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Stabilization of protein-protein interaction complexes through small molecules
Abstract
Most of the small molecules that have been identified thus far to modulate protein-protein interactions (PPIs) are inhibitors. Another promising way to interfere with PPI-associated biological processes is to promote PPI stabilization. Even though PPI stabilizers are still scarce, stabilization of PPIs by small molecules is gaining momentum and offers new pharmacological options. Therefore, we have performed a literature survey of PPI stabilization using small molecules. From this, we propose a classification of PPI stabilizers based on their binding mode and the architecture of the complex to facilitate the structure-based design of stabilizers.
... Thus, these features of PPI interfaces make it difficult to design selective and potent smallmolecule inhibitors [16]. Stabilization of PPI complexes is an alternative way to interfere with the PPI-associated biological functions [113,125]. Instead of competing with any of the protein partners, PPI stabilizers target the regions at or near the PPI interfaces. Thus, PPI stabilizers are able to exert desired biological response with relatively low binding affinity (micromolar range) and are more likely to achieve specificity [74,113,125]. ...
... Instead of competing with any of the protein partners, PPI stabilizers target the regions at or near the PPI interfaces. Thus, PPI stabilizers are able to exert desired biological response with relatively low binding affinity (micromolar range) and are more likely to achieve specificity [74,113,125]. Recently, there is an increase of research interests in investigating the mode of action, molecular design, and therapeutic effects of PPI stabilizers (e.g., stabilizers of 14-3-3 PPI) [74,113,125]. ...
... Thus, PPI stabilizers are able to exert desired biological response with relatively low binding affinity (micromolar range) and are more likely to achieve specificity [74,113,125]. Recently, there is an increase of research interests in investigating the mode of action, molecular design, and therapeutic effects of PPI stabilizers (e.g., stabilizers of 14-3-3 PPI) [74,113,125]. ...
Protein–protein interactions (PPIs) represent promising drug targets of broad-spectrum therapeutic interests due to their critical implications in both health and disease circumstances. Hence, they are widely accepted as the Holy Grail of drug development. Historically, PPIs were rendered “undruggable” for their large, flat, and pocket-less structures. Current attempts to drug these “intractable” targets include orthosteric and allosteric methodologies. Previous efforts employing orthosteric approaches like protein therapeutics and orthosteric small molecules frequently suffered from poor performance caused by the difficulties in directly targeting PPI interfaces. As structural biology progresses rapidly, allosteric modulators, which direct to the allosteric regulatory sites remote to the PPI surfaces, have gradually established as a potential solution. Allosteric pockets are topologically distal from the PPI orthosteric sites, and their ligands do not need to compete with the PPI partners, which helps to improve the physiochemical and pharmacological properties of allosteric PPI modulators. Thus, exploiting allostery to tailor PPIs is regarded as a tempting strategy in future PPI drug discovery. Here, we provide a comprehensive review of our representative achievements along the way we utilize allosteric effects to tame the difficult PPI systems into druggable targets. Importantly, we provide an in-depth mechanistic analysis of this success, which will be instructive to future related lead optimizations and drug design. Finally, we discuss the current challenges in allosteric PPI drug discovery. Their solutions as well as future perspectives are also presented.
... Others, like brefeldin A, forskolin and the diterpene glycosides fusicoccin A and cotylenin A, are tremendously useful biological tool compounds. As these natural product PPI stabilizers have been known for a long time, they have already been extensively reviewed on multiple occasions [1][2][3][4] and will not be covered in depth in this review. This review will focus on synthetic PPI stabilizers after a brief update on natural product actin stabilizers that have not been reviewed before, and a reflection on natural product PPI stabilizers in drug discovery. ...
... That being said, we acknowledge that there are other compounds in the literature which effectively stabilize single protein entities [37,38] or for which biochemical assays suggest PPI stabilization as the mechanism [39,40], but which have not yet been confirmed by structural data. In their 2016 review, Zarzycka et al. classify different PPI stabilizers according to the type of complex that they stabilize [2]. In the light of drug development we have, however, chosen to divide the compounds into (I) compounds for which post hoc mechanism determination showed them to be PPI stabilizers and (II) compounds which were identified in studies specifically looking for PPI stabilizers. ...
... None of the compounds exhibited binding at the dimer interface, but rather in a shallow pocket on the protein surface. In their review, Zarzycka et al. classified these compounds as allosteric protein-protein stabilizers [2], however, in our view the experimental data from two different groups are contradictory and there is no clear agreement that those compounds are SOD1 dimer stabilizers. This example underlines the crucial importance of experimental structural data in unraveling the binding mode of small molecules. ...
Introduction: PPIs are involved in every disease and specific modulation of these PPIs with small molecules would significantly improve our prospects of developing therapeutic agents. Both industry and academia have engaged in the identification and use of PPI inhibitors. However in comparison, the opposite strategy of employing small-molecule stabilizers of PPIs is underrepresented in drug discovery.
Areas covered: PPI stabilization has not been exploited in a systematic manner. Rather, this concept validated by a number of therapeutically used natural products like rapamycin and paclitaxel has been shown retrospectively to be the basis of the activity of synthetic molecules originating from drug discovery projects among them lenalidomide and tafamidis. Here, the authors cover the growing number of synthetic small-molecule PPI stabilizers to advocate for a stronger consideration of this as a drug discovery approach.
Expert opinion: Both the natural products and the growing number of synthetic molecules show that PPI stabilization is a viable strategy for drug discovery. There is certainly a significant challenge to adapt compound libraries, screening techniques and downstream methodologies to identify, characterize and optimize PPI stabilizers, but the examples of molecules reviewed here in our opinion justify these efforts.
... Whereas immunosuppressants rapamycin, cyclosporine, and FK506, and the antitumor drug paclitaxel have been long used in the clinic [8][9][10] , interest in PPI stabilization as a conceptual strategy has only recently surged, due to the success of synthetically engineered hetero-bifunctional probes (proteolysis-targeting chimera; PROTACs) 13,14 and the revelation of the molecular mechanism of lenalidomide and thalidomide (immunomodulatory drugs; IMiDs®) as PPI stabilizers 15,16 . Nevertheless, the majority of reported PPI stabilizers have been serendipitous discoveries and systematic design, screening, and technology platforms for PPI stabilizer discovery are largely lacking 17,18 . There is thus an urgent need for conceptual strategies for hit finding and rational optimization, empowering PPI stabilization. ...
... A crystallographic overlay of 12 (binding to 14-3-3), with 3 (binding to the 14-3-3/ChREBP binary complex) shows two rotations of the molecules with respect to each other in their orientation in the binding pocket; around the phosphonate and around the central axis of the phenylphosphonate, which drags the side chain around (Fig. 4b), with this turn in binding orientation resembling a molecular switch between the two distinct modes. Further SAR revealed substitutions of the phenylphosphonic moiety were either not tolerated (Me, [18][19][20] or did not significantly enhance the activity (F, 21-23). The second phenyl on the other hand, was hypothesized to provide an interesting opportunity for structure variations, for which substitutions on all positions might result in engaging the 14-3-3 side chains D215, K122, or N175 (Supplementary Fig. 9). ...
The systematic stabilization of protein–protein interactions (PPI) has great potential as innovative drug discovery strategy to target novel and hard-to-drug protein classes. The current lack of chemical starting points and focused screening opportunities limits the identification of small molecule stabilizers that engage two proteins simultaneously. Starting from our previously described virtual screening strategy to identify inhibitors of 14-3-3 proteins, we report a conceptual molecular docking approach providing concrete entries for discovery and rational optimization of stabilizers for the interaction of 14-3-3 with the carbohydrate-response element-binding protein (ChREBP). X-ray crystallography reveals a distinct difference in the binding modes between weak and general inhibitors of 14-3-3 complexes and a specific, potent stabilizer of the 14-3-3/ChREBP complex. Structure-guided stabilizer optimization results in selective, up to 26-fold enhancement of the 14-3-3/ChREBP interaction. This study demonstrates the potential of rational design approaches for the development of selective PPI stabilizers starting from weak, promiscuous PPI inhibitors. Small molecule stabilizers of protein–protein interactions hold great therapeutic potential. Based on virtual screening and molecular docking, the authors here develop a strategy to evolve weak, promiscuous inhibitors of 14-3-3 interactions into selective stabilizers of the 14-3-3/ChREBP complex.
... Of note, PPIs play a key role in various biological processes (Zarzycka et al., 2016). Similar to PPI inhibition, stabilization of dimers or oligomers can lead to either the activation or inhibition of a biological function. ...
... momentum and offers new pharmacological options (Zarzycka et al., 2016). Our findings also demonstrated that D39 combined with NMMHC IIA to inhibit the dissociation of NMMHC IIA from TNFR2 (Figure 4), which was first reported using natural products. ...
BACKGROUND AND PURPOSE
Non-muscular myosin heavy chain IIA (NMMHC IIA) plays a key role in tissue factor expression and venous thrombosis. Natural products might inhibit thrombosis through effects on NMMHC IIA. Here, we have shown that a natural saponin, D39, from Liriope muscari exerted anti-thrombotic activity in vivo, by targeting NMMHC IIA.
EXPERIMENTAL APPROACH
Expression and activity of tissue factor in endothelial cells were analysed in vitro by Western blot and simplified chromogenic assays. Interactions between D39 and NMMHC IIA were assessed by serial affinity chromatography and molecular docking
analysis. D39-dependent interactions between NMMHC IIA and TNF receptor 2 (TNFR2) were measured by immunofluorescence, co-immunoprecipitation and proximity ligation assays. Anti-thrombotic activity of D39 in vivo was evaluated with a model of inferior vena cava ligation injury in mice.
KEY RESULTS
D39 inhibited tissue factor expression and procoagulant activities in HUVECs and decreased thrombus weight in inferior vena cava-ligated mice dose-dependently. Serial affinity chromatography and molecular docking analysis suggested that D39 bound to NMMHC IIA. In HEK293T cells, D39 inhibited tissue factor expression evoked by NMMHC IIA overexpression. This effect was blocked by NMMHC IIA knockdown in HUVECs. D39 inhibited dissociation of NMMHC IIA from TNFR2, which subsequently modulated the Akt/GSK3β–NF-κB signalling pathways.
CONCLUSIONS AND IMPLICATIONS
D39 inhibited tissue factor expression and thrombus formation by modulating the Akt/GSK3β and NF-κB signalling pathways through NMMHC IIA. We identified a new natural product that targeted NMMHC IIA, as a potential treatment for thrombotic disorders and other vasculopathies.
... Although most of the efforts on small molecules targeting PPIs have been focused on inhibitors, the possibility to develop drug-like molecules able to stabilize the interaction among two or more protein partners has recently become an attractive possibility. A number of PPI stabilizers have been already identified [48,52], including some natural compounds and compounds validated as stabilizers in post hoc analyses (e.g., the mushroom toxin phalloidin that stabilizes actin filaments, [53]). Based on their mode of action, two different categories of PPI stabilizers can be identified: (i) molecules acting through allosteric stabilization, i.e., ligands that bind to an allosteric site of a specific target and induce a conformational change toward a structure showing higher affinity for a protein partner, and (ii) molecules that directly bind to an interfacial cage, thus improving complementarity and stabilizing the complex [48]. ...
Patients with cystic fibrosis (PwCF) have recently experienced an unprecedented breakthrough with the adoption of modulator therapy in clinical practice. This remarkable achievement has led to the reconsideration of disease management as the increased life expectancy has gradually shifted the attention over a spectrum of extra-pulmonary manifestations that become prevalent in the aging population. It comes to be that complementary approaches that target patient co-morbidities are needed for the optimal clinical management of PwCF. A strategy would be to adjuvate the cystic fibrosis transmembrane conductance regulator (CFTR) in performing its functions in the different organs in which it is expressed. Solute carrier family 26 (SLC26) members appear ideal in this context. Indeed, they not only cooperate with CFTR in the organ-dependent regulation of ion fluxes but physically interact with it to reciprocally modulate their function. In this opinion, we summarize available evidence pointing to a physical and functional interaction between CFTR and SLC26 members, with a particular focus on SLC26A6 for its wider expression and broader anion selectivity, and then discuss how restoring the physical interaction between CFTR and SLC26A6 might be beneficial in the treatment of PwCF in the era of modulator therapy.
