No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Structure-based discovery of a new class of Hsp90 inhibitors
Abstract
Docking-based virtual screening identified 1-(2-phenol)-2-naphthol compounds as a new class of Hsp90 inhibitors of low to sub-micromolar potency. Here we report the binding affinities and cellular activities of several members of this class. A high resolution crystal structure of the most potent compound reveals its binding mode in the ATP binding site of Hsp90, providing a rationale for the observed activity of the series and suggesting strategies for developing compounds with improved properties.
... The heat shock protein 90 (Hsp90) is a molecular chaperone implicated in the progression and survival of cancer, making it a target for cancer therapy (Bickel & Gohlke, 2019). The techniques of docking-based virtual screening for potential Hsp90 inhibitors has been validated elsewhere (Barril et al., 2005;Vilenchik et al., 2004). ATP binds to the N-terminal domain of Hsp90, thereby driving the activity of protein chaperone (Barril et al., 2005). ...
... The techniques of docking-based virtual screening for potential Hsp90 inhibitors has been validated elsewhere (Barril et al., 2005;Vilenchik et al., 2004). ATP binds to the N-terminal domain of Hsp90, thereby driving the activity of protein chaperone (Barril et al., 2005). The region, therefore represents a target for Hsp90 inhibitors. ...
Cancer is a rapidly growing non-communicable disease worldwide that is responsible for high mortality rates, which account for 9.6 million death in 2018. Dihydroartemisinin (DHA) is an active metabolite of artemisinin, an active principle present in the Chinese medicinal plant Artemisia annua used for malaria treatment. Dihydroartemisinin possesses remarkable and selective anticancer properties however the underlying mechanism of the antitumor effects of DHA from the structural point of view is still not yet elucidated. In the present study, we employed molecular docking simulation techniques using Autodock suits to access the binding properties of dihydroartemisinin to multiple protein targets implicated in cancer pathogenesis. Its potential targets with comprehensive pharmacophore were predicted using a PharmMapper database. The co-crystallised structures of the protein were obtained from a Protein Data Bank and prepared for molecular docking simulation. Out of the 24 selected protein targets, DHA has shown about 29% excellent binding to the targets compared to their co-crystallised ligand. Additionally, 75% of the targets identified for dihydroartemisinin binding are protein kinases, and 25% are non-protein kinases. Hydroxyl functional group of dihydroartemisinin contributed to 58.5% of the total hydrogen interactions, while pyran (12.2%), endoperoxide (9.8%), and oxepane (19.5%) contributed to the remaining hydrogen bonding. The present findings have elucidated the possible antitumor properties of dihydroartemisinin through the structural-based virtual studies, which provides a lead to a safe and effective anticancer agent useful for cancer therapy.
Communicated by Ramaswamy H. Sarma
... Developed at the company now known as Vernalis (http://www.vernalis.com), the software, scoring functions, and search protocols have been refined continuously over a number of years to meet the demands of inhouse discovery projects on heat-shock proteins [7][8][9], kinases [10][11][12][13] and other targets. The major components of the platform now include fast intermolecular scoring functions (vdW, polar, desolvation) validated against protein and RNA targets, a Genetic Algorithm (GA)-based stochastic search engine, a wide variety of external restraint terms (tethered template, pharmacophoric restraints), and novel Genetic Programming-based post-docking filtering [14]. ...
... This is an essential step common to all successful docking-based VS undertakings [3,27]. For this reason, we have compared the outcome of VS on Hsp90, a DUD system for which we have developed and used optimal docking protocols [7,8,28]. The cavity includes 2 interstitial water molecules and two pharmacophoric points. ...
Identification of chemical compounds with specific biological activities is an important step in both chemical biology and drug discovery. When the structure of the intended target is available, one approach is to use molecular docking programs to assess the chemical complementarity of small molecules with the target; such calculations provide a qualitative measure of affinity that can be used in virtual screening (VS) to rank order a list of compounds according to their potential to be active. rDock is a molecular docking program developed at Vernalis for high-throughput VS (HTVS) applications. Evolved from RiboDock, the program can be used against proteins and nucleic acids, is designed to be computationally very efficient and allows the user to incorporate additional constraints and information as a bias to guide docking. This article provides an overview of the program structure and features and compares rDock to two reference programs, AutoDock Vina (open source) and Schrödinger's Glide (commercial). In terms of computational speed for VS, rDock is faster than Vina and comparable to Glide. For binding mode prediction, rDock and Vina are superior to Glide. The VS performance of rDock is significantly better than Vina, but inferior to Glide for most systems unless pharmacophore constraints are used; in that case rDock and Glide are of equal performance. The program is released under the Lesser General Public License and is freely available for download, together with the manuals, example files and the complete test sets, at http://rdock.sourceforge.net/
... membrane proteins), the selection of the ligand database, the flexibility of the molecules and the receptor, the evaluation and ranking of each ligand active conformation through the scoring functions, the entropy penalty for immobilization of rotatable bonds in binding and the influence of water molecules are some of the subjects in constant discussion [1,2]. However, it was demonstrated that this kind of VS has made an important contribution to the generation of novel active structures as well to the understanding of proteing-ligand interactions [1,[3][4][5][6][7][8]. ...
... The predicted pKi values were very close to the experimental ones. In particular, one of the derivatives (4-[3- [1,2,4]triazolo [1,5c] pyrimidin-5-yl)ureido]phenyacetic acid ethyl ester) presents activity in a sub-nanomolar range (0.82nM); which was properly predicted by the regression model. Fig. (3) represents the combined design strategy used by the authors. ...
The progress in chemical knowledge and synthetic technologies over the last fifty-years has dramatically increased the synthetic accessible chemical entities. Exploration of natural products rich chemodiversity has also expanded the vast chemical universe where medicinal chemist can pursue the identification of new therapeutic agents. Virtual Screening (VS) benefits from computational technology to explore the increasingly vast chemical universe in an efficient manner. The different VS approaches may be characterized by the computational and human time they require, from the highly automated and fast 2D-QSAR ligand-based VS to the more demanding 3D QSAR and target-based (docking) methodologies. Recently, several studies based on the integration of different VS approaches have been proposed, demonstrating that the hit recovery rate may be maintained (or even increased) with a substantial reduction of computing times. Combined virtual screening methodologies usually begin with the least-demanding approaches at the beginning of the VS process and progress to the more accurate, time consuming techniques in the last stages. This review discusses recent 2D/3D QSAR and ligand-based/target-based “synergistic” combinations that allow speeding-up the VS process, permitting accurate and efficient studies on large databases. The impact of the combination of different techniques on the chemical diversity of the compounds retrieved is also discussed.
... These issues have led to significant efforts to identify novel rationally designed small molecular inhibitors of Hsp90 19 . The main focus of recent efforts toward the development of new Hsp90 inhibitors concentrate on structure-based ligand design [20][21][22] and highthroughput screening 23 , with a few ligand-based examples 24,25 . ...
The pharmacophoric features of the virtual cocrystallized protein of 178 Hsp90 proteins were obtained from the protein data bank and explored to generate 1260 pharmacophores evaluated using the decoy list composed of 1022 compounds. Accordingly, 51 pharmacophores were selected with high receiver operating characteristic (ROC) value for further processing. Subsequently, genetic algorithm and multiple linear regression analysis were employed to select an optimal combination of pharmacophoric models and 2D physicochemical descriptors capable of accessing a self-consistent quantitative structure-activity relationship (QSAR) of optimal predictive potential (R 2 67 ¼ 0.819, F ¼ 43.0, R 2 LOO ¼ 0.782, R 2 PRESS against 16 external test inhibitors equal 0.735). Two orthogonal pharmacophores emerged in the QSAR equation suggesting the existence of at least two binding modes accessible to ligands within the Hsp90 binding pocket. The fifth generated pharmacophoric model from Hsp90 protein 2XJX (2XJX_2_05), and the forth generated cocrystallized pharmacophoric model from Hsp90 protein 4LWF (4LWF_2_04) with area under the curve AUC-ROC values 0.812 and 0.876, respectively were selected to be used as a searching tool sequentially of the National Cancer Institute (NCI) database. The captured hits were mapped based on successful hypotheses and the best predicted hits were selected. Twenty-four hits showed Hsp90 inhibition, 15 hits were measured with low micromolar IC 50 ranged from 5.0 mM to 77.1 mM
... This indicates that Hsp90 inhibitors can be effective therapeutic molecules against multiple cancer types. Various parent structures like resorcinol, purine analogs and others are being pursued in order to identify newer derivatives as anticancer molecules, which offers improved binding affinities towards Hsp90 proteins and are effective against various phenotypes of cancers compared to first generation ansamycin analogs [10,11]. ...
Drugs targeting heat shock protein 90 (Hsp90) have been extensively explored for their anticancer potential in advanced clinical trials. Nanoformulations have been an important drug delivery platform for the anticancer molecules like Hsp90 inhibitors. It has been reported that bovine serum albumin (BSA) nanoparticles (NPs) serve as carriers for anticancer drugs, which have been extensively explored for their therapeutic efficacy against cancers. Luminespib (also known as NVP-AUY922) is a new generation Hsp90 inhibitor that was introduced recently. It is one of the most studied Hsp90 inhibitors for a variety of cancers in Phase I and II clinical trials and is similar to its predecessors such as the ansamycin class of molecules. To our knowledge, nanoformulations for luminespib remain unexplored for their anticancer potential. In the present study, we developed aqueous dispensable BSA NPs for controlled delivery of luminespib. The luminespib-loaded BSA NPs were characterized by SEM, TEM, FTIR, XPS, UV-visible spectroscopy and fluorescence spectroscopy. The results suggest that luminespib interacts by non-covalent reversible interactions with BSA to form drug-loaded BSA NPs (DNPs). Our in vitro evaluations suggest that DNP-based aqueous nanoformulations can be used in both pancreatic (MIA PaCa-2) and breast (MCF-7) cancer therapy.
... The center of binding site of five inhibitors to protein HSP90 lies between three helices α2, α4, and α7 and two β sheets (Figure 1a), and molecular structures of five inhibitors are shown in Figure 1b-f. These five small molecules have better cellular activity, and their IC 50 values are 19, 58, 700, 1,560, and 7,600 nM for inhibitors of BSM, 2Kl, AB4, ZZ4, and YJW, respectively (Barril et al., 2005;Brough et al., 2009;Bruncko et al., 2010;Vallée et al., 2011). ...
