Jean-Didier Maréchal

Autonomous University of Barcelona | UAB · Department of Chemistry

J-domain proteins tune the specificity of Hsp70s, engaging them in precise functions. Despite their essential role, the structure and function of many J-domain proteins remain largely unknown. We explore human DNAJA2, finding that it reversibly forms highly-ordered, tubular structures that can be dissociated by Hsc70, the constitutively expressed H...

Graphical analysis of the molecular structure of proteins can be very complex. Full-atom representations retain most geometric information but are generally crowded, and key structural patterns can be challenging to identify. Non-full atom representations could be more instructive on physicochemical aspects but be insufficiently detailed regarding...

One of Alzheimer’s disease major hallmarks is the aggregation of β-amyloid peptide, a process in which metal ions play an important role. In the present work, an integrative computational study has been performed to identify the metal-binding regions and determine the conformational impact of Cu(II) and Al(III) ion binding to the β-amyloid (Aβ42) f...

Graphical analysis of the molecular structure of proteins can be very complex. Full atom representations retain most of the geometric information but are generally crowded and key structural patterns can be difficult to catch. Non-full atom representations could be more instructive on physicochemical aspects but be insufficiently detailed regarding...

The covalent insertion of a cobalt heme into the cavity of an artificial protein named alpha Rep (αRep) leads to an artificial cobalt hemoprotein that is active as a catalyst not only for the photo-induced production of H2, but also for the reduction of CO2 in a neutral aqueous solution. This new artificial metalloenzyme has been purified and chara...

Many biological systems obtain their activity by the inclusion of metalloporphyrins into one or several binding pockets. However, decoding the molecular mechanism under which these compounds bind to their receptors is something that has not been widely explored and is a field with open questions. In the present work, we apply computational techniqu...

In the barley β-D-glucan glucohydrolase, a glycoside hydrolase family 3 (GH3) enzyme, the Trp286/Trp434 clamp ensures β-D-glucosides binding, which is fundamental for substrate hydrolysis during plant growth and development. We employ mutagenesis, high-resolution X-ray crystallography, and multi-scale molecular modelling methods to examine the bind...

Disaccharide complexes have been shown experimentally to be useful for drug delivery or as an antifouling surface biofilm, and are promising drug-encapsulation and delivery candidates. Although such complexes are intended for medical applications, to date no studies at the molecular level have been devoted to the influence of complexation on the en...

The Nazarov cyclization is investigated in solution and within K 12 [Ga 4 L 6 ] supramolecular organometallic cage by means of computational methods. The reaction needs acidic condition in solution but works at neutral pH in the presence of the metallocage. The reaction steps for the process are analogous in both media: (a) protonation of the alcoh...

RAS oncoproteins are molecular switches associated with critical signaling pathways that regulate cell proliferation and differentiation. Mutations in the RAS family, mainly in the KRAS isoform, are responsible for some of the deadliest cancers, which has made this protein a major target in biomedical research. Here we demonstrate that a designed b...

We describe a new approach to target non-canonical DNA 3-Way Junctions (3WJs) that relies on the cooperative and sequence-selective recognition of A/T-rich duplex DNA branches by three AT-Hook peptides attached to a three-fold symmetric and fluorogenic 1,3,5-tristyrylbenzene core.

The encapsulation of molecular guests into supramolecular hosts is a complex molecular recognition process in which the guest displaces the solvent from the host cavity, while the host deforms to let the guest in. An atomistic description of the association would provide valuable insights on the physicochemical properties that guide it. This unders...

Artificial metalloenzymes result from anchoring an organometallic catalyst within an evolvable protein scaffold. Thanks to its dimer of dimers quaternary structure, streptavidin allows the precise positioning of two metal cofactors to activate a single substrate, thus expanding the reaction scope accessible to artificial metalloenzymes. To validate...

Combining coordination chemistry and peptide engineering offers extraordinary opportunities for developing novel molecular (supra)structures. Here, we demonstrate that the β-annulus motif is capable of directing the stereoselective assembly of designed peptides containing 2,2'-bipyridine ligands into parallel three-stranded chiral peptide helicates...