... A plethora of excellent review articles on molecular glues and the complexes they stabilize have been published in the recent years, each focusing on a slightly different aspect of the topic, with the majority of them focusing on the discovery history, mechanism of action, and design strategy [28][29][30][31][32][33][34][35][36][37] . This review seeks to compile and analyze the current, published molecular glue ternary complex structures with the aim of identifying and quantifying any structural requirements for PPIs that are induced by molecular glues, as well as surveying the best computational methods to predict potential 'gluable' interfaces. ...
Molecular glues are a class of small molecules that stabilize the interactions between proteins. Naturally occurring molecular glues are present in many areas of biology where they serve as central regulators of signaling pathways. Importantly, several clinical compounds act as molecular glue degraders that stabilize interactions between E3 ubiquitin ligases and target proteins, leading to their degradation. Molecular glues hold promise as a new generation of therapeutic agents, including those molecular glue degraders that can redirect the protein degradation machinery in a precise way. However, rational discovery of molecular glues is difficult in part due to the lack of understanding of the protein-protein interactions they stabilize. In this review, we summarize the structures of known molecular glue-induced ternary complexes and the interface properties. Detailed analysis shows different mechanisms of ternary structure formation. Additionally, we also review computational approaches for predicting protein-protein interfaces and highlight the promises and challenges. This information will ultimately help inform future approaches for rational molecular glue discovery.
... Another approach for modulating PPI interactions is through PPI stabilizers 14 . These small molecules stabilize the protein-protein complex by targeting the pocket formed at the interface of two proteins 15 . In 2021, approximately 15 targeted protein degraders and molecular glues have entered the market including orally bioavailable protein degrader CFT7455 16 . ...
The featureless interface formed by protein–protein interactions (PPIs) is notorious for being considered a difficult and poorly druggable target. However, recent advances have shown PPIs to be druggable, with the discovery of potent inhibitors and stabilizers, some of which are currently being clinically tested and approved for medical use. In this study, we assess the druggability of 12 commonly targeted PPIs using the computational tool, SiteMap. After evaluating 320 crystal structures, we find that the PPI binding sites have a wide range of druggability scores. This can be attributed to the unique structural and physiochemical features that influence their ligand binding and concomitantly, their druggability predictions. We then use these features to propose a specific classification system suitable for assessing PPI targets based on their druggability scores and measured binding-affinity. Interestingly, this system was able to distinguish between different PPIs and correctly categorize them into four classes (i.e. very druggable, druggable, moderately druggable, and difficult). We also studied the effects of protein flexibility on the computed druggability scores and found that protein conformational changes accompanying ligand binding in ligand-bound structures result in higher protein druggability scores due to more favorable structural features. Finally, the drug-likeness of many published PPI inhibitors was studied where it was found that the vast majority of the 221 ligands considered here, including orally tested/marketed drugs, violate the currently acceptable limits of compound size and hydrophobicity parameters. This outcome, combined with the lack of correlation observed between druggability and drug-likeness, reinforces the need to redefine drug-likeness for PPI drugs. This work proposes a PPI-specific classification scheme that will assist researchers in assessing the druggability and identifying inhibitors of the PPI interface.
... 1−4 PPI stabilization and inhibition are related approaches but based on profoundly different underlying principles. 5,6 The stabilization of protein complexes by cooperatively binding ligands could have tremendous benefit in terms of client selectivity since druggable pockets at binding interfaces are constituted of residues of both protein partners and thus only exist in the context of the complex. 2,7,8 In contrast, PPI inhibitors typically affect multiple interactions of the target protein, an important consideration when aiming to therapeutically target interactions of "hub" proteins that have a large number of binding partners. ...
The systematic discovery of functional fragments binding to the composite interface of protein complexes is a first critical step for the development of orthosteric stabilizers of protein–protein interactions (PPIs). We have previously shown that disulfide trapping successfully yielded covalent stabilizers for the PPI of 14-3-3 with the estrogen receptor ERα. Here we provide an assessment of the composite PPI target pocket and the molecular characteristics of various fragments binding to a specific subpocket. Evaluating structure–activity relationships highlights the basic principles for PPI stabilization by these covalent fragments that engage a relatively large and exposed binding pocket at the protein/peptide interface with a “molecular glue” mode of action.
... Indeed, contributors indicate (step-by-step), the architecture of the PPI complex(es), the chemical compounds tested for modulation and the various assays in which these compounds were tested. An important step consists for the contributor in indicating a PDB ID for the entry containing the investigated PPIs and select the associated class of PPI architecture from a list of provided schematics as described in (Zarzycka et al., 2016). This input from the expert curator is a key element to accurately define the PPI target and the mode of action of the active compounds. ...
Motivation
One avenue to address the paucity of clinically testable targets is to reinvestigate the druggable genome by tackling complicated types of targets such as Protein-Protein Interactions (PPIs). Given the challenge to target those interfaces with small chemical compounds, it has become clear that learning from successful examples of PPI modulation is a powerful strategy. Freely-accessible databases of PPI modulators that provide the community with tractable chemical and pharmacological data, as well as powerful tools to query them, are therefore essential to stimulate new drug discovery projects on PPI targets.
Results
Here, we present the new version iPPI-DB, our manually curated database of PPI modulators. In this completely redesigned version of the database, we introduce a new web interface relying on crowdsourcing for the maintenance of the database. This interface was created to enable community contributions, whereby external experts can suggest new database entries. Moreover, the data model, the graphical interface, and the tools to query the database have been completely modernized and improved. We added new PPI modulators, new PPI targets, and extended our focus to stabilizers of PPIs as well.
Availability and Implementation
The iPPI-DB server is available at https://ippidb.pasteur.fr The source code for this server is available at https://gitlab.pasteur.fr/ippidb/ippidb-web/ and is distributed under GPL licence (http://www.gnu.org/licences/gpl). Queries can be shared through persistent links according to the FAIR data standards. Data can be downloaded from the website as csv files.
Supplementary information
Supplementary data are available at Bioinformatics online.
... The PPI stabilization represents a promising modulation approach since the combination with pre-existing complexes is more advantageous in energy saving compared to the inhibition of complexes formation. [60][61][62] However, the development of PPIs stabilizers has not received sufficient attention as compared to the development of PPIs inhibitors. 63 Three types of PPIs modulators Up to date, the PPI modulators can be classified into three categories ( Table 2). ...
Protein-protein interactions (PPIs) have pivotal roles in life processes. The studies showed that aberrant PPIs are associated with various diseases, including cancer, infectious diseases, and neurodegenerative diseases. Therefore, targeting PPIs is a direction in treating diseases and an essential strategy for the development of new drugs. In the past few decades, the modulation of PPIs has been recognized as one of the most challenging drug discovery tasks. In recent years, some PPIs modulators have entered clinical studies, some of which been approved for marketing, indicating that the modulators targeting PPIs have broad prospects. Here, we summarize the recent advances in PPIs modulators, including small molecules, peptides, and antibodies, hoping to provide some guidance to the design of novel drugs targeting PPIs in the future.
... Consequently, osteoporotic patients will require very mild mechanical activation, if any, via localised vibrating devices to induce a therapeutic effect in combination with anabolic treatment such as iPTH. This is plausible considering the advances in developing small-molecule drugs interfering with intracellular scaffold proteins, and their success in clinical trials [73][74][75]. ...
Background:
Mechanotransduction in bone cells plays a pivotal role in osteoblast differentiation and bone remodelling. Mechanotransduction provides the link between modulation of the extracellular matrix by mechanical load and intracellular activity. By controlling the balance between the intracellular and extracellular domains, mechanotransduction determines the optimum functionality of skeletal dynamics. Failure of this relationship was suggested to contribute to bone-related diseases such as osteoporosis.
Results:
A hybrid mechanical and agent-based model (Mech-ABM), simulating mechanotransduction in a single osteoblast under external mechanical perturbations, was utilised to simulate and examine modulation of the activation dynamics of molecules within mechanotransduction on the cellular response to mechanical stimulation. The number of molecules and their fluctuations have been analysed in terms of recurrences of critical events. A numerical approach has been developed to invert subordination processes and to extract the direction processes from the molecular signals in order to derive the distribution of recurring events. These predict that there are large fluctuations enclosing information hidden in the noise which is beyond the dynamic variations of molecular baselines. Moreover, studying the system under different mechanical load regimes and altered dynamics of feedback loops, illustrate that the waiting time distributions of each molecule are a signature of the system's state.
Conclusions:
The behaviours of the molecular waiting times change with the changing of mechanical load regimes and altered dynamics of feedback loops, presenting the same variation of patterns for similar interacting molecules and identifying specific alterations for key molecules in mechanotransduction. This methodology could be used to provide a new tool to identify potent molecular candidates to modulate mechanotransduction, hence accelerate drug discovery towards therapeutic targets for bone mass upregulation.
... The success of the kinetic-stabilizers approach for generating diseasemodifying drugs for TTR amyloidosis raises the question whether a similar approach could be used for other amyloidogenic proteins. However, although small-molecule stabilizers of protein-protein interaction have been studied for many proteins, 24,25 their use in the proteinopathy filed is rare. When considering this question, an immediate realization is that for this approach to be successful, the protein under consideration must have a stable structure. ...
Disease-modifying therapies for proteinopathies are urgently needed yet clinical trials for the major neurodegenerative diseases, Alzheimer's and Parkinson's, have been failing at an alarming rate leaving patients and caregivers scrambling for any sign of hope. At the same time, for one family of proteinopathies, the rare TTR amyloidoses, disease-modifying therapy has existed for almost 3 decades and two new types of disease-modifying therapy have become available more recently. In this chapter, I discuss those therapies, examine to what extent they can be generalized for other diseases, and consider what we may learn from their relative success.
... A small chemical compound with biological activity can have an affect on PPI via its effects on the enzymatic properties, the state of chemical modification, or the direct interruption of the ability to form PPI, resulting in a re-wiring of the PPI network; i.e. resulting in reconstruction of protein complexes in the cell [4]. Such a chemical compound may be useful as a therapeutic drug, but sometimes exhibits unwanted side effects [5,6]. Therefore, the investigation of protein complexes affected by a drug should contribute towards elucidating the mechanism underlying the therapeutic drug action. ...
Protein–protein interactions (PPIs) lead the formation of protein complexes that perform biochemical reactions that maintain the living state of the living cell. Although therapeutic drugs should influence the formation of protein complexes in addition to PPI network, the methodology analyzing such influences remain to be developed. Here, we demonstrate that a new approach combining HPLC (high performance liquid chromatography) for separating protein complexes, and the SILAC (stable isotope labeling using amino acids in cell culture) method for relative protein quantification, enable us to identify the protein complexes influenced by a drug. We applied this approach to the analysis of thalidomide action on HepG2 cells, assessed the identified proteins by clustering data analyses, and assigned 135 novel protein complexes affected by the drug. We propose that this approach is applicable to elucidating the mechanisms of actions of other therapeutic drugs on the PPI network, and the formation of protein complexes.
... Some of the most extensively studied proteins for the development of PPI stabilizers are the 14-3-3 proteins which are a family of conserved regulatory molecules that can bind to different partners and are involved in many cellular functions such as apoptosis, cell cycle regulation and signal transduction [124]. Fortunately, x-ray structures of the 14-3-3 proteins in complex with different binding partners are available from the Protein Data Bank allowing molecular modelers to use these structures for rational design of selective stabilizers for different protein-protein complexes [22,125,126]. For instance, recently, MD simulations were applied to investigate the interaction networks of human 14-3-3 sigma in complex with TASK-3 peptide and the stabilizer Fusicoccin A (PDB code 3P1O). ...