Heat shock protein 90 (HSP90) is a promising target for treatment of cancer, and inhibitor bindings can generate efficient suppression on tumor in multiple ways. In this work, 140‐ns molecular dynamics (MD) simulations were performed on six systems. Principal component analysis was subsequently carried out to explore the conformational diversity of HSP90. The results suggest that inhibitor bindings induce large conformational changes of HSP90, which tends to enlarge the volume of the binding pocket to facilitate the entrance of inhibitors. Hierarchical clustering analyses, the calculation of the energy contribution of each atom and the analyses of hydrogen bonding interactions were performed. The results indicate that 20 residues in group A of the hierarchical tree are responsible for major contributions, and van der Waals interactions as well as hydrogen bonding interactions between important residues in HSP90 and key regions of inhibitors are the main force for promoting inhibitor bindings. We expect that this work can provide useful theoretical information for development of efficient inhibitors targeting HSP90. Hierarchical clustering analysis was performed on individual contribution of residues to further investigate the similarity shared by five inhibitors in the binding site of HSP90 and reveal the hot interaction spot of inhibitors with HSP90. The calculation of individual contribution of atoms in key residues was achieved to better understand the binding mechanism of inhibitors to HSP90.
... In particular, the ligand efficiency metrics for 1 (0.40) and 2 (0.44) show promise for further optimization 42 . Several papers have reported new hits against Hsp90N using SBVS [43][44][45][46] . One of them employed 2D NMR to quantify the inhibition of three hits with K d values in the range of 2 to 20 μM 43 . ...
Heat shock protein 90 (Hsp90) is one of the most abundant cellular proteins and plays a substantial role in the folding of client proteins. The inhibition of Hsp90 has been regarded as an attractive therapeutic strategy for treating cancer because many oncogenic kinases are Hsp90 client proteins. In this study, we report new inhibitors that directly bind to N-terminal ATP-binding pocket of Hsp90. Optimized structure-based virtual screening predicted candidate molecules, which was followed by confirmation using biophysical and cell-based assays. Among the reported crystal structures, we chose the two structures that show the most favourable early enrichments of true-positives in the receiver operating characteristic curve. Four molecules showed significant changes in the signals of 2D [1H, 15N] correlation NMR spectroscopy. Differential scanning calorimetry analysis supported the results indicating direct binding. Quantified dissociation constant values of the molecules, determined by a series of 2D NMR experiments, lie in the range of 0.1-33 μM. Growth inhibition assay with breast and lung cancer cells confirmed the cellular activities of the molecules. Cheminformatics revealed that the molecules share limited chemical similarities with known inhibitors. Molecular dynamics simulations detailed the putative binding modes of the inhibitors.
... These issues have led to significant efforts to identify novel rationally designed small molecular inhibitors of Hsp90 19 . The main focus of recent efforts toward the development of new Hsp90 inhibitors concentrate on structure-based ligand design [20][21][22] and highthroughput screening 23 , with a few ligand-based examples 24,25 . ...
The pharmacophoric features of the virtual cocrystallized protein of 178 Hsp90 proteins were obtained from the protein data bank and explored to generate 1260 pharmacophores evaluated using the decoy list composed of 1022 compounds. Accordingly, 51 pharmacophores were selected with high receiver operating characteristic (ROC) value for further processing. Subsequently, genetic algorithm and multiple linear regression analysis were employed to select an optimal combination of pharmacophoric models and 2D physicochemical descriptors capable of accessing a self-consistent quantitative structure-activity relationship (QSAR) of optimal predictive potential (R67(2) = 0.819, F = 43.0, R(2)LOO( )= 0.782, R(2)PRESS against 16 external test inhibitors equal 0.735). Two orthogonal pharmacophores emerged in the QSAR equation suggesting the existence of at least two binding modes accessible to ligands within the Hsp90 binding pocket. The fifth generated pharmacophoric model from Hsp90 protein 2XJX (2XJX_2_05), and the forth generated cocrystallized pharmacophoric model from Hsp90 protein 4LWF (4LWF_2_04) with area under the curve AUC-ROC values 0.812 and 0.876, respectively were selected to be used as a searching tool sequentially of the National Cancer Institute (NCI) database. The captured hits were mapped based on successful hypotheses and the best predicted hits were selected. Twenty-four hits showed Hsp90 inhibition, 15 hits were measured with low micromolar IC50 ranged from 5.0 μM to 77.1 μM.
... 32 In this case, the 'guided' protocol was similar to that reported by Barril and co-workers. 43 In brief, a hydrogen bond donor and hydrogen bond acceptor groups from the ligand were set to a distance of 4.0 ± 0.75 Å from C c of Asp 93, which was also the centre of a sphere of radius 24 Å that enclosed the docking cavity. Each compound was subjected to 100 iterations of the genetic algorithm using default scoring parameters. ...
In the framework of the 2015 D3R inaugural grand challenge, blind binding pose and affinity predictions were performed for a set of 180 ligands of the Heat Shock Protein HSP 90-α protein, a relevant cancer target. Spectral clustering was used to rapidly identify alternative binding site conformations in publicly available crystallographic HSP90-alpha structures. Subsequently, multiple docking and scoring protocols employing the software Autodock Vina and rDock were applied to predict binding modes and rank order ligands. Alchemical free energy calculations were performed with the software FESetup and Sire/OpenMM to predict binding affinities for three congeneric series subsets. Some of the protocols used here were ranked among the top submissions according to most of the evaluation metrics. Docking performance was excellent, but the scoring results were disappointing. A critical assessment of the results is reported, as well as suggestions for future similar competitions.
... Virtual screening based molecular docking method has been enlisted the best lead compound among the library of large number of compounds (Barril et al. 2005;Burello et al. 2002;Hou and Xu 2003;Kitchen et al. 2004;Li et al. 2006;Liu et al. 2005;Pintore and Chretien 2004;Seneci and Miertus 2000). Therefore, computational molecular docking methods have proved to be cost effective and help in reducing the time and load for selection of best hit compound as compared to experimental techniques (Li et al. 2010). ...
... Lys7 and Glu8 could indirectly affect ATP binding or directly comprise an ATP-binding site, as suggested by the results of the docking studies (Fig. 1D). To assess the latter possibility further, we docked ATP to an area centered on the Cα atom of Lys7, followed by molecular dynamics (MD) simulations of the ATP configuration with the lowest predicted binding energy (30)(31)(32). The simulations showed that Lys7 interacts with the α-phosphate of ATP (Fig. 2B). ...
Significance
Calreticulin mutants that disrupt ATP binding are shown to prolong cellular MHC class I interactions with calreticulin and with the transporter associated with antigen processing (TAP). To our knowledge, no previous studies have implicated a role for endoplasmic reticulum (ER) luminal ATP as a determinant of MHC class I assembly complex dynamics. These studies also reveal a role for the ATP–calreticulin interaction in broadly regulating the binding of calreticulin to cellular substrates. Because a large number of cell surface and secreted glycoproteins are calreticulin/calnexin substrates, these studies have broad significance toward understanding the cellular mechanisms of protein quality control.
... Of the numerous small-molecules that have been found to bind HSP90, many of these prevent folding activity through the interactions in ATP pocket. In addition to the natural product radicicol [55] (and its derivatives [56][57][58]), other classes of small-molecules that target the HSP90 N-terminal ATP-binding site include the synthetic heterocyles including purine ATP-mimetics [59][60][61][62][63], pyrazoles [64][65][66][67], and isoxazoles [68,69], among other scaffolds [51,[70][71][72][73][74]. The HSP90 ATP pocket has proven to be quite amenable to small-molecule binding, and many inhibitors bind this region with high affinity (comparable to geldanamycin's nanomolar binding constant). ...
... The validity of Hsp90α as an anticancer target for drug discovery [4, 5] was further established by emerging clinical and preclinical trials employing the potent Hsp90α inhibitor 17-allylamino-17-desmethoxygeldanamycin as well as the natural Hsp90α inhibitors geldanamycin [6], radicicol [7], and other small molecules [8]. The significance of heat shock protein (Hsp90) as a target in anticancer research1234591011121314 , combined with the availability of appropriate crystallographic structures for this target [15, 16], prompted us to apply our newly developed computational technique—docking-based intermolecular contacts analysis (dbCICA) [17]—to this target, aiming at the discovery of new Hsp90α inhibitors. Molecular docking, which is basically a conformational sampling procedure in which various docked conformations are explored to identify the right one, can be a very challenging problem given the degree of conformational ...
Heat shock protein (Hsp90α) has been recently implicated in cancer, prompting several attempts to discover and optimize new Hsp90α inhibitors. Towards this end, we docked 83 diverse Hsp90α inhibitors into the ATP-binding site of this chaperone using several docking-scoring settings. Subsequently, we applied our newly developed computational tool-docking-based comparative intramolecular contacts analysis (dbCICA)-to assess the different docking conditions and select the best settings. dbCICA is based on the number and quality of contacts between docked ligands and amino acid residues within the binding pocket. It assesses a particular docking configuration based on its ability to align a set of ligands within a corresponding binding pocket in such a way that potent ligands come into contact with binding site spots distinct from those approached by low-affinity ligands, and vice versa. The optimal dbCICA models were translated into valid pharmacophore models that were used as 3D search queries to mine the National Cancer Institute's structural database for new inhibitors of Hsp90α that could potentially be used as anticancer agents. The process culminated in 15 micromolar Hsp90α ATPase inhibitors.
Completely revised and updated, the 2nd edition of The Handbook of Medicinal Chemistry draws together contributions from authoritative practitioners to provide a comprehensive overview of the field as well as insight into the latest trends and research. An ideal companion for students in medicinal chemistry, drug discovery and drug development, while also communicating core principles, the book places the discipline within the context of the burgeoning platform of new modalities now available to drug discovery. The book also highlights the role chemistry has to play in wider target validation and translational technologies.
This is a carefully curated compilation of writing from global experts using their broad experience of medicinal chemistry, project leadership and drug discovery and development from an industry, academic and charity perspective to provide unparalleled insight into the field.