Heat shock protein (Hsp) synthesis is upregulated in a wide range of cancers to provide the appropriate environment for tumor progression. The Hsp110 and Hsp70 families have been associated to cancer cell survival and resistance to chemotherapy. In this study, we explore the strategy of drug repurposing to find new Hsp70 and Hsp110 inhibitors that...

Metal ions have been found to play an important role in the formation of extracellular β-amyloid plaques, a major hallmark of Alzheimer's disease. In the present study, the conformational landscape of Aβ42 with Al(iii) and Cu(ii) has been explored using Gaussian accelerated molecular dynamics. Both metals reduce the flexibility of the peptide and e...

A new family of hybrid β,γ-peptidomimetics consisting of a repetitive unit formed by a chiral cyclobutane-containing trans-β-amino acid plus a Nα-functionalized trans-γ-amino-l-proline joined in alternation were synthesized and evaluated as cell penetrating peptides (CPP). They lack toxicity on the human tumoral cell line HeLa, with an almost negli...

Decoding the interactions of transition metal complexes with proteins is still an open challenge in many fields, like biology and medicinal chemistry, or in the design of de novo enzymes, including artificial metalloenzymes. Instrumental techniques like X-ray crystallography or nuclear magnetic resonance can provide an atomistic description of the...

Three novel dinuclear Cu(II) complexes based on a N,N,O-chelating salphen-like ligand scaffold and bearing varying aromatic substituents (-H, -Cl, and -Br) have been synthesized and characterized. The experimental and computational data obtained suggest that all three complexes exist in the dimeric form in the solid state and adopt the same conform...

Molecular modelling applications in metalloenzyme design are still scarce due to a series of challenges. On top of that, the simulations of metal-mediated binding and the identification of catalytic competent geometries require both large conformational exploration and simulation of fine electronic properties. Here, we demonstrate how the incorpora...

With a large amount of research dedicated to decoding how metallic species bind to proteins, in silico methods are interesting allies for experimental procedures. To date, computational predictors mostly work by identifying the best possible sequence or structural match of the target protein with metal-binding templates. These approaches are fundam...

Although largely overlooked in peptide engineering, coordination chemistry offers a new set of interactions that opens unexplored design opportunities for developing complex molecular structures. In this context, we report new artificial peptide ligands that fold into chiral helicates in the presence of labile metal ions such as Fe(II) and Co(II)....

Artificial bipyridine‐containing peptide ligands encode in their sequence the stereoselective folding into chiral three‐stranded FeII or CoII peptide helicates and as kinetically inert dinuclear CoIII complexes by in‐situ oxidation. These peptide helicates selectively label DNA replication foci in functional cells. Abstract Although largely overlo...

We present an artificial metalloenzyme based on the transcriptional regulator LmrR that exhibits dynamics involving the positioning of its abiological metal cofactor. The position of the cofactor, in turn, was found to be related to the preferred catalytic reactivity, which is either the enantioselective Friedel-Crafts alkylation of indoles with β-...

a> Peptide engineering has been extremely successful in creating new structures with defined properties and functions. Although generally overlooked in this context, coordination chemistry offers an additional set of interactions that opens unexplored design opportunities for developing complex molecular structures. With this in mind, we report the...

Two series of new hybrid γ/γ-peptides, γ-CC and γ-CT, formed by (1S,2R)-3-amino-2,2,dimethylcyclobutane-1-carboxylic acid joined in alternation to a Nα-functionalized cis- or trans-γ-amino-l-proline derivative, respectively, have been synthesized and evaluated as cell penetrating peptides (CPP) and as selective vectors for anti-Leishmania drug deli...

COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2. Presently, there is no effective treatment for COVID-19. As part of the worldwide efforts to find efficient therapies and preventions, it has been reported the crystalline structure of the SARS-CoV-2 main protease Mpro (also called 3CLpro) bound to a synthetic inhibito...

div> With a large amount of research dedicated to decoding how metallic species bind to protein, in silico methods are interesting allies for experimental procedures. To date, computational predictors mostly work by identifying the best possible sequence or structural match of the target protein with metal binding templates. These approaches are f...

A new inducible artificial metalloenzyme was obtained by covalent attachment of a Mn(III)‐tetraphenylporphyrin to the artificial bidomain repeat protein (A3A3’)Y26C. The biohybrid was characterized by MALDI‐ToF MS, circular dichroism and UV‐Vis spectroscopies. Its peroxidase activity was tested as well as its monooxygenase activity for the oxidatio...

COVID-19 is a novel severe acute respiratory syndrome coronavirus. Presently, there is no effective treatment for COVID-19. As part of the worldwide efforts to find efficient therapies and preventions, it has been reported the crystalline structure of the SARS-CoV-2 main protease Mpro (also called 3CLpro) bound to a synthetic inhibitor which repres...

Among vanadium compounds with potential medicinal applications, [VIVO(acac)2] is one of the most promising for its antidiabetic and anticancer activity. In the organism, however, interconversion of the oxidation state to +III and +V and binding to proteins are possible. In this report, the transformation of VIII(acac)3, VIVO(acac)2, and VVO2(acac)...

Human serum albumin (HSA) is involved in the transport of metal ions and potential metallodrugs. Depending on the metal, several sites are available, among which N ‐terminal (NTS) and multi‐metal binding site (MBS). Despite the large number of X‐ray determinations for albumins, only one structure with Zn2+ is available. In this work, the binding to...

ConspectusArtificial metalloenzymes (ArMs) are obtained by inserting homogeneous catalysts into biological scaffolds and are among the most promising strategies in the quest for new-to-nature biocatalysts. The quality of their design strongly depends on how three partners interact: the biological host, the "artificial cofactor," and the substrate....

We present an artificial metalloenzyme based on the transcriptional regulator LmrR that exhibits a unique form of structural dynamics involving the positioning of its abiological cofactor. The position of the cofactor was found to relate to the preferred catalytic activity, which is either the enantioselective Friedel-Crafts alkylation of indoles w...

In the present study the dependence of the reaction rate of carbon‐carbon reductive elimination from R 3 PAu(MeOH)(CH 3 ) 2 complexes inside [Ga 4 L 6 ] 12‐ metallocage on the nature of the phosphine ligand is investigated by computational means. The reductive elimination mechanism is analyzed in methanol solution and inside the metallocage. Classi...

Cis and trans‐copper(II) porphyrin dimers have been synthesized in which two Cu(II) porphyrin macrocycles are bridged through a rigid ethene‐linker for possible through‐space and through‐bond spin‐couplings between the paramagnetic Cu(II) centers. It has been found that the two macrocycles come closer after 1e‐oxidation which, however, move far apa...

The visible region of the electronic absorption spectra of Cu(II) complexes was studied by time-dependent density functional theory (TD-DFT). The performance of twelve functionals in the prediction of absorption maxima (λmax) was tested on eleven compounds with different geometry, donors and charge. The ranking of the functionals for λmax was deter...

The host effect of the supramolecular [Ga4L6]12- tetrahedral metallocage on reductive elimination of substrate by encapsulated Au(III) complexes is investigated by means of computational methods. The behavior of the reactants in solution and within the metallocage is initially evaluated by means of classical molecular dynamics simulations. These re...

Congenital hypogonadotropic hypogonadism (CHH) is a condition characterized by absent puberty and infertility due to gonadotropin releasing hormone (GnRH) deficiency, which is often associated with anosmia (Kallmann syndrome, KS). We identified loss-of-function heterozygous mutations in anti-Müllerian hormone (AMH) and its receptor, AMHR2, in 3% of...

Protein–ligand docking is a widely used method to generate solutions for the binding of a small molecule with its target in a short amount of time. However, these methods provide identification of physically sound protein–ligand complexes without a complete view of the binding process dynamics, which has been recognized to be a major discriminant i...