The horizon of drug discovery is currently expanding to target and modulate protein-protein interactions (PPIs) in globular proteins and intrinsically disordered proteins that are involved in various diseases. To either interrupt or stabilize PPIs, the 3D structure of target protein-protein (or protein-peptide) complexes can be exploited to rationally design PPI modulators (inhibitors or stabilizers) through structure-based molecular design. In this review, we present an overview of experimental and computational methods that can be used to determine 3D structures of protein-protein complexes. Several approaches including rational and in silico methods that can be applied to design peptides, peptidomimetics and small compounds by utilization of determined 3D protein-protein/peptide complexes are summarized and illustrated.
... 5−7 Therapeutic proof-of-concept for PPI stabilization has been provided by natural products, including the antitumor drug paclitaxel and immune suppressants rapamycin and FK506. 6,7 Additionally, a number of successes using synthetic molecules have been reported, such as the BRD4-dimer stabilizer (biBET) 8 and the allosteric stabilizer of the tetramer transthyretin (tafamidis). 9 Synthetic approachesproteolysis targeting chimeras (PROTACs) and immunomodulatory drugs (iMiDs)apply this principle to drive the association of two proteins that would not otherwise interact. ...
Modulation of Protein-Protein Interactions (PPIs) by small molecules has emerged as a valuable approach in drug discovery. Compared to direct inhibition, PPI stabilization is vastly underexplored but has strong advantages, including the ability to gain selectivity by targeting an interface formed only upon association of proteins. Here, we present the application of a site-directed screening technique based on disulfide trapping (tethering) to select for fragments that enhance the affinity between protein partners. We target the phosphorylation-dependent interaction between the hub protein 14-3-3sigma and a peptide derived from Estrogen Receptor alpha (ERalpha), an important breast cancer target that is negatively regulated by 14-3-3sigma. We identify orthosteric stabilizers that increase 14-3-3sigma/ERalpha affinity up to 40-fold and propose the mechanism of stabilization based on X-ray crystal structures. These fragments already display partial selectivity towards ERalpha-like motifs over other representative 14-3-3 clients. This first of its kind study illustrates the potential of the tethering approach to overcome the hurdles in systematic PPI stabilizer discovery.
... Finally, these structural data revealed that the surface of interaction between the N C-arm and the RNA groove could constitute a second target to develop antivirals against the N 0 -P complex. In this case, stabilization of the interaction using small molecules could represent an attractive strategy (32). ...
As all the viruses belonging to the Mononegavirales order, the non-segmented negative strand RNA genome of respiratory syncytial virus (RSV) is encapsidated by the viral nucleoprotein N. N protein polymerizes along the genomic and anti-genomic RNAs during replication. This requires the maintenance of the neosynthesized N protein in a monomeric and RNA-free form by the viral phosphoprotein P that plays the role of a chaperone protein, forming a soluble N⁰-P complex. We have previously demonstrated that residues 1-30 of P specifically bind to N⁰. Here, to isolate a stable N⁰-P complex suitable for structural studies, we used the N-terminal peptide of P (P40) to purify truncated forms of the N protein. We show that to purify a stable N⁰-P-like complex, a deletion of the first 30 N-terminal residues of N (NΔ30) is required to impair N oligomerization, whereas the presence of a full-length C-arm of N is required to inhibit RNA binding. We generated structural models of the RSV N⁰-P with biophysical approaches, including hydrodynamic measurements and small-angle X-ray scattering (SAXS), coupled with biochemical and functional analyses of human RSV (hRSV) NΔ30 mutants. These models suggest a strong structural homology between the hRSV and the human metapneumovirus (hMPV) N⁰-P complexes. In both complexes, the P40-binding sites on N⁰ appear to be similar, and the C-arm of N provides a high flexibility and a propensity to interact with the N RNA groove. These findings reveal two potential sites to target on N⁰-P for the development of RSV antivirals.
... Aberrant or inappropriate interactions may be associated with the pathogenesis of several diseases; therefore, the modulation of certain PPIs constitutes a challenging approach for therapeutic intervention in pathological situations [1]. In recent years, a lot of work in this direction has been reported describing different PPI disrupting agents both small molecules and peptides [2][3][4][5]. Some of them have even progressed to clinical development, especially for the inhibition of the interaction of p53 with its suppressor HDM2 (Human Double Minute 2) which is highly implicated in cancer [6][7][8]. ...
The interaction between vascular endothelial growth factor (VEGF) and its receptors (VEGFR) has important implications in angiogenesis and cancer, which moved us to search for peptide derivatives able to block this protein–protein interaction. In a previous work we had described a collection of linear 13-mer peptides specially designed to adopt helical conformations (Ac-SSEEX5ARNX9AAX12N-NH2), as well as the evaluation of seven library components for the inhibition of the interaction of VEGF with its Receptor 1 (VEGFR1). This study led to the discovery of some new, quite potent inhibitors of this protein–protein system. The results we found prompted us to extend the study to other peptides of the library. We describe here the evaluation of a new selection of peptides from the initial library that allow us to identify new VEGF-VEGFR1 inhibitors. Among them, the peptide sequence containing F, W, and I residues at the 5, 9, and 12 positions, show a very significant nanomolar IC50 value, competing with VEGF for its receptor 1, VEGFR1 (Flt-1), which could represent a new tool within the therapeutic arsenal for cancer detection and therapy.
... Imbalances in enzyme activity are etiological factors for numerous diseases, including inflammation, metabolic disorders, cardiovascular irregularities and cancers. Therefore, modulation of enzyme function by bioactive small molecules is a commonly employed therapeutic strategy and many successful drugs are enzyme inhibitors or poisons (1). The majority of drugs bind their targets via noncovalent forces, rendering the interactions reversible in nature. ...
Human type II topoisomerase (Top2) isoforms, hTop2α and hTop2β, are targeted by some of the most successful anticancer drugs. These drugs induce Top2-mediated DNA cleavage to trigger cell-death pathways. The potency of these drugs correlates positively with their efficacy in stabilizing the enzyme-mediated DNA breaks. Structural analysis of hTop2α and hTop2β revealed the presence of methionine residues in the drug-binding pocket, we therefore tested whether a tighter Top2-drug association may be accomplished by introducing a methionine-reactive Pt2+ into a drug to further stabilize the DNA break. Herein, we synthesized an organoplatinum compound, etoplatin-N2β, by replacing the methionine-juxtaposing group of the drug etoposide with a cis-dichlorodiammineplatinum(II) moiety. Compared to etoposide, etoplatin-N2β more potently inhibits both human Top2s. While the DNA breaks arrested by etoposide can be rejoined, those captured by etoplatin-N2β are practically irreversible. Crystallographic analyses of hTop2β complexed with DNA and etoplatin-N2β demonstrate coordinate bond formation between Pt2+ and a flanking methionine. Notably, this stable coordinate tether can be loosened by disrupting the structural integrity of drug-binding pocket, suggesting that Pt2+ coordination chemistry may allow for the development of potent inhibitors with protein conformation-dependent reversibility. This approach may be exploited to achieve isoform-specific targeting of human Top2s.
... gp120, was approved by FDA in 2007 to treat HIV infection.247 Compound 44, an inhibitor of cell division in Escherichia coli and Bacillus subtilis, binds to ZipA at FtsZ-binding site.248 ...
Targeting protein–protein interactions (PPIs) for therapeutic development was once considered undruggable due to the large and flat interactive surfaces that lack cavities. Facilitated by the development of new concepts, such as hotspots, screening techniques, and computational tools, various small molecules modulating PPIs have been achieved with a number of them having progressed into different phases of clinical trials and a portion recently reaching the market. In this article, we discuss the critical role of PPIs associated with various human diseases and different approaches to the identification of small molecular inhibitors targeting PPIs. We also highlight recent advances in developing such modulators as novel therapeutics.
... Also, in the assay we developed, two kinds of beads were used, and many compounds may interact with the reaction system, leading to the nonspecific interference shown in Fig. 5A. It was reported that compounds which modulate the protein-protein interaction include two types: inhibitor and stabilizer 30 . In our manuscript, the target was LEDGF/p75-IN interaction, therefore, several compounds may stabilize the target and indicated as enhancers. ...
HIV-1 integrase (IN) plays an essential role in viral replication and thus serves as an important target for chemotherapeutic intervention against HIV-1 infection. However, the current three clinical IN inhibitors, raltegravir, elvitegravir and dolutegravir share the same inhibitory mechanism, resulting in a common clinical resistance profile which have emerged in infected patients receiving treatment. Therefore, it is important to develop small molecule inhibitors that impair IN function with distinct mechanisms of action. In this work, a magnetic-beads based biochemical assay targeting the protein-protein interaction (PPI) between HIV IN and the cellular cofactor LEDGF/p75 was developed for identification of HIV-1 IN inhibitors. Furthermore, a library containing 1000 US. Food and Drug Administration (FDA)-approved drugs currently used for human medication was screened to identify inhibitors targeting the PPI. The assay was proved to be quite robust and with the novel assay we successfully identified dexlansoprazole (IC50 of 4.8 μM), a FDA-approved proton pump inhibitor, as a potential inhibitor for the PPI between IN and LEDGF/p75, which bound to the LEDGF/p75 partner with a kinetic dissociation (Kd) constant of 330 nM ± 2.6 nM.
... PPI stabilization represents a promising mode of modulation because binding to a preexisting complex is more energetically favorable relative to inhibition of complex formation [31,35,36]. Roche has described synthetic stabilizers, RO-2443 and RO-5963, which activate p53 signaling and induce apoptosis in breast cancer cells by stabilizing MdmX dimers. ...
Over the past decade, protein-protein interactions (PPIs) have gone from being neglected as 'undruggable' to being considered attractive targets for the development of therapeutics. Recent advances in computational analysis, fragment-based screening, and molecular design have revealed promising strategies to address the basic molecular recognition challenge: how to target large protein surfaces with specificity. Several systematic and complementary workflows have been developed to yield successful inhibitors of PPIs. Here we review the major contemporary approaches utilized for the discovery of inhibitors and focus on a structure-based workflow, from the selection of a biological target to design.
This review describes an unprecedented class of biocompatible protein‐based microfibers obtained by exploiting the ability of small thiophene fluorophores: (1) to be spontaneously incorporated by living cells (2D or 3D) without causing any harm, (2) to act as protein self‐assembly inducers, and (3) to transfer their long‐lasting fluorescence and electroactivity properties to the protein‐fluorophore microfibers. The process is driven by cell's own metabolism and leads to the generation of stable multifunctional microfibers exhibiting hierarchical order across several length‐scales with morphologies varying from helical wires to rigid rods. Analogous microfibers are obtained following uptake of an appropriate thiophene fluorophore by small living organisms ( Hydra vulgaris ). Due to the high photostability of thiophene fluorophores, the entire process of fibers formation can be tracked in real time by LSCM. Moreover, the microfibers can be picked up and separated by their environment to assess their composition and properties by a variety of techniques including electrophoretic analyses and Q‐TOF mass spectrometry, Tr‐TUNA AFM and KPFM. This review also reports DFT calculations aimed to provide indications for the design of appropriate thiophene fluorophores for microfibers formation inside live cells.
There is an increasing interest to develop therapeutics that modulate challenging or undruggable target proteins via a mechanism that involves ternary complexes. In general, such compounds can be characterized by...
Protein-protein interactions (PPIs) are essential for biological processes including immune reactions and diseases. Inhibition of PPIs by drug-like compounds is a common basis for therapeutic approaches. In many cases the flat interface of PP complexes prevents discovery of specific compound binding to cavities on one partner and PPI inhibition. However, frequently new pockets are formed at the PP interface that allow accommodation of stabilizers which is often as desirable as inhibition but a much less explored alternative strategy. Herein, we employ molecular dynamics simulations and pocket detection to investigate 18 known stabilizers and associated PP complexes. For most cases, we find that a dual-binding mechanism, a similar stabilizer interaction strength with each protein partner, is an important prerequisite for effective stabilization. A few stabilizers follow an allosteric mechanism by stabilizing the protein bound structure and/or increase the PPI indirectly. On 226 protein-protein complexes, we find in >75% of the cases interface cavities suitable for binding of drug-like compounds. We propose a computational compound identification workflow that exploits new PP interface cavities and optimizes the dual-binding mechanism and apply it to 5 PP complexes. Our study demonstrates a great potential for in silico PPI stabilizers discovery with a wide range of therapeutic applications.