Structure-based (SBDD) and ligand-based (LBDD) drug design are extremely important and active areas of research in both the academic and commercial realms. This book provides a complete snapshot of the field of computer-aided drug design and associated experimental approaches. Topics covered include X-ray crystallography, NMR, fragment-based drug design, free energy methods, docking and scoring, linear-scaling quantum calculations, QSAR, pharmacophore methods, computational ADME-Tox, and drug discovery case studies. A variety of authors from academic and commercial institutions all over the world have contributed to this book, which is illustrated with more than 200 images. This is the only book to cover the subject of structure and ligand-based drug design, and it provides the most up-to-date information on a wide range of topics for the practising computational chemist, medicinal chemist, or structural biologist. Professor Kenneth Merz has been selected as the recipient of the 2010 ACS Award for Computers in Chemical & Pharmaceutical Research that recognizes the advances he has made in the use of quantum mechanics to solve biological and drug discovery problems.
Structure-based (SBDD) and ligand-based (LBDD) drug design are extremely important and active areas of research in both the academic and commercial realms. This book provides a complete snapshot of the field of computer-aided drug design and associated experimental approaches. Topics covered include X-ray crystallography, NMR, fragment-based drug design, free energy methods, docking and scoring, linear-scaling quantum calculations, QSAR, pharmacophore methods, computational ADME-Tox, and drug discovery case studies. A variety of authors from academic and commercial institutions all over the world have contributed to this book, which is illustrated with more than 200 images. This is the only book to cover the subject of structure and ligand-based drug design, and it provides the most up-to-date information on a wide range of topics for the practising computational chemist, medicinal chemist, or structural biologist. Professor Kenneth Merz has been selected as the recipient of the 2010 ACS Award for Computers in Chemical & Pharmaceutical Research that recognizes the advances he has made in the use of quantum mechanics to solve biological and drug discovery problems.
Structure-based (SBDD) and ligand-based (LBDD) drug design are extremely important and active areas of research in both the academic and commercial realms. This book provides a complete snapshot of the field of computer-aided drug design and associated experimental approaches. Topics covered include X-ray crystallography, NMR, fragment-based drug design, free energy methods, docking and scoring, linear-scaling quantum calculations, QSAR, pharmacophore methods, computational ADME-Tox, and drug discovery case studies. A variety of authors from academic and commercial institutions all over the world have contributed to this book, which is illustrated with more than 200 images. This is the only book to cover the subject of structure and ligand-based drug design, and it provides the most up-to-date information on a wide range of topics for the practising computational chemist, medicinal chemist, or structural biologist. Professor Kenneth Merz has been selected as the recipient of the 2010 ACS Award for Computers in Chemical & Pharmaceutical Research that recognizes the advances he has made in the use of quantum mechanics to solve biological and drug discovery problems.
Structure-based (SBDD) and ligand-based (LBDD) drug design are extremely important and active areas of research in both the academic and commercial realms. This book provides a complete snapshot of the field of computer-aided drug design and associated experimental approaches. Topics covered include X-ray crystallography, NMR, fragment-based drug design, free energy methods, docking and scoring, linear-scaling quantum calculations, QSAR, pharmacophore methods, computational ADME-Tox, and drug discovery case studies. A variety of authors from academic and commercial institutions all over the world have contributed to this book, which is illustrated with more than 200 images. This is the only book to cover the subject of structure and ligand-based drug design, and it provides the most up-to-date information on a wide range of topics for the practising computational chemist, medicinal chemist, or structural biologist. Professor Kenneth Merz has been selected as the recipient of the 2010 ACS Award for Computers in Chemical & Pharmaceutical Research that recognizes the advances he has made in the use of quantum mechanics to solve biological and drug discovery problems.
Structure-based (SBDD) and ligand-based (LBDD) drug design are extremely important and active areas of research in both the academic and commercial realms. This book provides a complete snapshot of the field of computer-aided drug design and associated experimental approaches. Topics covered include X-ray crystallography, NMR, fragment-based drug design, free energy methods, docking and scoring, linear-scaling quantum calculations, QSAR, pharmacophore methods, computational ADME-Tox, and drug discovery case studies. A variety of authors from academic and commercial institutions all over the world have contributed to this book, which is illustrated with more than 200 images. This is the only book to cover the subject of structure and ligand-based drug design, and it provides the most up-to-date information on a wide range of topics for the practising computational chemist, medicinal chemist, or structural biologist. Professor Kenneth Merz has been selected as the recipient of the 2010 ACS Award for Computers in Chemical & Pharmaceutical Research that recognizes the advances he has made in the use of quantum mechanics to solve biological and drug discovery problems.
Structure-based (SBDD) and ligand-based (LBDD) drug design are extremely important and active areas of research in both the academic and commercial realms. This book provides a complete snapshot of the field of computer-aided drug design and associated experimental approaches. Topics covered include X-ray crystallography, NMR, fragment-based drug design, free energy methods, docking and scoring, linear-scaling quantum calculations, QSAR, pharmacophore methods, computational ADME-Tox, and drug discovery case studies. A variety of authors from academic and commercial institutions all over the world have contributed to this book, which is illustrated with more than 200 images. This is the only book to cover the subject of structure and ligand-based drug design, and it provides the most up-to-date information on a wide range of topics for the practising computational chemist, medicinal chemist, or structural biologist. Professor Kenneth Merz has been selected as the recipient of the 2010 ACS Award for Computers in Chemical & Pharmaceutical Research that recognizes the advances he has made in the use of quantum mechanics to solve biological and drug discovery problems.
Structure-based (SBDD) and ligand-based (LBDD) drug design are extremely important and active areas of research in both the academic and commercial realms. This book provides a complete snapshot of the field of computer-aided drug design and associated experimental approaches. Topics covered include X-ray crystallography, NMR, fragment-based drug design, free energy methods, docking and scoring, linear-scaling quantum calculations, QSAR, pharmacophore methods, computational ADME-Tox, and drug discovery case studies. A variety of authors from academic and commercial institutions all over the world have contributed to this book, which is illustrated with more than 200 images. This is the only book to cover the subject of structure and ligand-based drug design, and it provides the most up-to-date information on a wide range of topics for the practising computational chemist, medicinal chemist, or structural biologist. Professor Kenneth Merz has been selected as the recipient of the 2010 ACS Award for Computers in Chemical & Pharmaceutical Research that recognizes the advances he has made in the use of quantum mechanics to solve biological and drug discovery problems.
Structure-based (SBDD) and ligand-based (LBDD) drug design are extremely important and active areas of research in both the academic and commercial realms. This book provides a complete snapshot of the field of computer-aided drug design and associated experimental approaches. Topics covered include X-ray crystallography, NMR, fragment-based drug design, free energy methods, docking and scoring, linear-scaling quantum calculations, QSAR, pharmacophore methods, computational ADME-Tox, and drug discovery case studies. A variety of authors from academic and commercial institutions all over the world have contributed to this book, which is illustrated with more than 200 images. This is the only book to cover the subject of structure and ligand-based drug design, and it provides the most up-to-date information on a wide range of topics for the practising computational chemist, medicinal chemist, or structural biologist. Professor Kenneth Merz has been selected as the recipient of the 2010 ACS Award for Computers in Chemical & Pharmaceutical Research that recognizes the advances he has made in the use of quantum mechanics to solve biological and drug discovery problems.
Structure-based (SBDD) and ligand-based (LBDD) drug design are extremely important and active areas of research in both the academic and commercial realms. This book provides a complete snapshot of the field of computer-aided drug design and associated experimental approaches. Topics covered include X-ray crystallography, NMR, fragment-based drug design, free energy methods, docking and scoring, linear-scaling quantum calculations, QSAR, pharmacophore methods, computational ADME-Tox, and drug discovery case studies. A variety of authors from academic and commercial institutions all over the world have contributed to this book, which is illustrated with more than 200 images. This is the only book to cover the subject of structure and ligand-based drug design, and it provides the most up-to-date information on a wide range of topics for the practising computational chemist, medicinal chemist, or structural biologist. Professor Kenneth Merz has been selected as the recipient of the 2010 ACS Award for Computers in Chemical & Pharmaceutical Research that recognizes the advances he has made in the use of quantum mechanics to solve biological and drug discovery problems.
Structure-based (SBDD) and ligand-based (LBDD) drug design are extremely important and active areas of research in both the academic and commercial realms. This book provides a complete snapshot of the field of computer-aided drug design and associated experimental approaches. Topics covered include X-ray crystallography, NMR, fragment-based drug design, free energy methods, docking and scoring, linear-scaling quantum calculations, QSAR, pharmacophore methods, computational ADME-Tox, and drug discovery case studies. A variety of authors from academic and commercial institutions all over the world have contributed to this book, which is illustrated with more than 200 images. This is the only book to cover the subject of structure and ligand-based drug design, and it provides the most up-to-date information on a wide range of topics for the practising computational chemist, medicinal chemist, or structural biologist. Professor Kenneth Merz has been selected as the recipient of the 2010 ACS Award for Computers in Chemical & Pharmaceutical Research that recognizes the advances he has made in the use of quantum mechanics to solve biological and drug discovery problems.
Background
The -SO2NH- group is of great significance in modern pharmaceutical use since in sulfa-drugs it is possible to introduce easily chemical modifications, and even small changes may lead to an improved version of an already existing drug.
Objective
This paper aims to describe updated information in the sulfonamide field with a particular focus on new mechanisms of action, especially if discovered employing computational approaches.
Methods
Research articles that focused on the use of the sulfonamide moiety for the design, synthesis, and in vitro/in vivo tests of various diseases were collected from various search engines like PubMed, Science Direct, Google Scholar, and Scopus, using keywords like sulfonamide moiety, aryl/heteroarylsulfonamides, alkylsulfonamides, in silico drug design.
Conclusion
The more relevant reports highlighting the prominent role of sulfonamide moiety in drug discovery have been critically analyzed. Sulfonamides can be considered as “molecular chimera” which are found to form hydrogen bonds as well as interact with unipolar environments within proteins. Therefore, based on the analysis reported herein, it is strongly foresight that new entities can be developed easily to improve the available machinery helpful in the fight of new and emerging diseases.