Breast cancer is the most commonly diagnosed cancer among women and leading the second most cause of cancer death worldwide in 2020. Human Epidermal Growth Factor Receptor 2 (HER2) is part of four members of the HER2 receptor family leading to proliferation, differentiation, and inhibition of apoptosis. Overexpression of HER2 is associated with a more aggressive disease with higher recurrence rates. The various bioactivity of the active substances from natural compounds has been tested as inhibitors, including white turmeric (Curcuma zedoaria). In several studies, extracts and essential oil of this plant showed promising antioxidant properties and cytotoxic against cancer cell lines. Therefore, this study predicts the potential of bioactive compounds of C. zedoaria targeting HER2 through molecular docking simulations. The conformational stability formed is the main parameter in the docking affinity assessment. The result showed that six out of 33 compounds from C. zedoria had potential as HER2 inhibitors. The binding affinity of dihydrocurcumin, curcumin, tetrahydrodemethoxycurcumin, zerumin A, demethoxycurcumin and bisdemethoxycurcumin were -7.4359 kcal/mol, -6.8372 kcal/mol, -6.6454 kcal/mol, -6.3360 kcal/mol, -6.3148 kcal/mol and -6.3148 kcal/mol, respectively. The inhibitory action of the compounds was also validated by comparing it with the reference compound lapatinib. Further research is needed to validate the above data.
Targeting protein-protein interactions (PPIs) has become a common approach to tackle various diseases whose pathobiology is driven by their mis-regulation in important signalling pathways. Modulating PPIs has tremendous untapped therapeutic potential and different approaches can be used to modulate PPIs. Initially, therapeutic effects were mostly sought by inhibiting PPIs. However, by gaining insight in the mode of action of certain therapeutic compounds, it became clear that stabilising (i.e. enhancing) PPIs can also be useful. The latter strategy is recently gaining a lot of attention, as stabilising physiologic, or even inducing novel interactions of a target protein with E3 ubiquitin ligases forms the basis of the targeted protein degradation (TPD) approach. An emerging additional example for drug discovery based on PPI stabilisation are the 14-3-3 proteins, a family of regulatory proteins, which engages in many protein-protein interactions, some of which might become therapeutical targets.
Molecules that induce interactions between proteins, often referred to as “molecular glues”, are increasingly recognized as important therapeutic modalities and as entry points for rewiring cellular signaling networks. Here, we report a new PACE-based method to rapidly select and evolve molecules that mediate interactions between otherwise non-interacting proteins: rapid evolution of Protein-Protein Interaction Glues (rePPI-G). Proof-of-concept evolutions demonstrated that rePPI-G reduces the “hook” effect of the engineered molecular glues, due at least in part to tuning the interaction affinities of each individual component of the bifunctional molecule. Altogether, this work validates rePPI-G as a continuous, phage-based evolutionary technology for optimizing molecular glues, providing a strategy for developing molecules that reprogram protein-protein interactions.
New genomic information has revealed the crucial role that protein–protein interactions (PPIs) play in regulating numerous cellular functions. Aberrant forms of these interactions are common in numerous diseases and thus PPIs have emerged as a vast class of critical drug targets. Despite the importance of PPIs in biology, it has been extremely challenging to convert targets into therapeutics and targeting PPIs had long been considered a very difficult task. However, over the past decade the field has advanced with increasing growth in the number of successful PPI regulators. Protein–Protein Interaction Regulators surveys the latest advances in the structural understanding of PPIs as well as recent developments in modulator discovery.
Modulation of interactome networks, essentially protein-protein interactions (PPIs), might represent valuable therapeutic approaches to different pathological conditions. Since a high percentage of PPIs are mediated by α-helical structures at the interacting surface, the development of compounds able to reproduce the amino acid side-chain organization of α-helices (e.g. stabilized α-helix peptides and β-derivatives, proteomimetics, and α-helix small-molecule mimetics) focuses the attention of different research groups. This appraisal describes the recent progress in the non-peptide α-helix mimetics field, which has evolved from single-face to multi-face reproducing compounds and from oligomeric to monomeric scaffolds able to bear different substituents in similar spatial dispositions as the side-chains in canonical helices. Grouped by chemical structures, the review contemplates terphenyl-like molecules, oligobenzamides and heterocyclic analogues, benzamide-amino acid conjugates and non-oligomeric small-molecules mimetics, among others, and their effectiveness to stabilize/disrupt therapeutically relevant PPIs. The X-ray structures of a couple of oligomeric peptidomimetics and of some small-molecules complexed with the MDM2 protein, as well as the state of the art on their development in clinical trials, are also remarked. The discovery of a Journal Pre-proof
continuously increasing number of new disease-relevant PPIs could offer future opportunities for these and other forthcoming α-helix mimetics.
Small molecule modulation of protein-protein interactions is a very promising but also challenging area in drug discovery. The tumor suppressor protein p53 is one of the most frequently altered proteins in human cancers, making it an attractive target in oncology. 14-3-3 proteins have been shown to bind to and positively regulate p53 activity by protecting it from MDM2-dependent degradation or activating its DNA binding affinity. Protein-protein interactions can be modulated by inhibiting or stabilizing specific interactions by small molecules. Whereas inhibition has been widely explored by pharmaceutical industry and academia, the opposite strategy of stabilizing protein-protein interactions still remains relatively underexploited. This is rather interesting considering the number of natural compounds like rapamycin, forskolin and fusicoccin that exert their activity by stabilizing specific protein-protein interactions. In this review, we give an overview of 14-3-3 interactions with p53, explain isoform specific stabilization of the tumor suppressor protein, explore the approach of stabilizing the 14-3-3σ - p53 complex and summarize some promising small-molecules inhibiting the p53 - MDM2 protein-protein interaction.
Protein-protein interactions (PPI) offer the unique opportunity to tailor ligands aimed at specifically stabilizing or disrupting the corresponding interfaces and providing a safer alternative to conventional ligands targeting monomeric macromolecules. Selecting biologically relevant protein-protein interfaces for either stabilization or disruption by small molecules is usually biology-driven, on a case-by-case basis and does not follow a structural rationale that could be applied to an entire interactome. We herewith provide a first step to the latter goal by using a fully automated and structure-based workflow, applicable to any PPI of known three-dimensional (3D) structure, to identify and prioritize druggable cavities at and nearby PPIs of pharmacological interest. When applied to the entire Protein Data Bank, 164,514 druggable cavities were identified and classified in four groups (interfacial, rim, allosteric, orthosteric) according to their properties and spatial locations. Systematic comparison of PPI cavities with pockets deduced from druggable protein-ligand complexes shows almost no overlap in property space, suggesting that even the most druggable PPI cavities are unlikely to be addressed with conventional drug-like compound libraries. The archive is freely accessible at http://drugdesign.unistra.fr/ppiome.
Alzheimer's disease (AD) has been proposed to begin in a cryptic form long before clinical symptoms appear. If this is the case, there might be an initial trigger leading to AD that we have not yet seen. Such a trigger might occur far away from the brain regions that are currently identified as affected sites, and might start long before either functional or histological changes are apparent. How might we detect this putative trigger? In this chapter, I propose an experimental approach using matrix-assisted laser desorption ionization (MALDI)-based imaging mass spectrometry (IMS), combined with pathological and functional connectivity studies, to track down the initial trigger of AD. The deficits in AD brains do not spread randomly, and even though we do not know where to find the initial deficit or which biomolecule is involved, the brain region where the initial change occurs is surely connected functionally to the brain regions that subsequently show detectable damage. Therefore, MALDI IMS taking account of the brain's functional connectivity and the spread of AD symptoms should be a powerful strategy for uncovering molecular signatures related to the AD trigger(s).
During the last decade, great progress has been made in mass spectrometry rendering the identification of 6000 proteins in an hour and up to 10 000 proteins in half a day. The proteome has been widely applied in a variety of studies in the life sciences, for dissecting protein profiling, protein–protein interactions, post‐translational‐modification, etc. Since the improvement of the proteome screening efficiency and the decreasing of the cost in sample measurement, the growing requirement of deep application of proteomics has been raised recently in clinical research, foretelling an era in which proteomics will enable personally tailored therapies for patients. This review describes the cutting‐edge progression of next‐generation proteomics and highlights its potential in precision medicine in the future.
Protein-protein interactions (PPIs) provide a rich source of drug targets for the development of new generation of clinical therapeutics. However, targeting PPIs by small-molecule inhibitors remains a significant challenge due to large, flat, and hydrophobic features of the PPI interfaces. Recently, important advances have been made in the discovery and development of small-molecule PPI inhibitors. This chapter aims to give an overview of the structural features of PPIs as well as the design strategies of small-molecule PPI inhibitors. Moreover, PPI inhibitors under clinical development will be briefly introduced and two successful examples in PPI-based drug development (venetoclax and lifitegrast) will be highlighted.
Background:
The significant number of protein-protein interactions (PPIs) discovered by harnessing concomitant advances in the fields of sequencing, crystallography, spectrometry and two-hybrid screening suggests astonishing prospects for remodelling drug discovery. The PPI space which includes up to 650 000 entities is a remarkable reservoir of potential therapeutic targets for every human disease. In order to allow modern drug discovery programs to leverage this we should be able to discern complete PPI maps associated with a specific disorder and corresponding normal physiology.
Objective:
Here, we will review community available computational programs for predicting PPIs and web-based resources for storing experimentally annotated interactions.
Methods:
We compared the capacities of prediction tools: iLoops, Struck2Net, HOMCOS, COTH, PrePPI, InterPreTS and PRISM to predict recently discovered protein interactions.
Results:
We described sequence-based and structure-based PPI prediction tools and addressed their peculiarities. Additionally, since the usefulness of prediction algorithms critically depends on the quality and quantity of the experimental data they are built on, we extensively discussed community resources for protein interactions. We focused on the active and recently updated primary and secondary PPI databases, repositories specialized to the subject or species, as well as databases that include both experimental and predicted PPIs.
Conclusion:
PPI complexes are the basis of important physiological processes and therefore, possible targets for cell-penetrating ligands. Reliable computational PPI predictions can speed up new target discoveries through prioritization of therapeutically relevant protein-protein complexes for experimental studies.
The nuclear factor (NF)-κB essential modulator (NEMO) is a key regulator in NF-κB-mediated signaling. By transmitting extracellular or intracellular signals, NEMO can control NF-κB-regulated genes. NEMO dysfunction is associated with inherited diseases such as incontinentia pigmenti (IP), ectodermal dysplasia, anhidrotic, with immunodeficiency (EDA-ID), and some cancers. We focus on molecular studies, human case reports, and mouse models emphasizing the significance of NEMO molecular interactions and modifications in health and diseases. This knowledge opens new opportunities to engineer suitable drugs that may putatively target precise NEMO functions attributable to various diseases, while leaving other functions intact, and eliminating cytotoxicity. Indeed, with the advent of novel gene editing tools such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)9, treating some inherited diseases may in the long run, become a reality.
Protein–protein interactions are central to all biological processes, and their modulation has enormous potential for therapeutic intervention in a range of diseases. However, protein–protein interactions have long been considered intractable targets because of the nature of their contact surfaces, which tend to be larger and flatter than typical druggable sites with most of the binding energy localized in “hot spots.” Protein–protein interfaces are typically formed by primary, secondary, or tertiary epitopes from the partner proteins, and modulation becomes progressively more challenging as the epitope becomes more complex. The majority of protein–protein interaction modulators are small molecules, peptides, or peptidomimetics, which directly disrupt the interface. Several hit-finding strategies have been used to identify starting points for drug discovery efforts with a number of protein–protein interaction modulators advancing to clinical trials. Here, we discuss how hit identification and qualification methods can be tailored toward protein–protein interaction modulator development.
Our research and teaching group called MTi (Molécules Thérapeutiques in silico) has developed numerous applications available online, thanks to the RPBS platform (Ressource Parisienne en Bioinformatique Structurale), in the field of chemoinformatics, structural bioinformatics and drug design. Since its opening in 2009, over 200 articles/reviews have been reported and involve virtual screening studies, prediction of druggability, analysis of protein-protein interaction inhibitors, development of databases, data mining and knowledge discovery, as well as combined in silico-in vitro work to search for new hits and chemical probes acting on original targets in several therapeutic areas. An international training program has also been developed pertaining to the field of in silico drug design. In this review, we present some tools developed in our laboratory with a special emphasis on the prediction of some ADMET properties, compound collection preparation and 3D-ADMET computations.
Protein-protein interactions (PPIs) are receiving increasing interest, much sparked by the realization they represent druggable targets. Recently, we successfully developed a peptidic inhibitor, RRYGTSKYQ ("SKY" peptide), that shows high potential in vitro and in vivo to interrupt a PPI between the platelet-borne chemokine CCL5 and the neutrophil-derived granule protein HNP1. This PPI plays a vital role in monocyte adhesion, representing a key mechanism in acute and chronic inflammatory diseases. Here, we present extensive and detailed computational methods applied to develop the SKY peptide. We combined experimentally determined binding affinities (KD) of several orthologs of CCL5 with HNP1 with in silico studies to identify the most likely heterodimeric CCL5-HNP1 complex which was subsequently used as a starting structure to rationally design peptidic inhibitors. Our method represents a fast and simple approach which can be widely applied to determine other protein-protein complexes and moreover, to design inhibitors or stabilizers of protein-protein interaction.
Dynamic instability, the stochastic switching between growth and shrinkage, is essential for microtubule function. This behavior is driven by GTP hydrolysis in the microtubule lattice and is inhibited by anticancer agents like Taxol. We provide insight into the mechanism of dynamic instability, based on high-resolution cryo-EM structures (4.7-5.6 Å) of dynamic microtubules and microtubules stabilized by GMPCPP or Taxol. We infer that hydrolysis leads to a compaction around the E-site nucleotide at longitudinal interfaces, as well as movement of the α-tubulin intermediate domain and H7 helix. Displacement of the C-terminal helices in both α- and β-tubulin subunits suggests an effect on interactions with binding partners that contact this region. Taxol inhibits most of these conformational changes, allosterically inducing a GMPCPP-like state. Lateral interactions are similar in all conditions we examined, suggesting that microtubule lattice stability is primarily modulated at longitudinal interfaces.
Weak protein interactions between ubiquitin and the ubiquitin-proteasome system (UPS) enzymes that mediate its covalent attachment to substrates serve to position ubiquitin for optimal catalytic transfer. We show that a small-molecule inhibitor of the E2 ubiquitin-conjugating enzyme Cdc34A, called CC0651, acts by trapping a weak interaction between ubiquitin and the E2 donor ubiquitin-binding site. A structure of the ternary CC0651-Cdc34A-ubiquitin complex reveals that the inhibitor engages a composite binding pocket formed from Cdc34A and ubiquitin. CC0651 also suppresses the spontaneous hydrolysis rate of the Cdc34A-ubiquitin thioester without decreasing the interaction between Cdc34A and the RING domain subunit of the E3 enzyme. Stabilization of the numerous other weak interactions between ubiquitin and UPS enzymes by small molecules may be a feasible strategy to selectively inhibit different UPS activities.
The nucleoprotein (NP) of influenza virus covers the viral RNA entirely and it is this NP-RNA complex that is the template for transcription and replication by the viral polymerase. Purified NP forms a dynamic equilibrium between monomers and small oligomers, but only the monomers can oligomerize onto RNA. Therefore, drugs that stabilize the monomers or that induce abnormal oligomerization may have an antiviral effect, as would drugs that interfere with RNA binding. Crystal structures have been produced for monomeric and dimeric mutants, and for trimers and tetramers; high-resolution electron microscopy structures have also been calculated for the viral NP-RNA complex. We explain how these structures and the dynamic oligomerization equilibrium of NP can be and have been used for anti-influenza drug development.
Steroid Receptor Signaling
Plant brassinosteroids signal to diverse pathways in plant physiology. These steroid hormones are perceived at the cell surface, where they bind to the receptor BRASSINOSTEROID INSENSITIVE 1 (BRI1). Santiago et al. (p. 889 , published online 8 August) now show that somatic embryogenesis receptor kinase 1 (SERK1) complexes with BRI1. Together, these receptor kinases form the steroid binding site, with the hormone acting as a “molecular glue” that stabilizes the interaction. Hormone-induced heteromerization of BRI1 with SERK1 leads to the activation of the cytoplasmic signaling cascade, triggering plant growth and differentiation.
Nuclear receptors (NRs) comprise a family of 49 members that share a common structural organization and act as ligand-inducible transcription factors with major (patho)physiological impact. For some NRs ("orphan receptors"), cognate ligands have not yet been identified or may not exist. The principles of DNA recognition and ligand binding are well understood from both biochemical and crystal structure analyses. The 3D structures of several DNA-binding domains (DBDs), in complexes with a variety of cognate response elements, and multiple ligand-binding domains (LBDs), in the absence (apoLBD) and presence (holoLBD) of agonist, have been established and reveal canonical structural organization. Agonist binding induces a structural transition in the LBD whose most striking feature is the relocation of helix H12, which is required for establishing a coactivator complex, through interaction with members of the p160 family (SRC1, TIF2, AIB1) and/or the TRAP/DRIP complex. The p160-dependent coactivator complex is a multiprotein complex that comprises histone acetyltransferases (HATs), such as CBP, methyltransferases, such as CARM1, and other enzymes (SUMO ligase, etc.). The agonist-dependent recruitment of the HAT complex results in chromatin modification in the environment of the target gene promoters, which is requisite to, or may in some cases be sufficient for, transcription activation. In the absence of ligands, or in the presence of some antagonists, certain NRs are bound to distinct multiprotein complexes through the interaction with corepressors, such as NCoR and SMRT. Corepressor complexes comprise histone deacetylases (HDACs) that have the capacity to condense chromatin over target gene promoters. Ligands have been designed that selectively modulate the interaction between NRs and their coregulators. Both HATs and HDACs can also modify the acetylation status of nonhistone proteins, but the significance in the context of NR signaling is unclear. NRs communicate with other intracellular signaling pathways on a mutual basis, and their functionality may be altered, positively or negatively, by post-translational modification. The majority of NRs act as retinoid X receptor (RXR) heterodimers in which RXR cannot a priori respond autonomously to its cognate ligand to activate target gene transcription. This RXR subordination allows signaling pathway identity for the RXR partner. The corresponding mechanism is understood and reveals cell and NR selectivity, indicating that RXR can, under certain conditions, act autonomously. NRs are regulators of cell life and death, and NR malfunction can be at the basis of both disease and therapy, as is impressively documented in the case of acute promyelocytic leukemia. Recently, several pathways have been uncovered that link NR action with cell proliferation and apoptosis.
TIMBAL is a database holding molecules of molecular weight <1200 Daltons that modulate protein–protein interactions. Since its first release, the database has been extended to cover 50 known protein–protein interactions drug targets, including protein complexes that can be stabilized by small molecules with therapeutic effect. The resource contains 14 890 data points for 6896 distinct small molecules. UniProt codes and Protein Data Bank entries are also included.
Database URL:
http://www-cryst.bioc.cam.ac.uk/timbal
Estrogen receptor alpha (ERα) is involved in numerous physiological and pathological processes, including breast cancer. Breast cancer therapy is therefore currently directed at inhibiting the transcriptional potency of ERα, either by blocking estrogen production through aromatase inhibitors or antiestrogens that compete for hormone binding. Due to resistance, new treatment modalities are needed and as ERα dimerization is essential for its activity, interference with receptor dimerization offers a new opportunity to exploit in drug design. Here we describe a unique mechanism of how ERα dimerization is negatively controlled by interaction with 14-3-3 proteins at the extreme C terminus of the receptor. Moreover, the small-molecule fusicoccin (FC) stabilizes this ERα/14-3-3 interaction. Cocrystallization of the trimeric ERα/14-3-3/FC complex provides the structural basis for this stabilization and shows the importance of phosphorylation of the penultimate Threonine (ERα-T(594)) for high-affinity interaction. We confirm that T(594) is a distinct ERα phosphorylation site in the breast cancer cell line MCF-7 using a phospho-T(594)-specific antibody and by mass spectrometry. In line with its ERα/14-3-3 interaction stabilizing effect, fusicoccin reduces the estradiol-stimulated ERα dimerization, inhibits ERα/chromatin interactions and downstream gene expression, resulting in decreased cell proliferation. Herewith, a unique functional phosphosite and an alternative regulation mechanism of ERα are provided, together with a small molecule that selectively targets this ERα/14-3-3 interface.
Mutations in the gene encoding Cu/Zn superoxide dismutase-1 cause amyotrophic lateral sclerosis. Superoxide dismutase-1 mutations decrease protein stability and promote aggregation. The mutant monomer is thought to be an intermediate in the pathway from the superoxide dismutase-1 dimer to aggregate. Here we find that the monomeric copper-apo, zinc-holo protein is structurally perturbed and the apo-protein aggregates without reattainment of the monomer-dimer equilibrium. Intervention to stabilize the superoxide dismutase-1 dimer and inhibit aggregation is regarded as a potential therapeutic strategy. We describe protein-ligand interactions for two compounds, Isoproterenol and 5-fluorouridine, highlighted as superoxide dismutase-1 stabilizers. We find both compounds interact with superoxide dismutase-1 at a key region identified at the core of the superoxide dismutase-1 fibrillar aggregates, β-barrel loop II-strand 3, rather than the proposed dimer interface site. This illustrates the need for direct structural observations when developing compounds for protein-targeted therapeutics.
Most proteins, such as ion channels, form well-organized 3D structures to carry out their specific functions. A typical voltage-gated potassium channel subunit has six transmembrane segments (S1-S6) to form the voltage-sensing domain and the pore domain. Conformational changes of these domains result in opening of the channel pore. Intrinsically disordered (ID) proteins/peptides are considered equally important for the protein functions. However, it is difficult to explore the structural features underlying the functions of ID proteins/peptides by conventional methods, such as X-ray crystallography, because of the flexibility of their secondary structures. Unlike voltage-gated potassium channels, families of small- and intermediate-conductance Ca(2+)-activated potassium (SK/IK) channels with important roles in regulating membrane excitability are activated exclusively by Ca(2+)-bound calmodulin (CaM). Upon binding of Ca(2+) to CaM, a 2 × 2 structure forms between CaM and the CaM-binding domain. A channel fragment that connects S6 and the CaM-binding domain is not visible in the protein crystal structure, suggesting that this fragment is an ID fragment. Here we show that the conformation of the ID fragment in SK channels becomes readily identifiable in the presence of NS309, the most potent compound that potentiates the channel activities. This well-defined conformation of the ID fragment, stabilized by NS309, increases the channel open probability at a given Ca(2+) concentration. Our results demonstrate that the ID fragment, itself a target for drugs modulating SK channel activities, plays a unique role in coupling Ca(2+) sensing by CaM and mechanical opening of SK channels.
Small- and intermediate-conductance Ca(2+)-activated potassium channels, activated by Ca(2+)-bound calmodulin, have an important role in regulating membrane excitability. These channels are also linked to clinical abnormalities. A tremendous amount of effort has been devoted to developing small molecule compounds targeting these channels. However, these compounds often suffer from low potency and lack of selectivity, hindering their potential for clinical use. A key contributing factor is the lack of knowledge of the binding site(s) for these compounds. Here we demonstrate by X-ray crystallography that the binding pocket for the compounds of the 1-ethyl-2-benzimidazolinone (1-EBIO) class is located at the calmodulin-channel interface. We show that, based on structure data and molecular docking, mutations of the channel can effectively change the potency of these compounds. Our results provide insight into the molecular nature of the binding pocket and its contribution to the potency and selectivity of the compounds of the 1-EBIO class.
Plant hormones are a group of naturally occurring, organic substances which influence physiological processes at low concentrations. The processes influenced consist mainly of growth, differentiation and development, though other processes, such as stomatal
movement, may also be affected. Plant hormones1 have also been referred to as ‘phytohormones’ though this term is infrequently used.