As of 2018, 18 Hsp90 inhibitors have entered clinical trials had been launched toward the treatment of human cancers. The 90 kDa heat shock proteins (Hsp90) are molecular chaperones required for the conformational maturation of a number of key signaling proteins that are often overexpressed and/or mutated in transformed cells. Consequently, small molecule inhibitors of Hsp90 exert a combinatorial attack on cancer cells that may be comparable to the administration of multiple chemotherapeutic agents.
This book aims to provide a comprehensive examination of the field of molecular chaperone inhibition and its application to pharmaceutical research. With several small molecule inhibitors in oncology clinical development, there is clearly intense interest in the chaperones as a molecular target. Filling a significant gap in the market by providing a detailed comparison of discovery programs across the industry, this text will find broad interest among researchers in the field of molecular chaperone pharmaceutical research, oncology research, and medicinal chemistry.
Arranged into three main sections the book covers structure and function, small molecule inhibitors and concludes with a section discussing clinical perspectives. With specific chapters covering the discovery of key molecules such as, BIIB028, STA-9090, Serenex Hsp90 inhibitor, NVP-AUY922 and NVP-HSP990, this comprehensive text is an essential treatise for researchers working in academia and industry.
New series of compounds bearing 2-thioquinazolinone scaffold were designed, synthesized as HSP90 inhibitors. Anti-proliferative activity of the synthesized compounds was evaluated against HCT-116, Hela and MCF-7 cell lines and compound 5k was found to be the most active member of the entire study with IC50 of 4.47, 7.55 and 4.04 μM, respectively, compared to DOX (IC50 of 5.23, 5.57 and 4.17μM, respectively). Most of the tested compounds revealed lower cytotoxicity against normal fibroblast cells WI-38. Compounds 5b, 5k and 8a showed potent HSP90 inhibitory activities with IC50 values in nanomolar range; 71.32, 25.07 and 56.78 nm, respectively, against Tanespimycin (IC50 of 86.45 nm). Their HSP90 inhibitory activities were confirmed by their down regulation of HSP90 client protein Her2 and up regulation of chaperone HSP70 levels. Compound 5k had shown potent multi-target inhibitory activities against EGFR, VEGFR-2 and Topoisomerase-2 with IC50 values in nanomolar range; 38.5, 126.95 and 25.85 nm, respectively. Compound 5k was further evaluated for cell cycle distribution and apoptosis induction on MCF-7 cells using flow cytometry. Compound 5k arrested the cell cycle on MCF-7 at a G2/M phase by 35.06 % and induced apoptosis by 19.82 %. Mechanistic evaluation of apoptosis induction was studied by following ways triggering mitochondrial apoptotic pathway through inducing ROS accumulation, increasing Bax/Bcl-2 ratio and activation of caspases 6, 7 and 9. Comparative molecular modeling study was performed between active and inactive HSP90 inhibitors. Docking studies into the active site of HSP90 N-terminal domain showed good agreement with the obtained biological results. ADMET analysis and parameters of Lipinski’s rule of five were calculated where compound 5k had reasonable drug-likeness with acceptable physicochemical properties so it could be used as promising orally absorbed antibreast targeted therapy.
The methods of fragment‐based lead discovery (FBLD) have matured considerably and are an accepted part of the armory of techniques used to identify initial hit compounds for initiating either a chemical biology or drug discovery project. This chapter reviews the evolution of the methods and summarizes the essential features of a fragment‐based discovery platform, illustrated with some recent success stories. It presents some extended discussion of some of the practical aspects of fragments based on the author's experiences and the literature. A fragment‐based discovery campaign has three main components ‐ a library of fragments, a method for identifying which fragments bind to the target (screening), and a strategy for evolving the fragments to hits that register in conventional assays. One key point is that as many orthogonal techniques should be applied, and their output interpreted skeptically, to identify an optimal set of validated fragment hits.
Ten new molecules of sulfa drugs including pyrazolyl acylthiourea groups (3a-3j) were synthesized and characterized with the help of elemental analysis, HRMS, FT-IR, ¹H NMR, ¹³C NMR and UV measurements. Theoretical calculations were carried out by DFT method using B3LYP functional and 6-311 + G(d,p) basis set. For theoretical IR, NMR (with GIAO method), UV, NLO, MEP, HOMO-LUMO energies analysis of 3a-3j compounds were performed over the optimized structures. Additionally, molecular docking studies were performed to explain the interaction between title molecules and four receptors such as 1UY6, 1YET, 5AML and 3HS4.
Heat shock protein 90 (Hsp90) has emerged as an important target in cancer therapy, in which case screening inhibitors targeted Hsp90 attracted special attention on anti-cancer research. Recent progress in the development of screening technique for Hsp90 inhibitors has taken place. Particular emphasis is focused on ligand fishing screening assay based on protein affinity such as fluorescent ligand fishing that serve as a screening platform show case. This context will focus on strategies to screen and validate potential Hsp90 inhibitors from natural products and the development of screening techniques that are currently applied for the discovery of bioactive compounds from complex mixtures.
There are over 100 different types of cancer, and each is classified based on the type of cell that is initially affected. If left untreated, cancer can result in serious health problems and eventually death. Recently the paradigm of cancer chemotherapy has evolved to use a combination approach, which involves the use of multiple drugs each of which targets an individual protein. Inhibition of heat shock protein 90 (Hsp90) is one of the novel key cancer targets. Because of its ability to target several signaling pathways, Hsp90 inhibition emerged as a useful strategy to treat a wide variety of cancers. Molecular modeling approaches and methodologies have become " close counterparts " to experiments in drug design and discovery workflows. A wide-range of molecular modeling approaches have been developed, each of which has different objectives and outcomes. In this review, we provide an up-to-date systematic overview on the different computational models implemented towards the design of Hsp90 inhibitors as anti-cancer agents. Although this is the main emphasis of this review, different topics such as; background and current statistics of cancer, different anti-cancer targets including Hsp90, the structure and function of Hsp90 from an experimental perspective e.g. X-ray and NMR are also addressed in this report. To the best of our knowledge, this review is the first account, which comprehensively outlines various molecular modeling efforts directed towards identification of anti-cancer drugs targeting Hsp90. We believe that the information, methods and perspectives highlighted in this report would assist researchers in the discovery of potential anti-cancer agents.
Introduction Biophysical Methods Applied to BACE Fragment Screens BACE Inhibitors Identified by Fragment Screening Final Remarks References
This chapter focuses on the virtual screening techniques for the prediction of bioactive compounds using various in silico methods. Administration of docking, pharmacophore, and QSAR-based virtual screening methods would be a cost-effective strategy to envisage novel therapeutic bioactive molecules. The principal success of virtual screening lies in its potential to remove the bulk of inactive compounds, rather than to select bioactive molecules for a specified target. However, the development of advanced virtual screening programs leading to higher prediction accuracy and greater reliability has shown the potential to predict compounds that exhibit the intended biological activity. In this chapter, we have reported various available docking-based programs that are helpful in selecting or screening of biologically active compounds using different commonly available databases. We have also shown how QSAR can be used as a virtual screening tool to predict and rank the bioactivity of the molecules. Moreover, we also included some pharmacophore-based case studies accomplished in our own lab to reflect how such a strategy can be applied to predict the bioactivity of the chosen molecule toward the specified process. Since there are several pitfalls in the scoring functions, the consensus approach that will combine all the available three methods would be more beneficial to get the actual leads.
Publisher Summary
This chapter provides an update on the status of existing and emerging classes of HSP90 inhibitors. The story of HSP90 inhibitors illustrates the use of natural products as chemical biology tools to understand biological systems and define new molecular targets, together with the application of a range of powerful technologies in contemporary drug design. Understanding the importance of the molecular chaperone Heat Shock Protein 90 (HSP90) in cell biology, and also as a target in cancer therapy. To a remarkable extent, the advances in basic chaperone biology and in drug development have been mutually beneficial. In particular, natural product HSP90 inhibitors have been invaluable as chemical tools in the elucidation of chaperone function, while the structural biology of HSP90 has underpinned the design of novel, small-molecule inhibitors. This chapter reviews the discovery and status of present and emerging classes of HSP90 inhibitors. This focuses on target validation and the pharmacology and clinical results with HSP90 inhibitors. The involvement of a large number of chaperone clients in the molecular processes that are responsible for the initiation and progression of the malignant phenotype has led to the recognition that inhibition of HSP90 can deliver a powerful anticancer effect through the combinatorial depletion of multiple oncogenic client proteins and the consequent modulation of all the hallmark traits of cancer cells.
The Hsp90 molecular chaperones represent a promising target for the development of anticancer and neuroprotective agents as they are responsible for the conformational maturation of numerous signaling proteins and the refolding of aggregated proteins, respectively. In this chapter, a summary of recent developments toward the treatment of these diseases by small-molecule modulators of Hsp90 is provided.Keywords:cancer;Hsp90;neuroprotection
There are over 100 different types of cancer, and each is classified based on the type of cell that is initially affected. If left untreated, cancer can result in serious health problems and eventually death. Recently the paradigm of cancer chemotherapy has evolved to use a combination approach, which involves the use of multiple drugs each of which targets an individual protein. Inhibition of heat shock protein 90 (Hsp90) is one of the novel key cancer targets. Because of its ability to target several signaling pathways, Hsp90 inhibition emerged as a useful strategy to treat a wide variety of cancers.
Molecular modeling approaches and methodologies have become “close counterparts” to experiments in drug design and discovery workflows. A wide-range of molecular modeling approaches have been developed, each of which has different objectives and outcomes. In this review, we provide an up-to-date systematic overview on the different computational models implemented towards the design of Hsp90 inhibitors as anti-cancer agents. Although this is the main emphasis of this review, different topics such as; background and current statistics of cancer, different anti-cancer targets including Hsp90, the structure and function of Hsp90 from an experimental perspective e.g. X-ray and NMR are also addressed in this report.
To the best of our knowledge, this review is the first account, which comprehensively outlines various molecular modeling efforts directed towards identification of anti-cancer drugs targeting Hsp90. We believe that the information, methods and perspectives highlighted in this report would assist researchers in the discovery of potential anti-cancer agents.
Some case studies for small molecule modulators of protein-protein interactions (PPI) are reviewed. It has been shown that in general natural products are proven to be highly effective in modulating PPI, and in many cases, this is achieved through the interactions utilizing the allosteric sites. As shown through some specific case studies, the structural information about the PP interface has also been highly useful in designing synthetic compounds. There is a growth in activity in building chemical toolboxes having compounds that are closer to bioactive natural products. This would also challenge the synthetic community to develop new approaches to access a wide variety of natural product-like or natural product inspired scaffolds. One such area that is gaining momentum is to establish methods that allows building the macrocyclic-based chemical toolboxes. Discovery of functional small molecule modulators of PPI demands a close interaction of the synthesis community working closely with other skill sets that are specialized in various aspects of studying these interactions.
Novel small molecule inhibitors of heat shock protein 90 (Hsp90) were discovered with the help of a fragment based drug discovery approach (FBDD) and subsequent optimization with a combination of structure guided design, parallel synthesis and application of medicinal chemistry principles. These efforts led to the identification of compound 18 (NMS-E973), which displayed significant efficacy in a human ovarian A2780 xenograft tumor model, with a mechanism of action confirmed in vivo by typical modulation of known Hsp90 client proteins, and with a favorable pharmacokinetic and safety profile.
In this review, 100 diverse chemical derivatives were either designed, synthesized or naturally screen ed and tested as Hsp90 inhibitors, miscellaneous derivatives were synthesized that represent different scaffolds. Anti-Hsp90 activities of these compounds were examined and diverse activities were observed. Although Hsp90 inhibition had activities against cancerous cell line, there is no Hsp90 inhibitor as anticancer FDA approved drug ye t, however some clinically investigated Hsp90 inhibitors are in phase I and phase II. Hsp90 inhibitors could act as a new strategy for treatment of cancer as a chronic disea se rather than using typically aggressive chemotherapeutic agents.
The experimental roots of fragment-based drug discovery can be found in the work of Petsko, Ringe, and coworkers, who were the first to report flooding of protein crystals with small organic solutes (e.g., compounds such as benzene with ten or fewer nonhydrogen atoms) to identify bound functional groups that might ultimately be transformed into targeted ligands. The concept of linking fragments together to increase binding affinity was described as early as 1992 by Verlinde et al. Computational screening of fragments, using tools such as DOCK or MCSS, was also described in the early 1990s. Pharmaceutical industry application of fragment screening began at Abbott Laboratories, where Fesik and coworkers pioneered 'SAR by NMR' (structure/activity relationship by nuclear magnetic resonance). In this spectroscopic approach, bound fragments are detected by NMR screening and subsequently linked together to increase affinity, as envisaged by Verlinde and coworkers. Application of x-ray crystallography to detect and identify fragment hits was also pursued at Abbott. Fragment-based drug discovery has now been under way for more than a decade. Although Fesik and coworkers popularized the notion of linking fragments (as in their highly successful BCL-2 program), tactical emphasis appears to have largely shifted from fragment condensation to fragment engineering (or growing the fragment) to increase binding affinity and selectivity. Various biotechnology companies, including SGX Pharmaceuticals, Astex, and Plexxikon, have recently demonstrated that fragment-based approaches can indeed produce development candidates suitable for Phase I studies of safety and tolerability in patients (www.clinicaltrials.gov).
The pharmacophoric space of cyclin dependent kinase-1 (CDK1) and heat shock protein 90
(HSP90) inhibitors were explored using several sets of inhibitors to identify high quality
binding models. Subsequently, genetic algorithm and multiple linear regression analysis
were employed to select an optimal combination of pharmacophoric models and two
dimensional physicochemical descriptors capable of accessing self-consistent quantitative
structure activity relationship (QSAR) of optimal predictive potential for HSP90 ( r2 =
0.811 , F = 42.814 , r2
LOO = 0.748 , r 2
PRESS = 0.619 ) and for CDK1 ( r2 = 0.945 , F =
79.720 , r2
LOO = 0.884 , r 2
PRESS = 0.864 ). Interestingly, three orthogonal pharmacophoric
models of HSP90 (Hypo19/7, Hyp26/8 and Hypo27/1) with cross correlation r2 < 0.4
emerged in the QSAR equation suggesting the existence of at least three distinct binding
modes accessible to ligands within HSP90 that is different from CDK1 pharmacophoric
models (Hypo1/8 and Hypo17/8). The validity of the QSAR equation and the associated
pharmacophoric models were experimentally established by the identification of selective
diverse inhibitors of CDK1 and HSP90 retrieved from our in house built structural database
of established drug molecules using ligand based method. Eight NCI compounds, a drug;
Isoxsuprine, and an agrochemical; foramsulfuran exert low micromolar anti-CDK1
bioactivities in vitro but without significant effect on HSP90, while 20 NCI and 18 drugs
exert variable anti-HSP90 bioactivities, from which 4 drugs; formoterol, amodaquine,
primaquine and, midodrine, are nanomolar inhibitors as follows; 3 nM, 5 nM, 6 nM and, 20
nM but without significant effect on CDK1. However; using structure based method
(SCID) for HSP90 lead to 22 NCI hits with IC50 in micromolar range. Eight sulfonamide
drugs were docked into the binding pocket of HSP90 and analyzed in vitro; torsemide
sulfadiazine and sulfathiazole were found the most potent with IC50; 1.0 µM, 1.5 µM, and
2.6 µM respectively. Chemical modification of cationic pyridinium derivatives was carried
to resemble thiamine in fitting to Hypo19/7. It was found that 16 synthetic compounds
exerts HSP90 inhibitory effects with IC50 in micromolar range from 7.0 µM to 49.6 µM but
with little effect on CDK1 while the rest compounds are weakly active on both HSP90 and
CDK1. Screened inhibitors are selective rather than dual.
The increasing use of fragment-based lead discovery (FBLD) in industry as well as in academia creates a high demand for sensitive and reliable methods to detect the binding of fragments to act as starting points in drug discovery programs. Nuclear magnetic resonance (NMR), surface plasmon resonance (SPR), and X-ray crystallography are well-established methods for fragment finding, and thermal shift and fluorescence polarization (FP) assays are used to a lesser extent. Weak affinity chromatography (WAC) was recently introduced as a new technology for fragment screening. The study presented here compares screening of 111 fragments against the ATPase domain of HSP90 by all of these methods, with isothermal titration calorimetry (ITC) used to confirm the most potent hits. The study demonstrates that WAC is comparable to the established methods of ligand-based NMR and SPR as a hit-id method, with hit correlations of 88% and 83%, respectively. The stability of HSP90 WAC columns was also evaluated and found to give 90% reproducibility even after 207 days of storage. A good correlation was obtained between the various technologies, validating WAC as an effective technology for fragment screening.
An adenosine tri-phosphate (ATP)-dependent molecular chaperone heat shock protein (Hsp90) is of current interest as a potential anticancer drug target. It has several oncogenic client proteins involved in signal transduction, cell cycle regulation and apoptosis. In order to identify essential chemical functional features for Hsp90 inhibition, a pharmacophore model consisting of one hydrogen bond donor, two hydrogen bond acceptor lipid and one hydrophobic feature has been developed using Hypogen (Catalyst 2.0 software) on a total set of 103 inhibitors consisting of 16 and 87 compounds in the training and the test set, respectively. The model shows good correlation for the training (r(2)= 0.887) and the test set ( [image omitted] = 0.692). In view of the X-ray data structure of Hsp90, GOLD 3.2 docking software was used to dock the 16 training set compounds. A good correlation (r(2)= 0.699) was observed between the experimental biological activity and the top-ranked Goldscore. The analysis of conserved patterns across the Hsp90 family, using the human Hsp90 X-ray structure as an alignment template, led to the identification of important amino acids involved in the ligand-binding interactions, which were found to be similar to those observed in docking studies. Hence, the best-generated pharmacophore model can be used for designing new Hsp90 inhibitors.
The design through Energy-Based Pharmacophore Virtual screening has led to aminocyanopyridine derivatives as efficacious new inhibitors of Hsp90. The synthesized compounds showed a good affinity for Hsp90 ATP binding site in the competitive binding assay. Moreover, they showed an excellent antiproliferative activity against a large number of human tumor cell lines. Further biological studies on the derivative with the higher EC50 confirmed its specific influence on the cellular pathways involving Hsp90.
Background:
Virtual screening has become an established tool for lead generation. In recent years, the computational science behind these tools has evolved to become ever more sophisticated and diverse, whilst the quantity of published successes has continued to increase.
Objective:
By understanding the origins of virtual screening, the theoretical limitations behind it, and the published examples of success, to understand the current and potential value of these techniques to drug discovery.
Method:
By reviewing the underlying science and current practice of virtual screening, this article demonstrates the ability of the methods to generate lead molecules.
Conclusion:
Based on current literature and comparison with 'wet' screening techniques such as high-throughput screening and fragment screening, the author suggests areas that need to be addressed if the science of virtual screening is to fulfil its potential.
Owing to the key role of heat-shock protein 90 (Hsp90) in the evolution, development and disease pathogenesis of cancer, it has been an important target for anti-cancer chemotherapy over the years. A five-nanosecond molecular dynamics simulation combined with the calculation of the binding free energy was carried out to investigate the binding mechanisms of three Hsp90 inhibitors 4BH, 2E1 and 2D9 to Hsp90. The binding free energy of each complex was computed using the molecular mechanics–generalised Born surface area method. Detailed binding free energies between each inhibitor and residues of Hsp90 were calculated using a per-residue basis decomposition method. The detailed inhibitor–residue interaction provides insights into binding mechanisms and in-depth understanding of the structure–affinity relationship. This study suggests that van der Waals energy is primarily responsible for driving the binding of the inhibitors to Hsp90, and the three inhibitors bind to Hsp90 in a similar binding mode. However, a substituent in 2D9 leads to higher binding free energy than the other two inhibitors. These data may assist in designing new potent drugs to combat cancer.
Hsp90 is a highly abundant and ubiquitous molecular chaperone which plays an essential role in many cellular processes including cell cycle control, cell survival, hormone and other signalling pathways. It is important for the cell's response to stress and is a key player in maintaining cellular homeostasis. In the last ten years, it has become a major therapeutic target for cancer, and there has also been increasing interest in it as a therapeutic target in neurodegenerative disorders, and in the development of anti-virals and anti-protozoan infections. The focus of this review is the structural and mechanistic studies which have been performed in order to understand how this important chaperone acts on a wide variety of different proteins (its client proteins) and cellular processes. As with many of the other classes of molecular chaperone, Hsp90 has a critical ATPase activity, and ATP binding and hydrolysis known to modulate the conformational dynamics of the protein. It also uses a host of cochaperones which not only regulate the ATPase activity and conformational dynamics but which also mediate interactions with Hsp90 client proteins. The system is also regulated by post-translational modifications including phosphorylation and acetylation. This review discusses all these aspects of Hsp90 structure and function.