The transthyretin amyloidoses (ATTR) are invariably fatal diseases characterized by progressive neuropathy and/or cardiomyopathy. ATTR are caused by aggregation of transthyretin (TTR), a natively tetrameric protein involved in the transport of thyroxine and the vitamin A-retinol-binding protein complex. Mutations within TTR that cause autosomal dominant forms of disease facilitate tetramer dissociation, monomer misfolding, and aggregation, although wild-type TTR can also form amyloid fibrils in elderly patients. Because tetramer dissociation is the rate-limiting step in TTR amyloidogenesis, targeted therapies have focused on small molecules that kinetically stabilize the tetramer, inhibiting TTR amyloid fibril formation. One such compound, tafamidis meglumine (Fx-1006A), has recently completed Phase II/III trials for the treatment of Transthyretin Type Familial Amyloid Polyneuropathy (TTR-FAP) and demonstrated a slowing of disease progression in patients heterozygous for the V30M TTR mutation. Herein we describe the molecular and structural basis of TTR tetramer stabilization by tafamidis. Tafamidis binds selectively and with negative cooperativity (K(d)s ~2 nM and ~200 nM) to the two normally unoccupied thyroxine-binding sites of the tetramer, and kinetically stabilizes TTR. Patient-derived amyloidogenic variants of TTR, including kinetically and thermodynamically less stable mutants, are also stabilized by tafamidis binding. The crystal structure of tafamidis-bound TTR suggests that binding stabilizes the weaker dimer-dimer interface against dissociation, the rate-limiting step of amyloidogenesis.
Proliferating cell nuclear antigen (PCNA), a potential anticancer target, forms a homotrimer and is required for DNA replication and numerous other cellular processes. The purpose of this study was to identify novel small molecules that modulate PCNA activity to affect tumor cell proliferation. An in silico screen of a compound library against a crystal structure of PCNA and a subsequent structural similarity search of the ZINC chemical database were carried out to derive relevant docking partners. Nine compounds, termed PCNA inhibitors (PCNA-Is), were selected for further characterization. PCNA-I1 selectively bound to PCNA trimers with a dissociation constant (K(d)) of ~0.2 to 0.4 μM. PCNA-Is promoted the formation of SDS-refractory PCNA trimers. PCNA-I1 dose- and time-dependently reduced the chromatin-associated PCNA in cells. Consistent with its effects on PCNA trimer stabilization, PCNA-I1 inhibited the growth of tumor cells of various tissue types with an IC(50) of ~0.2 μM, whereas it affected the growth of nontransformed cells at significantly higher concentrations (IC(50), ~1.6 μM). Moreover, uptake of BrdU was dose-dependently reduced in cells treated with PCNA-I1. Mechanistically the PCNA-Is mimicked the effect of PCNA knockdown by siRNA, inducing cancer cell arrest at both the S and G(2)/M phases. Thus, we have identified a class of compounds that can directly bind to PCNA, stabilize PCNA trimers, reduce PCNA association with chromatin, and inhibit tumor cell growth by inducing a cell cycle arrest. They are valuable tools in studying PCNA function and may be useful for future PCNA-targeted cancer therapy.
Influenza nucleoprotein (NP) plays multiple roles in the virus life cycle, including an essential function in viral replication as an integral component of the ribonucleoprotein complex, associating with viral RNA and polymerase within the viral core. The multifunctional nature of NP makes it an attractive target for antiviral intervention, and inhibitors targeting this protein have recently been reported. In a parallel effort, we discovered a structurally similar series of influenza replication inhibitors and show that they interfere with NP-dependent processes via formation of higher-order NP oligomers. Support for this unique mechanism is provided by site-directed mutagenesis studies, biophysical characterization of the oligomeric ligand:NP complex, and an X-ray cocrystal structure of an NP dimer of trimers (or hexamer) comprising three NP_A:NP_B dimeric subunits. Each NP_A:NP_B dimeric subunit contains two ligands that bridge two composite, protein-spanning binding sites in an antiparallel orientation to form a stable quaternary complex. Optimization of the initial screening hit produced an analog that protects mice from influenza-induced weight loss and mortality by reducing viral titers to undetectable levels throughout the course of treatment.
Jasmonates are a family of plant hormones that regulate plant growth, development and responses to stress. The F-box protein CORONATINE INSENSITIVE 1 (COI1) mediates jasmonate signalling by promoting hormone-dependent ubiquitylation and degradation of transcriptional repressor JAZ proteins. Despite its importance, the mechanism of jasmonate perception remains unclear. Here we present structural and pharmacological data to show that the true Arabidopsis jasmonate receptor is a complex of both COI1 and JAZ. COI1 contains an open pocket that recognizes the bioactive hormone (3R,7S)-jasmonoyl-l-isoleucine (JA-Ile) with high specificity. High-affinity hormone binding requires a bipartite JAZ degron sequence consisting of a conserved α-helix for COI1 docking and a loop region to trap the hormone in its binding pocket. In addition, we identify a third critical component of the jasmonate co-receptor complex, inositol pentakisphosphate, which interacts with both COI1 and JAZ adjacent to the ligand. Our results unravel the mechanism of jasmonate perception and highlight the ability of F-box proteins to evolve as multi-component signalling hubs.
In the absence of ligand, some nuclear receptors, including retinoic acid receptor (RAR), act as transcriptional repressors by recruiting corepressor complexes to target genes. This constitutive repression is crucial in metazoan reproduction, development and homeostasis. However, its specific molecular determinants had remained obscure. Using structural, biochemical and cell-based assays, we show that the basal repressive activity of RAR is conferred by an extended beta-strand that forms an antiparallel beta-sheet with specific corepressor residues. Agonist binding induces a beta-strand-to-alpha-helix transition that allows for helix H11 formation, which in turn provokes corepressor release, repositioning of helix H12 and coactivator recruitment. Several lines of evidence suggest that this structural switch could be implicated in the intrinsic repressor function of other nuclear receptors. Finally, we report on the molecular mechanism by which inverse agonists strengthen corepressor interaction and enhance gene silencing by RAR.
S100A4, a member of the S100 family of Ca(2+)-binding proteins, regulates carcinoma cell motility via interactions with myosin-IIA. Numerous studies indicate that S100A4 is not simply a marker for metastatic disease, but rather has a direct role in metastatic progression. These observations suggest that S100A4 is an excellent target for therapeutic intervention. Using a unique biosensor-based assay, trifluoperazine (TFP) was identified as an inhibitor that disrupts the S100A4/myosin-IIA interaction. To examine the interaction of S100A4 with TFP, we determined the 2.3 A crystal structure of human Ca(2+)-S100A4 bound to TFP. Two TFP molecules bind within the hydrophobic target binding pocket of Ca(2+)-S100A4 with no significant conformational changes observed in the protein upon complex formation. NMR chemical shift perturbations are consistent with the crystal structure and demonstrate that TFP binds to the target binding cleft of S100A4 in solution. Remarkably, TFP binding results in the assembly of five Ca(2+)-S100A4/TFP dimers into a tightly packed pentameric ring. Within each pentamer most of the contacts between S100A4 dimers occurs through the TFP moieties. The Ca(2+)-S100A4/prochlorperazine (PCP) complex exhibits a similar pentameric assembly. Equilibrium sedimentation and cross-linking studies demonstrate the cooperative formation of a similarly sized S100A4/TFP oligomer in solution. Assays examining the ability of TFP to block S100A4-mediated disassembly of myosin-IIA filaments demonstrate that significant inhibition of S100A4 function occurs only at TFP concentrations that promote S100A4 oligomerization. Together these studies support a unique mode of inhibition in which phenothiazines disrupt the S100A4/myosin-IIA interaction by sequestering S100A4 via small molecule-induced oligomerization.
Atrial fibrillation (AF) is the most common sustained arrhythmia. Previous studies have identified several genetic loci associated with typical AF. We sought to identify common genetic variants underlying lone AF. This condition affects a subset of individuals without overt heart disease and with an increased heritability of AF. We report a meta-analysis of genome-wide association studies conducted using 1,335 individuals with lone AF (cases) and 12,844 unaffected individuals (referents). Cases were obtained from the German AF Network, Heart and Vascular Health Study, the Atherosclerosis Risk in Communities Study, the Cleveland Clinic and Massachusetts General Hospital. We identified an association on chromosome 1q21 to lone AF (rs13376333, adjusted odds ratio = 1.56; P = 6.3 x 10(-12)), and we replicated this association in two independent cohorts with lone AF (overall combined odds ratio = 1.52, 95% CI 1.40-1.64; P = 1.83 x 10(-21)). rs13376333 is intronic to KCNN3, which encodes a potassium channel protein involved in atrial repolarization.
Genomic and proteomic profiling of human tumor samples and tumor-derived cell lines are essential for the realization of personalized therapy in oncology. Identification of the changes required for tumor initiation or maintenance will likely provide new targets for small-molecule and biological therapeutics. For example, inactivation of the p53 tumor suppressor pathway occurs in most human cancers. Although this can be due to frank p53 gene mutation, almost half of all cancers retain the wild-type p53 allele, indicating that the pathway is disabled by other means. Alternate mechanisms include deletion or epigenetic inactivation of the p53-positive regulator arf, methylation of the p53 promoter, or elevated expression of the p53 regulators Mdm2 and Mdmx. This review discusses current models of p53 regulation by Mdm2 and Mdmx and presents the rationale for design of future Mdmx-specific therapeutics based on our knowledge of its structure and biological functions.
Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets. Here we describe a framework that uses an empirically-based approach to rigorously dissect quality parameters of currently available human interactome maps. Our results indicate that high-throughput yeast two-hybrid (HT-Y2H) interactions for human proteins are more precise than literature-curated interactions supported by a single publication, suggesting that HT-Y2H is suitable to map a significant portion of the human interactome. We estimate that the human interactome contains approximately 130,000 binary interactions, most of which remain to be mapped. Similar to estimates of DNA sequence data quality and genome size early in the Human Genome Project, estimates of protein interaction data quality and interactome size are crucial to establish the magnitude of the task of comprehensive human interactome mapping and to elucidate a path toward this goal.
Microtubules are formed from a 110,000-dalton dimeric subunit called tubulin. Two forms of 55,000-dalton monomer, alpha and beta, are found in all microtubule preparations. The dimers could thus theoretically be either heterodimers (alphabeta) or homodimers (alphaalpha and betabeta). This problem was investigated by stigated by chemical cross-linking using several bifunctional reagents, of which one, dimethyl-3,3-(tetrame thylenedioxy) dipropionimidate dihydrochloride (DTDI), was able to make intradimer bonds in tubulin. When soluble chick brain tubulin was cross-linked with DTDI and analyzed by electrophoresis in an acrylamide gel system capable of resolving alphaalpha, alphabeta, and betabeta, 60 to 90% of the cross-linked dimer was alphabeta. If tubulin was incubated at 24 degrees prior to cross-linking with DTDI the total yield of cross-linked dimer increased with time, indicating that tubulin was forming loose aggregates. The relative amounts of cross-linked dimer alphaalpha and betabeta also increase with time, indicating that soluble tubulin is largely alphabeta, and suggesting that cross-linked alphaalpha and betabeta arise from nonspecific aggregation during tubulin purification. The aggregation observed by cross-linking with DTDI was strongly influenced by colchicine and Vinca alkaloids in a pattern similar to the effects of these drugs on tubulin polymerization.
(Figure Presented) Two structurally unrelated small molecules that stabilize the interaction of a 14-3-3 protein with the proton pump PMA2 have been identified. The compounds are selective among different 14-3-3 protein-protein interactions and are active in vivo. Crystal structures of ternary complexes revealed that the molecules bind to different sites in the interface of the 14-3-3 protein and PMA2 (see picture), thus explaining the different binding kinetics.
Protein–protein interactions (PPIs) are implicated in every disease and mastering the ability to influence PPIs with small molecules would considerably enlarge the druggable genome. Whereas inhibition of PPIs has repeatedly been shown to work successfully, targeted stabilization of PPIs is underrepresented in the literature. This is all the more surprising because natural products like FK506, rapamycin, brefeldin, forskolin and fusicoccin confer their physiological activity by stabilizing specific PPIs. However, recently a number of very interesting synthetic molecules have been reported from drug discovery projects that indeed achieve their desired activities by stabilizing either homo- or hetero-oligomeric complexes of their target proteins.