Folding of Nascent Proteins In Vitro and In VivoMore Hsp90Protein Misfolding DiseasesHsp60 and Hsp70 InhibitorsPositive Therapeutic Effects of Hsp70 UpregulationHsp90 as a Novel Oncology TargetHsp90 Inhibitors in Preclinical and Clinical TrialsAlternative Hsp90 Targeting StrategiesPotential Problems in Hsp90 InhibitionVaccine Candidates Based on Heat Shock Protein-Substrate ComplexesReferences
The PROCHECK suite of programs provides a detailed check on the stereochemistry of a protein structure. Its outputs comprise a number of plots in PostScript format and a comprehensive residue-by-residue listing. These give an assessment of the overall quality of the structure as compared with well refined structures of the same resolution and also highlight regions that may need further investigation. The PROCHECK programs are useful for assessing the quality not only of protein structures in the process of being solved but also of existing structures and of those being modelled on known structures.
The molecular mechanisms by which oncogenic tyrosine kinases induce cellular transformation are unclear. Herbimycin A, geldanamycin, and certain other benzoquinone ansamycins display an unusual capacity to revert tyrosine kinase-induced oncogenic transformation. As an approach to the study of v-src-mediated transformation, we examined ansamycin action in transformed cells and found that drug-induced reversion could be achieved without direct inhibition of src phosphorylating activity. To identify mechanisms other than kinase inhibition for drug-mediated reversion, we prepared a solid phase-immobilized geldanamycin derivative and affinity precipitated the molecular targets with which the drug interacted. In a range of cell lines, immobilized geldanamycin bound elements of a major class of heat shock protein (HSP90) in a stable and pharmacologically specific manner. Consistent with these binding data, we found that soluble geldanamycin and herbimycin A inhibited specifically the formation of a previously described src-HSP90 heteroprotein complex. A related benzoquinone ansamycin that failed to revert transformed cells did not inhibit the formation of this complex. These results demonstrate that HSP participation in multimolecular complex formation is required for src-mediated transformation and can provide a target for drug modulation.
The cellular activity of several regulatory and signal transduction proteins, which depend on the Hsp90 molecular chaperone for folding, is markedly decreased by geldanamycin and by radicicol (monorden). We now show that these unrelated compounds both bind to the N-terminal ATP/ADP-binding domain of Hsp90, with radicicol displaying nanomolar affinity, and both inhibit the inherent ATPase activity of Hsp90 which is essential for its function in vivo. Crystal structure determinations of Hsp90 N-terminal domain complexes with geldanamycin and radicicol identify key aspects of their nucleotide mimicry and suggest a rational basis for the design of novel antichaperone drugs.
Molecular docking is an invaluable tool in modern drug discovery. This review focuses on methodological developments relevant to the field of molecular docking. The forces important in molecular recognition are reviewed and followed by a discussion of how different scoring functions account for these forces. More recent applications of computational chemistry tools involve library design and database screening. Last, we summarize several critical methodological issues that must be addressed in future developments.
To study the toxicity and pharmacokinetic-pharmacodynamic profile of 17-allylamino, 17- demethoxygeldanamycin (17-AAG) and to recommend a dose for phase II trials.
This was a phase I study examining a once-weekly dosing schedule of 17-AAG. Thirty patients with advanced malignancies were treated.
The highest dose level reached was 450 mg/m(2)/week. The dose-limiting toxicities (DLTs) encountered were grade 3 diarrhea in three patients (one at 320 mg/m(2)/week and two at 450 mg/m(2)/week) and grade 3 to 4 hepatotoxicity (AST/ALT) in one patient at 450 mg/m(2)/week. Two of nine DLTs were at the highest dose level. Two patients with metastatic melanoma had stable disease and were treated for 15 and 41 months, respectively. The dose versus area under the curve-relationship for 17-AAG was linear (r(2) = .71) over the dose range 10 to 450 mg/m(2)/week, with peak plasma concentrations of 8,998 mug/L (standard deviation, 2,881) at the highest dose level. After the demonstration of pharmacodynamic changes in peripheral blood leukocytes, pre- and 24 hours post-treatment, tumor biopsies were performed and demonstrated target inhibition (c-RAF-1 inhibition in four of six patients, CDK4 depletion in eight of nine patients and HSP70 induction in eight of nine patients) at the dose levels 320 and 450 mg/m(2)/week. It was not possible to reproducibly demonstrate these changes in biopsies taken 5 days after treatment.
It has been possible to demonstrate that 17-AAG exhibits a tolerable toxicity profile with therapeutic plasma concentrations and target inhibition for 24 hours after treatment and some indications of clinical activity at the dose level 450 mg/m(2)/week. We recommend this dose for phase II clinical trials.
The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecular structure determination by X-ray crystallography. The suite is designed to be flexible, allowing users a number of methods of achieving their aims and so there may be more than one program to cover each function. The programs are written mainly in standard Fortran77. They are from a wide variety of sources but are connected by standard data file formats. The package has been ported to all the major platforms under both Unix and VMS. The suite is distributed by anonymous ftp from Daresbury Laboratory and is widely used throughout the world.
A system has been developed that can automatically generate three-dimensional atomic coordinates from the constitution of a molecule as expressed by a connection table. The program, CORINA, is applicable to the entire range of organic chemistry. It can also handle structures that are beyond the scope of some other programs, e.g., macrocyclic and polymacrocyclic molecules. Computation times are short and the results compare favorably with data from X-ray crystallography and with those of molecular mechanics calculations.
Molecular chaperones are proteins that ensure the appropriate folding, stability and function of other proteins in the cell. There is increasing evidence that molecular chaperones are not only important in normal cell homeostasis and response to stresses, such as heat shock, but can also be involved in disease pathology. In particular, HSP90 has emerged as an important potential drug target in oncology. This is because it is essential for the stability of a long list of ‘client proteins’, including ErbB2/human epithelial growth factor receptor (HER)2, Raf-1, Akt/protein kinase B (PKB), Polo-1, Met, mutant p53 and human telomerase reverse transcriptase (hTERT), as well as the oestrogen and androgen receptor. Inhibition of HSP90 leads to depletion of these oncogenic clients by the ubiquitin proteasome pathway, thereby providing a simultaneous combinatorial attack on all of the hallmark phenotypic traits of cancer cells. Because of the rapid progress made, this review focuses on the patents dealing with the discovery and application of small molecule inhibitors of HSP90, although limited coverage of other applications in the area of HSP90 and additional chaperones is also included. Pioneering work with natural products, namely geldanamycin and related ansamycin antibiotics together with radicicol macrocycle derivatives, established the therapeutic potential of inhibiting the essential N-terminal ATPase of HSP90 by competing at the nucleotide binding site. A geldanamycin analogue, 17-(desmethoxy), 17-allylamino geldanamycin (17AAG), is completing Phase I clinical trials with promising initial results. The use of high-throughput screening and rational design based on X-ray crystal structures of HSP90 has led to the discovery of small molecule HSP90 inhibitors based on purine and pyrazole scaffolds. The continued progression of these various compound classes into clinical trials should help to establish proof of concept for inhibition of HSP90 as a viable therapeutic approach for the treatment of cancer and potentially other diseases. This would in turn validate protein folding as a strategy for drug development and encourage additional chaperones to be explored as molecular targets.
Citations in CAS SciFinder to the rule-of-five (RO5) publication will exceed 1000 by year-end 2004. Trends in the RO5 literature explosion that can be discerned are the further definitions of drug-like. This topic is explored in terms of drug-like physicochemical features, drug-like structural features, a comparison of drug-like and non-drug-like in drug discovery and a discussion of how drug-like features relate to clinical success. Physicochemical features of CNS drugs and features related to CNS blood–brain transporter affinity are briefly reviewed. Recent literature on features of non-oral drugs is reviewed and how features of lead-like compounds differ from those of drug-like compounds is discussed. Most recently, partly driven by NIH roadmap initiatives, considerations have arisen as to what tool-like means in the search for chemical tools to probe biology space. All these topics frame the scope of this short review/perspective.Section Editors:Han van de Waterbeemd, Christopher Kohl – Pfizer Global Research & Development, Sandwich Laboratories, PDM (Pharmacokinetics, Dynamics and Metabolism), Sandwich, Kent, UK CT13 9NJIn the past, many clinical candidates failed during development. The reasons for failure are now much better understood. The author of this contribution, Chris Lipinski, was among the first to point out that drugs typically have physicochemical and structural properties within certain ranges. This review discusses the original rule-of-five concept and its variants, to be used in the design of orally active compounds. He also compares the concepts of drug-like, lead-like, and CNS-like compounds and drugs. It is important to consider differences better oral and non-oral drugs. Finally, the new idea of tool-like compounds is presented.
Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallographic refinement and result in an incorrect structure. The normally quoted crystallographic residual is often a poor description for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations.
The Hsp90 chaperone is required for the activation of several families of eukaryotic protein kinases and nuclear hormone receptors, many of which are protooncogenic and play a prominent role in cancer. The geldanamycin antibiotic has antiproliferative and antitumor effects, as it binds to Hsp90, inhibits the Hsp90-mediated conformational maturation/refolding reaction, and results in the degradation of Hsp90 substrates. The structure of the geldanamycin-binding domain of Hsp90 (residues 9-232) reveals a pronounced pocket, 15 A deep, that is highly conserved across species. Geldanamycin binds inside this pocket, adopting a compact structure similar to that of a polypeptide chain in a turn conformation. This, and the pocket's similarity to substrate-binding sites, suggest that the pocket binds a portion of the polypeptide substrate and participates in the conformational maturation/refolding reaction.
The molecular chaperone Hsp90 plays an essential role in the folding and function of important cellular proteins including steroid hormone receptors, protein kinases and proteins controlling the cell cycle and apoptosis. A 15 A deep pocket region in the N-terminal domain of Hsp90 serves as an ATP/ADP-binding site and has also been shown to bind geldanamycin, the only specific inhibitor of Hsp90 function described to date. We now show that radicicol, a macrocyclic antifungal structurally unrelated to geldanamycin, also specifically binds to Hsp90. Moreover, radicicol competes with geldanamycin for binding to the N-terminal domain of the chaperone, expressed either by in vitro translation or as a purified protein, suggesting that radicicol shares the geldanamycin binding site. Radicicol, as does geldanamycin, also inhibits the binding of the accessory protein p23 to Hsp90, and interferes with assembly of the mature progesterone receptor complex. Radicicol does not deplete cells of Hsp90, but rather increases synthesis as well as the steady-state level of this protein, similar to a stress response. Finally, radicicol depletes SKBR3 cells of p185erbB2, Raf-1 and mutant p53, similar to geldanamycin. Radicicol thus represents a structurally unique antibiotic, and the first non-benzoquinone ansamycin, capable of binding to Hsp90 and interfering with its function.
The Hsp90s contain a conserved pocket that binds ATP/ADP and plays an important role in the regulation of chaperone function. Occupancy of this pocket by several natural products (geldanamycin (GM) and radicicol) alters Hsp90 function and results in the degradation of a subset of proteins (i.e. steroid receptors, Her2, Raf). We have used the structural features of this pocket to design a small molecule inhibitor of Hsp90.
The designed small molecule PU3 competes with GM for Hsp90 binding with a relative affinity of 15-20 microM. PU3 induces degradation of proteins, including Her2, in a manner similar to GM. Furthermore, PU3 inhibits the growth of breast cancer cells causing retinoblastoma protein hypophosphorylation, G1 arrest and differentiation.
PU3 is representative of a novel class of synthetic compounds that binds to Hsp90 and inhibits the proliferation of cancer cells. These reagents could provide a new strategy for the treatment of cancers.
Current anticancer drug development strategies involve identifying novel molecular targets which are crucial for tumourigenesis. The molecular chaperone heat shock protein (HSP) 90 is of interest as an anticancer drug target because of its importance in maintaining the conformation, stability and function of key oncogenic client proteins involved in signal transduction pathways leading to proliferation, cell cycle progression and apoptosis, as well as other features of the malignant phenotype such as invasion, angiogenesis and metastasis. The natural product HSP90 inhibitors geldanamycin and radicicol exert their antitumour effect by inhibiting the intrinsic ATPase activity of HSP90, resulting in degradation of HSP90 client proteins via the ubiquitin proteosome pathway. Anticancer selectivity may derive from the simultaneous combinatorial effects of HSP90 inhibitors on multiple cancer targets and pathways. 17-allylamino, 17-demethoxygeldanamycin (17AAG), a geldanamycin derivative, showed good activity and cancer selectivity in preclinical models and has now progressed to Phase I clinical trial in cancer patients with encouraging initial results. Phase II trials including combination studies with cytotoxic agents are now being planned and these should allow the therapeutic activity of 17AAG to be determined. Second generation HSP90 inhibitors may be designed to overcome some of the drawbacks of 17AAG, including limited oral bioavailability and solubility. They could also be engineered to target specific functions of HSP90, which may not only provide greater molecular selectivity and clinical benefit but may also increase understanding of the complex functions of this molecular chaperone. HSP90 inhibitors provide proof of concept for drugs directed at HSP90 and protein folding and this principle may be applicable to other medical conditions involving protein aggregation and stability.
17-allylamino, 17-demethoxygeldanamycin (17AAG; NSC 330507) is the first modulator of heat shock protein 90 (Hsp90) to enter clinical trials. Hsp90 serves a chaperone role to properly fold and deliver client proteins to appropriate intracellular locations. Interest in Hsp90 modulators for the experimental therapeutics of cancer has arisen based on pre-clinical evaluations suggesting that Hsp90 client proteins regulate signaling pathways critical to the molecular economy of many types of tumors, including oncogene signaling, cyclin-dependent kinase activation, steroid hormone receptors, and mediators of invasion and metastasis. Thus, Hsp90-directed agents could affect molecules upon which tumors depend for their proliferation and survival. Initial clinical studies have therefore sought to incorporate assessment of these endpoints into initial clinical evaluations. Three schedules of administration have been supported for initial evaluation in Phase I studies sponsored by the National Cancer Institute (NCI) or supported by NCI and sponsored by Cancer Research UK. In the daily times five schedule, a recommended Phase II dose (RPTD) of 40 mg/m(2) has been reached, while once weekly or three of four weekly schedules are defining RPTDs of 295 and 308 mg/m(2). Toxicity is tolerable and appears dominated by hepatic, gastrointestinal, and constitutional symptoms. Concentrations of drug at peak of ~1700-3000 nM are concordant with concentrations predictive of useful outcomes in pre-clinical model systems. Evidence of modulation of Hsp90 partner molecules has been obtained in both surrogate and some tumor compartments. These very early results encourage additional clinical evaluations of 17AAG and related molecules.
Multiple co-crystal structures of an adenine-based series of inhibitors bound to the molecular chaperone Hsp90 have been determined. These structures explain the observed SAR for previously described compounds and new compounds, which possess up to 8-fold improved potency against the isolated enzyme. Anti-tumour cell potency and mechanism of action data is also described for the most potent compounds. These data should enable the design of more potent Hsp90 inhibitors.
We have implemented five drug-like filters, based on 1D and 2D molecular descriptors, and applied them to characterize the drug-like properties of commercially available chemical compounds. In addition to previously published filters (Lipinski and Veber), we implemented a filter for medicinal chemistry tractability based on lists of chemical features drawn up by a panel of medicinal chemists. A filter based on the modeling of aqueous solubility (>1 microM) was derived in-house, as well as another based on the modeling of Caco-2 passive membrane permeability (>10 nm/s). A library of 2.7 million compounds was collated from the 23 compound suppliers and analyzed with these filters, highlighting a tendency toward highly lipophilic compounds. The library contains 1.6 M unique structures, of which 37% (607,223) passed all five drug-like filters. None of the 23 suppliers provides all the members of the drug-like subset, emphasizing the benefit of considering compounds from various compound suppliers as a source of diversity for drug discovery.
The molecular chaperone heat-shock protein 90 (HSP90) plays a key role in the cell by stabilizing a number of client proteins, many of which are oncogenic. The intrinsic ATPase activity of HSP90 is essential to this activity. HSP90 is a new cancer drug target as inhibition results in simultaneous disruption of several key signaling pathways, leading to a combinatorial approach to the treatment of malignancy. Inhibitors of HSP90 ATPase activity including the benzoquinone ansamycins, geldanamycin and 17-allylamino-17-demethoxygeldanamycin, and radicicol have been described. A high-throughput screen has been developed to identify small-molecule inhibitors that could be developed as therapeutic agents with improved pharmacological properties. A colorimetric assay for inorganic phosphate, based on the formation of a phosphomolybdate complex and subsequent reaction with malachite green, was used to measure the ATPase activity of yeast HSP90. The Km for ATP determined in the assay was 510+/-70 microM. The known HSP90 inhibitors geldanamycin and radicicol gave IC(50) values of 4.8 and 0.9 microM respectively, which compare with values found using the conventional coupled-enzyme assay. The assay was robust and reproducible (2-8% CV) and used to screen a compound collection of approximately 56,000 compounds in 384-well format with Z' factors between 0.6 and 0.8.
Agents that inhibit Hsp90 function hold significant promise in cancer therapy. Here we present PU24FCl, a representative of the first class of designed Hsp90 inhibitors. By specifically and potently inhibiting tumor Hsp90, PU24FCl exhibits wide-ranging anti-cancer activities that occur at similar doses in all tested tumor types. Normal cells are 10- to 50-fold more resistant to these effects. Its Hsp90 inhibition results in multiple anti-tumor-specific effects, such as degradation of Hsp90-client proteins involved in cell growth, survival, and specific transformation, inhibition of cancer cell growth, delay of cell cycle progression, induction of morphological and functional changes, and apoptosis. In concordance with its higher affinity for tumor Hsp90, in vivo PU24FCl accumulates in tumors while being rapidly cleared from normal tissue. Concentrations achieved in vivo in tumors lead to single-agent anti-tumor activity at non-toxic doses.
Inhibition of the ATPase activity of the chaperone protein HSP90 is a potential strategy for treatment of cancers. We have determined structures of the HSP90alpha N-terminal domain complexed with the purine-based inhibitor, PU3, and analogs with enhanced potency both in enzyme and cell-based assays. The compounds induce upregulation of HSP70 and downregulation of the known HSP90 client proteins Raf-1, CDK4, and ErbB2, confirming that the molecules inhibit cell growth by a mechanism dependent on HSP90 inhibition. We have also determined the first structure of the N-terminal domain of HSP90beta, complexed with PU3. The structures allow a detailed rationale to be developed for the observed affinity of the PU3 class of compounds for HSP90 and also provide a structural framework for design of compounds with improved binding affinity and drug-like properties.
This paper reviews the mathematical basis of maximum likelihood. The likelihood function for macromolecular structures is extended to include prior phase information and experimental standard uncertainties. The assumption that different parts of a structure might have different errors is considered. A method for estimating sigma(A) using 'free' reflections is described and its effects analysed. The derived equations have been implemented in the program REFMAC. This has been tested on several proteins at different stages of refinement (bacterial alpha-amylase, cytochrome c', cross-linked insulin and oligopeptide binding protein). The results derived using the maximum-likelihood residual are consistently better than those obtained from least-squares refinement.
An automated refinement procedure (ARP) for protein models is proposed, and its convergence properties discussed. It is comparable to the iterative least-squares minimization/difference Fourier synthesis approach for small molecules. ARP has been successfully applied to three proteins, and for two of them resulted in models very similar to those obtained by conventional least-squares refinement and rebuilding with FRODO. In real time ARP is about ten times faster than conventional refinement. In its present form ARP requires high (2.0 A or better) resolution data, which should be of high quality and a starting protein model having about 75% of the atoms in roughly the correct position. For the third protein at 2.4 A resolution, ARP was significantly less powerful but nevertheless gave definite improvement, in the density map at least.