Fusicoccin, a naturally occurring compound, stabilizes a 14-3-3 protein–protein interaction and induces wilting of plants by opening the gas-exchanging stomatal pores (gray). C. Ottmann and co-workers describe in their Communication on page 4129 ff. how easily available small molecules have been identified that mimic the action of fusicoccin. Crystal-structure and functional biophysical analyses reveal the binding modes of these molecules.
This study presents model extensions for a lattice Boltzmann (LB) approach to thermal axisymmetric flow including swirl or rotation. An incompressible axisymmetric lattice Boltzmann D2Q9 model was applied to solve the axial and radial velocities through inserting source terms into the two-dimensional lattice Boltzmann equation. The equations governing azimuthal (or swirling) velocity and the temperature were also solved by the LBM. It is found that this scheme is much more stable and consistent compared to previous hybrid schemes. It provides a significant advantage in simulation of melt flows with high Reynolds number and high Grashof number. The present scheme was validated by comparing the LB results with benchmark solutions for melt flow in Czochralski crystal growth. Unsteady flows with high Grashof numbers were studied in detail. The critical Grashof number for the onset of the oscillation is found to be about 2.5×1062.5×106. The oscillation amplitude ψmaxψmax is proportional to (Gr-Grc)0.5(Gr-Grc)0.5 for 2.5×106<Gr<6×1062.5×106<Gr<6×106. The frequencies and flow patterns of the unsteady flows are also analyzed. The distributions of the mean quantities of the temperature and rms of temperature at Grashof number as high as 6×1076×107 is found to be similar to those obtained by 3D simulations.
One third of all human cancers harbor somatic RAS mutations. This leads to aberrant activation of downstream signaling pathways involving the RAF kinases. Current ATP-competitive RAF inhibitors are active in cancers with somatic RAF mutations, such as BRAFV600-mutant melanomas. However, they paradoxically promote the growth of RAS-mutant tumors, partly due to the complex interplay between different homo- and heterodimers of A-RAF, B-RAF and C-RAF. Based on pathway analysis and structure-guided compound identification we describe the natural product cotylenin-A (CN-A) as stabilizer of the physical interaction of C-RAF with 14-3-3 proteins. CN-A binds to inhibitory 14-3-3 interaction sites of C-RAF, pSer233 and pSer259, but not to the activating interaction site, pSer621. While CN-A alone is inactive in RAS-mutant cancer models, combined treatment with CN-A and an anti-EGFR antibody synergistically suppresses tumor growth in vitro and in vivo. This defines a novel pharmacologic strategy for treatment of RAS-mutant cancers.
Most multicellular organisms use steroids as signalling molecules for
physiological and developmental regulation. Two different modes of
steroid action have been described in animal systems: the well-studied
gene regulation response mediated by nuclear receptors, and the rapid
non-genomic responses mediated by proposed membrane-bound receptors.
Plant genomes do not seem to encode members of the nuclear receptor
superfamily. However, a transmembrane receptor kinase,
brassinosteroid-insensitive1 (BRI1), has been implicated in
brassinosteroid responses. Here we show that BRI1 functions as a
receptor of brassinolide, the most active brassinosteroid. The number of
brassinolide-binding sites and the degree of response to brassinolide
depend on the level of BRI1 protein. The brassinolide-binding activity
co-immunoprecipitates with BRI1, and requires a functional BRI1
extracellular domain. Moreover, treatment of Arabidopsis seedlings with
brassinolide induces autophosphorylation of BRI1, which, together with
our binding studies, shows that BRI1 is a receptor kinase that
transduces steroid signals across the plasma membrane.
The development of small molecule drugs targeting protein-protein interactions (PPI) represents a major challenge, in part owing to the misunderstanding of the PPI chemical space. To this end, we have manually collected and stored structures, physicochemical and pharmacological profiles of 1650 PPI inhibitors across 13 families of PPI targets in an online database: iPPI-DB. Based on a large variety of query criteria and analysis tools, the functionalities of this expanding database could assist scientists to design the next generation of PPI drugs. In this review, we describe iPPI-DB in the context of other low molecular weight molecule databases.
Small-molecule stabilization of protein-protein interactions is an emerging field in chemical biology. We show how fusicoccanes, originally identified as fungal toxins acting on plants, promote the interaction of 14-3-3 proteins with the human potassium channel TASK-3 and present a semisynthetic fusicoccane derivative (FC-THF) that targets the 14-3-3 recognition motif (mode 3) in TASK-3. In the presence of FC-THF, the binding of 14-3-3 proteins to TASK-3 was increased 19-fold and protein crystallography provided the atomic details of the effects of FC-THF on this interaction. We also tested the functional effects of FC-THF on TASK channels heterologously expressed in Xenopus oocytes. Incubation with 10 μM FC-THF was found to promote the transport of TASK channels to the cell membrane, leading to a significantly higher density of channels at the surface membrane and increased potassium current.
In this review, we discuss the structural and functional diversity of protein–protein interactions (PPIs) based primarily on protein families for which three-dimensional structural data are available. PPIs play diverse roles in biology and differ based on the composition, affinity and whether the association is permanent or transient. In vivo, the protomer's localization, concentration and local environment can affect the interaction between protomers and are vital to control the composition and oligomeric state of protein complexes. Since a change in quaternary state is often coupled with biological function or activity, transient PPIs are important biological regulators. Structural characteristics of different types of PPIs are discussed and related to their physiological function, specificity and evolution.
The two-pore-domain potassium channels TASK-1 (KCNK3) and TASK-3 (KCNK9) modulate the electrical activity of neurons and many other cell types. We expressed TASK-1, TASK-3 and related reporter constructs in Xenopus oocytes, mammalian cell lines and various yeast strains to study the mechanisms controlling their transport to the surface membrane and the role of 14-3-3 proteins. We measured potassium currents with the voltage-clamp technique and fused N- and C-terminal fragments of the channels to various reporter proteins to study changes in subcellular localisation and surface expression. Mutational analysis showed that binding of 14-3-3 proteins to the extreme C-terminus of TASK-1 and TASK-3 masks a tri-basic motif, KRR, which differs in several important aspects from canonical arginine-based (RxR) or lysine-based (KKxx) retention signals. Pulldown experiments with GST fusion proteins showed that the KRR motif in the C-terminus of TASK-3 channels was able to bind to COPI coatomer. Disabling the binding of 14-3-3, which exposes the KRR motif, caused localisation of the GFP-tagged channel protein mainly to the Golgi complex. TASK-1 and TASK-3 also possess a di-basic N-terminal retention signal, KR, whose function was found to be independent of the binding of 14-3-3. Suppression of channel surface expression with dominant-negative channel mutants revealed that interaction with 14-3-3 has no significant effect on the dimeric assembly of the channels. Our results give a comprehensive description of the mechanisms by which 14-3-3 proteins, together with N- and C-terminal sorting signals, control the intracellular traffic of TASK-1 and TASK-3.
Activation of p53 tumor suppressor by antagonizing its negative regulator murine double minute (MDM)2 has been considered an attractive strategy for cancer therapy and several classes of p53-MDM2 binding inhibitors have been developed. However, these compounds do not inhibit the p53-MDMX interaction, and their effectiveness can be compromised in tumors overexpressing MDMX. Here, we identify small molecules that potently block p53 binding with both MDM2 and MDMX by inhibitor-driven homo- and/or heterodimerization of MDM2 and MDMX proteins. Structural studies revealed that the inhibitors bind into and occlude the p53 pockets of MDM2 and MDMX by inducing the formation of dimeric protein complexes kept together by a dimeric small-molecule core. This mode of action effectively stabilized p53 and activated p53 signaling in cancer cells, leading to cell cycle arrest and apoptosis. Dual MDM2/MDMX antagonists restored p53 apoptotic activity in the presence of high levels of MDMX and may offer a more effective therapeutic modality for MDMX-overexpressing cancers.
Until recently, the expression and primary function of the cell surface receptor CD40 and its ligand CD154 were considered
restricted to B and T lymphocytes, and their interactions required for the thymus-dependent humoral response. However, current
work from several groups challenges this view of the CD40/CD154 dyad as a mere mediator of lymphocyte communication. A variety
of non-lymphocytic cell types express both receptor and ligand, including hematopoetic and non-hematopoetic cells, such as
monocytes, basophils, eosinophils, dendritic cells, fibroblasts, smooth muscle, and endothelial cells. Accordingly, ligation
of CD40 mediates a broad variety of immune and inflammatory responses, such as the expression of adhesion molecules, cytokines,
matrix-degrading enzymes, prothrombotic activities, and apoptotic mediators. Consequently, CD40 signaling has been associated
with pathogenic processes of chronic inflammatory diseases, such as autoimmune diseases, neurodegenerative disorders, graft-versus-host
disease, cancer, and atherosclerosis. This review focuses on the synthesis and structure of CD40 and outlines CD154/CD40 signaling
pathways, and emphasizes the previously unexpected importance of the CD40/CD154 receptor/ligand dyad in a spectrum of immunoregulatory
processes and prevalent human diseases.
Modulation of protein-protein interactions (PPIs) is a highly demanding, but also a very promising approach in chemical biology and targeted drug discovery. In contrast to inhibiting PPIs with small, chemically tractable molecules, stabilisation of these interactions can only be achieved with complex natural products, like rapamycin, FK506, taxol, forskolin, brefeldin and fusicoccin. Fusicoccin stabilises the activatory complex of the plant H(+)-ATPase PMA2 and 14-3-3 proteins. Recently, we have shown that the stabilising effect of fusicoccin could be mimicked by a trisubstituted pyrrolinone (pyrrolidone1, 1). Here, we report the synthesis, functional activity and crystal structure of derivatives of 1 that stabilise the 14-3-3-PMA2 complex. With a limited compound collection three modifications that are important for activity enhancement could be determined: 1) conversion of the pyrrolinone scaffold into a pyrazole, 2) introduction of a tetrazole moiety to the phenyl ring that contacts PMA2, and 3) addition of a bromine to the phenyl ring that exclusively contacts the 14-3-3 protein. The crystal structure of a pyrazole derivative of 1 in complex with 14-3-3 and PMA2 revealed that the more rigid core of this molecule positions the stabiliser deeper into the rim of the interface, enlarging especially the contact surface to PMA2. Combination of the aforementioned features gave rise to a molecule (37) that displays a threefold increase in stabilising the 14-3-3-PMA2 complex over 1. Compound 37 and the other active derivatives show no effect on two other important 14-3-3 protein-protein interactions, that is, with CRaf and p53. This is the first study that describes the successful optimisation of a PPI stabiliser identified by screening.
The modulation of protein-protein interactions (PPIs) has been recognized as one of the most challenging tasks in drug discovery. While their systematic development has long been considered as intractable, this view has changed over the last years, with the first drug candidates undergoing clinical studies. To date, the vast majority of PPI modulators are interaction inhibitors. However, in many biological contexts a prolonged lifespan of a PPI might be desirable, calling for the complementary approach of PPI stabilization. In fact, nature offers impressive examples of this concept and some PPI-stabilizing natural products have already found application as important drugs. Moreover, directed small-molecule stabilization has recently been demonstrated. Therefore, it is time to take a closer look at the constructive side of modulating PPIs.
Histone deacetylase enzymes (HDACs) are emerging cancer drug targets. They regulate gene expression by removing acetyl groups from lysine residues in histone tails, resulting in chromatin condensation. The enzymatic activity of most class I HDACs requires recruitment into multi-subunit co-repressor complexes, which are in turn recruited to chromatin by repressive transcription factors. Here we report the structure of a complex between an HDAC and a co-repressor, namely, human HDAC3 with the deacetylase activation domain (DAD) from the human SMRT co-repressor (also known as NCOR2). The structure reveals two remarkable features. First, the SMRT-DAD undergoes a large structural rearrangement on forming the complex. Second, there is an essential inositol tetraphosphate molecule--D-myo-inositol-(1,4,5,6)-tetrakisphosphate (Ins(1,4,5,6)P(4))--acting as an 'intermolecular glue' between the two proteins. Assembly of the complex is clearly dependent on the Ins(1,4,5,6)P(4), which may act as a regulator--potentially explaining why inositol phosphates and their kinases have been found to act as transcriptional regulators. This mechanism for the activation of HDAC3 appears to be conserved in class I HDACs from yeast to humans, and opens the way to novel therapeutic opportunities.