Recent advances in structure determination and computational methods have encouraged the development of structure-based virtual screening. Here we survey progress in the field and review the most recent methods, validation experiments and real applications, including an in-house example of hit identification for the oncology target Hsp90. These results provide a basis for discussing the current state of structure-based virtual screening and to outline the developments that are expected to have a major impact in the near future.
Virtual screening uses computer-based methods to discover new ligands on the basis of biological structures. Although widely heralded in the 1970s and 1980s, the technique has since struggled to meet its initial promise, and drug discovery remains dominated by empirical screening. Recent successes in predicting new ligands and their receptor-bound structures, and better rates of ligand discovery compared to empirical screening, have re-ignited interest in virtual screening, which is now widely used in drug discovery, albeit on a more limited scale than empirical screening.
A series of dihydroxyphenylpyrazole compounds were identified as a unique class of reversible Hsp90 inhibitors. The crystal structures for two of the identified compounds complexed with the N-terminal ATP binding domain of human Hsp90alpha were determined. The dihydroxyphenyl ring of the compounds fits deeply into the adenine binding pocket with the C2 hydroxyl group forming a direct hydrogen bond with the side chain of Asp93. The pyrazole ring forms hydrogen bonds to the backbone carbonyl of Gly97, the hydroxyl group of Thr184 and to a water molecule, which is present in all of the published HSP90 structures. One of the identified compounds (G3130) demonstrated cellular activities (in Her-2 degradation and activation of Hsp70 promoter) consistent with the inhibition of cellular Hsp90 functions.
High-throughput screening identified the 3,4-diarylpyrazole CCT018159 as a novel and potent (7.1 microM) inhibitor of Hsp90 ATPase activity. Here, we describe the synthesis of CCT018159 and a number of close analogues together with data on their biochemical properties. Some initial structure-activity relationships are discussed, as well as the crystal structure of CCT018159 bound to Hsp90.
The crystal structure of a previously reported screening hit 1 (CCT018159) bound to the N terminal domain of molecular chaperone Hsp90 has been used to design 5-amide analogues. These exhibit enhanced potency against the target in binding and functional assays with accompanying appropriate cellular pharmacodynamic changes. Compound 11 (VER-49009) compares favorably with the clinically evaluated 17-AAG.
The molecular chaperone Hsp90 is not only of major current interest in fundamental biological research but also recognised as an exciting new target for the treatment of cancer and other diseases. In addition to playing an important role in response to proteotoxic heat shock and others stresses, Hsp90 is also critical for maintaining normal cellular homeostasis. Hsp90 is responsible for ensuring the conformational stability, shape and function of a selected range of key proteins, including many kinases and transcription factors. Furthermore, recent studies show that Hsp90 plays a key role in development and evolution. Hsp90 is overexpressed in cancer cells and is thought to be involved in dealing with the cellular stress associated with malignancy, as well as being essential for a range of key oncogenic proteins, including ErbB2, Raf-1, Akt/PKB, mutant p53 and many others. A major attraction of Hsp90 inhibitors is their potential to inhibit a range of 'mission critical' cancer pathways, thereby blocking all of the 'hallmark traits' of malignancy and exhibiting broad-spectrum antitumour activity. The first-in-class Hsp90 inhibitor 17AAG has entered clinical trials with promising early results and a range of other agents is under investigation and preclinical development. This article reviews the current status and future prospects for the exploitation of Hsp90 as a new molecular target for cancer treatment.
- A Maloney
- Workman
Maloney, A.; Workman, P. Expert. Opin. Biol. Ther. 2002,
2, 3.
- L Whitesell
- E G Mimnaugh
- B De Costa
- C E Myers
- L M Neckers
Whitesell, L.; Mimnaugh, E. G.; De Costa, B.; Myers, C.
E.; Neckers, L. M. Proc. Natl. Acad. Sci. U.S.A. 1994, 91,
8324.
- T W Schulte
- S Akinaga
- S Soga
- W Sullivan
- B Stensgard
- D Toft
- L M Neckers
Schulte, T. W.; Akinaga, S.; Soga, S.; Sullivan, W.;
Stensgard, B.; Toft, D.; Neckers, L. M. Cell Stress.
Chaperones 1998, 3, 100.
- E A Sausville
- J E Tomaszewski
- P Ivy
- Curr
Sausville, E. A.; Tomaszewski, J. E.; Ivy, P. Curr. Cancer
Drug Targets 2003, 3, 377.
- U Banerji
- A Oõdonnell
- M Scurr
- S Pacey
- S Stapleton
- Y Asad
- L Simmons
- A Maloney
- F Raynaud
- M Campbell
- M Walton
- S Lakhani
- S Kaye
- P Workman
- I Judson
Banerji, U.; OÕDonnell, A.; Scurr, M.; Pacey, S.; Stapleton, S.; Asad, Y.; Simmons, L.; Maloney, A.; Raynaud,
F.; Campbell, M.; Walton, M.; Lakhani, S.; Kaye, S.;
Workman, P.; Judson, I. J. Clin. Oncol. 2005, 23, 4152.
- M Vilenchik
- D Solit
- A Basso
- H Huezo
- B Lucas
- H He
- N Rosen
- C Spampinato
- P Modrich
- G Chiosis
Vilenchik, M.; Solit, D.; Basso, A.; Huezo, H.; Lucas, B.;
He, H.; Rosen, N.; Spampinato, C.; Modrich, P.; Chiosis,
G. Chem. Biol. 2004, 11, 787.
- A Kreusch
- S Han
- A Brinker
- V Zhou
- H S Choi
- Y He
- S A Lesley
- J Caldwell
- X J Gu
Kreusch, A.; Han, S.; Brinker, A.; Zhou, V.; Choi, H. S.;
He, Y.; Lesley, S. A.; Caldwell, J.; Gu, X. J. Bioorg. Med.
Chem. Lett. 2005, 15, 1475.
- K.-M Cheung
- T P Matthews
- K James
- M G Rowlands
- K J Boxall
- S Y Sharp
- A Maloney
- S M Roe
- C Prodromou
- L H Pearl
- G W Aherne
- E Mcdonald
- P Workman
Cheung, K.-M.; Matthews, T. P.; James, K.; Rowlands,
M. G.; Boxall, K. J.; Sharp, S. Y.; Maloney, A.; Roe, S.
M.; Prodromou, C.; Pearl, L. H.; Aherne, G. W.;
McDonald, E.; Workman, P. Bioorg. Med. Chem. Lett.
2005, 15, 3338.
- L Wright
- X Barril
- B Dymock
- L Sheridan
- A Surgenor
- M Beswick
- M Drysdale
- A Collier
- A Massey
- N Davies
- A Fink
- C Fromont
- W Aherne
- K Boxall
- S Sharp
- P Workman
- R E Hubbard
Wright, L.; Barril, X.; Dymock, B.; Sheridan, L.; Surgenor, A.; Beswick, M.; Drysdale, M.; Collier, A.; Massey,
A.; Davies, N.; Fink, A.; Fromont, C.; Aherne, W.;
Boxall, K.; Sharp, S.; Workman, P.; Hubbard, R. E.
Chem. Biol. 2004, 11, 775.
- B Dymock
- X Barril
- M Beswick
- A Collier
- N Davies
- M Drysdale
- A Fink
- C Fromont
- R E Hubbard
- A Massey
- A Surgenor
- L Wright
Dymock, B.; Barril, X.; Beswick, M.; Collier, A.; Davies,
N.; Drysdale, M.; Fink, A.; Fromont, C.; Hubbard, R. E.;
Massey, A.; Surgenor, A.; Wright, L. Bioorg. Med. Chem.
Lett. 2004, 14, 325.
- B Dymock
- X Barril
- P A Brough
- J E Cansfield
- A Massey
- E Mcdonald
- R E Hubbard
- A Surgenor
- S Roughley
- P Webb
- P Workman
- L Wright
- M Drysdale
Dymock, B.; Barril, X.; Brough, P. A.; Cansfield, J. E.;
Massey, A.; McDonald, E.; Hubbard, R. E.; Surgenor, A.;
Roughley, S.; Webb, P.; Workman, P.; Wright, L.;
Drysdale, M. J. Med. Chem. 2005, 48, 4212.
- N Brooijmans
- I D Kuntz
Brooijmans, N.; Kuntz, I. D. Annu. Rev. Biophys. Biomol.
Struct. 2003, 32, 335.
- X Barril
- R E Hubbard
- S D Morley
- Mini
Barril, X.; Hubbard, R. E.; Morley, S. D. Mini. Rev. Med.
Chem. 2004, 4, 779.
- B K Shoichet
Shoichet, B. K. Nature 2004, 432, 862.
- N Baurin
- R Baker
- C Richardson
- I Chen
- N Foloppe
- A Potter
- A Jordan
- S Roughley
- M Parratt
- P Greaney
- D Morley
- R E Hubbard
Baurin, N.; Baker, R.; Richardson, C.; Chen, I.; Foloppe,
N.; Potter, A.; Jordan, A.; Roughley, S.; Parratt, M.;
Greaney, P.; Morley, D.; Hubbard, R. E. J. Chem. Inf.
Comput. Sci. 2004, 44, 643.
- C A Lipinski
Lipinski, C. A. Drug Discov. Today 2004, 1, 337.
- J Gasteiger
- C Rudolph
- J Sadowski
Gasteiger, J.; Rudolph, C.; Sadowski, J. Tetrahedron
Comp. Method 1990, 3, 537.
A protocol of the assay is provided within Beswick
- R Howes
Howes, R. et al. A protocol of the assay is provided within
Beswick, M. C. et al., PCT Int Appl. WO 2004/050087,
submitted for publication.
- G N Murshudov
- A A Vagin
- E J Dodson
Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta
Crystallogr. D. Biol. Crystallogr. 1997, 53, 240.
- T A Jones
- J Y Zou
- S W Cowan
- M Kjeldgaard
Jones, T. A.; Zou, J. Y.; Cowan, S. W.; Kjeldgaard, M.
Acta Crystallogr. A. 1991, 47, 110.
- V S Lamzin
- K S Wilson
Lamzin, V. S.; Wilson, K. S. Acta. Crystallogr. D. Biol.
Crystallogr. 1993, 49, 129.
- R A Laskowski
- M W Macarthur
- D S Moss
- J M Thornton
Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.;
Thornton, J. M. J. Appl. Cryst. 1993, 26, 283.