Small-conductance Ca(2+)-activated K(+) channels (SK channels) are widely expressed throughout the central nervous system. These channels are activated solely by increases in intracellular Ca(2+). SK channels are stable macromolecular complexes of the ion pore-forming subunits with calmodulin, which serves as the intrinsic Ca(2+) gating subunit, as well as with protein kinase CK2 and protein phosphatase 2A, which modulate Ca(2+) sensitivity. Well-known for their roles in regulating somatic excitability in central neurons, SK channels are also expressed in the postsynaptic membrane of glutamatergic synapses, where their activation and regulated trafficking modulate synaptic transmission and the induction and expression of synaptic plasticity, thereby affecting learning and memory. In this review we discuss the molecular and functional properties of SK channels and their physiological roles in central neurons.
Phenylketonuria (PKU), the most common inborn error of metabolism, is caused by dysfunction of the liver enzyme phenylalanine hydroxylase (PAH), with more than 550 PAH gene mutations identified to date. A large number of these mutations result in mutant forms of the enzyme displaying reduced stability, increased propensity to aggregate, and accelerated in cellulo degradation. Loss or reduction of human PAH activity results in hyperphenylalaninemia (HPA) which, if untreated, results in severe mental retardation and impaired cognitive development. Until now, strict low phenylalanine diet has been the most effective therapy, but as a protein misfolding disease PKU is a good candidate for treatment by natural/chemical/pharmacological chaperones. The natural cofactor of human PAH, (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH(4)), has already been approved for oral treatment of HPA, giving a positive response in mild forms of the disease showing considerable residual enzymatic activity. In the case of the most severe forms of PKU, ongoing studies with chemical and pharmacological chaperones to rescue misfolded mutant proteins from aggregation and degradation are providing promising results. The PKU mutation G46S is associated with a severe form of the disease, resulting in an aggregation-prone protein. The human PAH mutant G46S is rapidly degraded in the cellular environment and, in vitro (upon removal of its stabilizing fusion partner maltose binding protein (MBP)) self-associates to form higher-order oligomers/fibrils. Here, we present an in vitro experimental model system to study the modulation of G46S aggregation by chemical/pharmacological chaperones, which may represent a useful approach to study the rescue of other severe PKU mutations by chemical/pharmacological chaperones.
Survivin is one of the most tumor-specific genes in the human genome and is an attractive target for cancer therapy. However, small-molecule ligands for survivin have not yet been described. Thus, an interrogation of survivin which could potentially both validate a small-molecule therapy approach, and determine the biochemical nature of any of survivin's functions has not been possible. Here we describe the discovery and characterization of a small molecule binding site on the survivin surface distinct from the Smac peptide-binding site. The new site is located at the dimer interface and exhibits many of the features of highly druggable, biologically relevant protein binding sites. A variety of small hydrophobic compounds were found that bind with moderate affinity to this binding site, from which one lead was developed into a group of compounds with nanomolar affinity. Additionally, a subset of these compounds are adequately water-soluble and cell-permeable. Thus, the structural studies and small molecules described here provide tools that can be used to probe the biochemical role(s) of survivin, and may ultimately serve as a basis for the development of small molecule therapeutics acting via direct or allosteric disruption of binding events related to this poorly understood target.
Worldwide research efforts have driven recent pharmaceutical successes, and consequently, the emerging role of Protein-Protein Interactions (PPIs) as drug targets has finally been widely embraced by the scientific community. Inhibitors of these Protein-Protein Interactions (2P2Is or i-PPIs) are likely to represent the next generation of highly innovative drugs that will reach the market over the next decade. This review describes up-to-date knowledge on this particular chemical space, with a specific emphasis on a subset of this ensemble. We also address current structural knowledge regarding both protein-protein and protein-inhibitor complexes, that is, the 2P2I database. Finally, ligand efficiency analyses permit us to relate potency to size and polarity and to discuss the need to co-develop nanoparticle drug delivery systems.
In the ubiquitin-proteasome system (UPS), E2 enzymes mediate the conjugation of ubiquitin to substrates and thereby control protein stability and interactions. The E2 enzyme hCdc34 catalyzes the ubiquitination of hundreds of proteins in conjunction with the cullin-RING (CRL) superfamily of E3 enzymes. We identified a small molecule termed CC0651 that selectively inhibits hCdc34. Structure determination revealed that CC0651 inserts into a cryptic binding pocket on hCdc34 distant from the catalytic site, causing subtle but wholesale displacement of E2 secondary structural elements. CC0651 analogs inhibited proliferation of human cancer cell lines and caused accumulation of the SCF(Skp2) substrate p27(Kip1). CC0651 does not affect hCdc34 interactions with E1 or E3 enzymes or the formation of the ubiquitin thioester but instead interferes with the discharge of ubiquitin to acceptor lysine residues. E2 enzymes are thus susceptible to noncatalytic site inhibition and may represent a viable class of drug target in the UPS.
BIO8898 is one of several synthetic organic molecules that have recently been reported to inhibit receptor binding and function of the constitutively trimeric tumor necrosis factor (TNF) family cytokine CD40 ligand (CD40L, aka CD154). Small molecule inhibitors of protein-protein interfaces are relatively rare, and their discovery is often very challenging. Therefore, to understand how BIO8898 achieves this feat, we characterized its mechanism of action using biochemical assays and X-ray crystallography. BIO8898 inhibited soluble CD40L binding to CD40-Ig with a potency of IC(50) = 25 μM and inhibited CD40L-dependent apoptosis in a cellular assay. A co-crystal structure of BIO8898 with CD40L revealed that one inhibitor molecule binds per protein trimer. Surprisingly, the compound binds not at the surface of the protein but by intercalating deeply between two subunits of the homotrimeric cytokine, disrupting a constitutive protein-protein interface and breaking the protein's 3-fold symmetry. The compound forms several hydrogen bonds with the protein, within an otherwise hydrophobic binding pocket. In addition to the translational splitting of the trimer, binding of BIO8898 was accompanied by additional local and longer-range conformational perturbations of the protein, both in the core and in a surface loop. Binding of BIO8898 is reversible, and the resulting complex is stable and does not lead to detectable dissociation of the protein trimer. Our results suggest that a set of core aromatic residues that are conserved across a subset of TNF family cytokines might represent a generic hot-spot for the induced-fit binding of trimer-disrupting small molecules.
The transcription factor c-Myc is overexpressed in many tumors in human beings and has been identified as a highly promising target for cancer therapy. Most biological functions of c-Myc require heterodimerization with its activation partner Max. Inhibition of the protein-protein interactions between c-Myc and Max by small molecules has been shown to be a feasible and powerful approach toward the inhibition of c-Myc functions. More recently, stabilization of Max homodimers to reduce the amount of Max available for activating c-Myc has also been demonstrated to counteract Myc activity. This review summarizes our current knowledge on small organic molecules that inhibit c-Myc by modulating protein-protein interactions relevant for the biological function of this important oncoprotein.
Many human cancers show constitutive or amplified expression of the transcriptional regulator and oncoprotein Myc, making Myc a potential target for therapeutic intervention. Here we report the down-regulation of Myc activity by reducing the availability of Max, the essential dimerization partner of Myc. Max is expressed constitutively and can form unstable homodimers. We have isolated stabilizers of the Max homodimer by applying virtual ligand screening (VLS) to identify specific binding pockets for small molecule interactors. Candidate compounds found by VLS were screened by fluorescence resonance energy transfer, and from these screens emerged a potent, specific stabilizer of the Max homodimer. In vitro binding assays demonstrated that the stabilizer enhances the formation of the Max-Max homodimer and interferes with the heterodimerization of Myc and Max in a dose-dependent manner. Furthermore, this compound interferes with Myc-induced oncogenic transformation, Myc-dependent cell growth, and Myc-mediated transcriptional activation. The Max-Max stabilizer can be considered a lead compound for the development of inhibitors of the Myc network.
Cotylenin A, a fungal metabolite originally described as a cytokinin-like bioactive substance against plants shows differentiation-inducing and anti-tumor activity in certain human cancers. Here, we present the crystal structure of cotylenin A acting on a 14-3-3 regulatory protein complex. By comparison with the closely related, but non-anticancer agent fusicoccin A, a rationale for the activity of cotylenin A in human cancers is presented. This class of fusicoccane diterpenoids are possible general modulators of 14-3-3 protein-protein interactions. In this regard, specificities for individual 14-3-3/target protein complexes might be achieved by varying the substituent pattern of the diterpene ring system. As the different activities of fusicoccin A and cotylenin A in human cancers suggest, hydroxylation of C12 might be a sufficient determinant of structural specificity.
The binding of linear and circular forms of DNA to yeast DNA topoisomerase II or its complex with AMPPNP, the nonhydrolyzable beta,gamma-imido analog of ATP, was carried out to probe the ATP analog-induced conformational change of the enzyme. Binding of the ATP analog is shown to convert the enzyme to a circular clamp with an annulet, through which only a linear DNA can pass; subsequent circularization of the bound linear DNA forms a salt-stable catenane between the protein circular clamp and the DNA ring. Analysis of catenane formation between a small DNA ring originally bound to the topoisomerase and a large DNA ring subsequently added, under conditions such that the two do not exchange, supports a model in which a second DNA double-helix can enter the open jaws of a DNA-bound protein clamp, and the closure of the jaws upon ATP-binding traps the second duplex and transports it through an enzyme-operated gate in the first DNA duplex.
CYCLOSPORIN A and the newly discovered immunosuppressant, FK-506, are potent inhibitors of T cell activation. In addition to their clinical importance in the prevention of allograft rejection, cyclosporin A and FK-506 represent important reagents for the study of the molecular mechanisms of lymphocyte activation. Cyclosporin A, a cyclic undecapeptide and FK-506, a macrolide, although chemically distinct, inhibit similar lymphocyte activation responses. The earliest responses inhibited in the T cell seem to be the expression of early phase T cell-activation genes for interleukins 2, 3 and 4, granulocyte-macrophage colony stimulating factor and gamma interferon. Although FK-506 and cyclosporin A seem to inhibit similar signal transduction processes, they do so be interacting with distinct cytosolic proteins. We report here the purification to homogeneity of a specific FK-506 binding protein that is distinct from the cyclosporin A-binding protein, cyclophilin. In addition, we show that this FK-506 binding protein, like cyclophilin, has peptidyl-prolyl isomerase activity.
A series of twelve structurally related bisdioxopiperazines that included ICRF-187 (dexrazoxane), ICRF-159 (razoxane), ICRF-193, and ICRF-154 were examined both for their ability to inhibit the growth of Chinese hamster ovary (CHO) cells and their ability to inhibit the catalytic activity of mammalian DNA topoisomerase II. The bisdioxopiperazines exhibited a wide range in both growth inhibitory effects (30,000-fold), and in their ability to inhibit the catalytic activity of topoisomerase II (150-fold). The cytotoxicity of the bisdioxopiperazines toward CHO cells was highly correlated (correlation coefficient r = 0.86, P = 0.0003) with their inhibition of the catalytic activity of DNA topoisomerase II. This result strongly suggests that DNA topoisomerase II is the functional target of the bisdioxopiperazines. The stereoisomers (+)-ICRF-187 and (-)-ICRF-186 were observed to be equally cytotoxic and equally inhibitory toward DNA topoisomerase II. This result indicates that the bisdioxopiperazine binding site on DNA topoisomerase II is large enough or flexible enough to accommodate either form of the drug. The strongly metal-ion binding fully rings-opened hydrolysis product of ICRF-187, ADR-925, demonstrated no measurable inhibitory activity toward DNA topoisomerase II or cytotoxicity toward CHO cells.