An integrated experimental/computational strategy to study the binding modes of metal species to proteins is presented. With this multistep method based on the combined application of spectrometric (ESI-MS), spectroscopic (EPR) and computational (docking and QM) techniques, the interaction of VIVO²⁺ and four potential drugs VIVOL2 (L = 1,2-dimethyl...

The interaction of two bis-chelated VIVO²⁺ complexes, formed by pipemidic (Hpip) and 8-hydroxyquinoline-5-sulfonic acids (Hhqs), with two small proteins, ubiquitin (Ub) and lysozyme (Lyz) was studied by EPR, ESI-MS, docking and DFT methods. The two complexes differ by electric charge (at neutral pH it is +2 and -2 for the species formed by Hpip and...

The interaction of VIVO2+ ion and five VIVOL2 compounds with potential pharmacological application, where L indicates maltolate (ma), kojate (koj), acetylacetonate (acac), 1,2-dimethyl-3-hydroxy-4(1 H)-pyridinonate (dhp), and l-mimosinate (mim), with ubiquitin (Ub) was studied by EPR, ESI-MS, and computational (docking and DFT) methods. The free me...

Substrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-covalently trapped glucose forms a stable enzyme-product complex. Here, we report that the alkyl β-d-g...

The design of Artificial Metalloenzymes (ArMs), that result from the incorporation of organometallic cofactors into biological structures, has grown steadily in the last two decades and important new-to-Nature reactions have been reached. This type of exercises could highly benefit from understanding the structural impact that the inclusion of orga...

Despite the increasing efforts in the last years, the identification of efficient catalysts able to perform the enantioselective addition of water to double bonds have not been reached yet. Natural hydratases represent an interesting pool of biocatalysts to generate chiral alcohols but modifying their substrate scope remains an issue. The use of Ar...

Substrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-covalently trapped glucose forms a stable enzyme-product complex. Here, we report that the alkyl β-D-g...

Reactive oxygen species (ROS) formation appears as one of the most promising pathways to induce cell death. The interesting Cu(II)/Cu(I) redox pair has been reported to biologically generate ROS and induce cell damage. Simple metal complexes, such as cisplatin, sometimes offer even better properties than others highly accurately synthesized, which...

With more than a third of the genome encoding for metal-containing biomolecules, the in silico prediction of how metal ions bind to proteins is crucial in chemistry, biology, and medicine. To date, algorithms for metal-binding site prediction are mainly based on sequence analysis. Those methods have reached enough quality to predict the correct reg...

ABSTRACT: αRep is a family of entirely artificial repeat proteins. Within the previously described αRep library, some variants are homodimers displaying interdomain cavities. Taking advantage of these properties, one of these homodimers called αRep A3 was converted into entirely artificial single chain bidomain metalloenzymes. A nonmutated A3 domai...

In the organism, cisplatin and its derivatives are known to interact with proteins besides their principal DNA target. These off-target interactions have major therapeutic consequences including undesired side effects, loss of bioavailability and emergence of resistance. Insulin is one of the prototypical protein targets of platinum drugs as it has...

With the aim to provide a general protocol to interpret electron paramagnetic resonance (EPR) spectra of paramagnetic copper(II) coordination compounds, density functional theory (DFT) calculations of spin Hamiltonian parameters g and A for fourteen Cu(II) complexes with different charges, donor sets, and geometry were carried out using ORCA softwa...

Decoding the interaction between coordination compounds and proteins is of fundamental importance in biology, pharmacy, and medicine. In this context, protein- ligand docking represents a particularly interesting asset to predict how small compounds could interact with biomolecules, but to date, very little information is available to adapt these m...

The ONIOM method, developed in the group of Keiji Morokuma, is one of the most successful examples of quantum mechanics / molecular mechanics (QM/MM) treatments, and of multilayer methods in general. Its implementation in the Gaussian program package is in particular widely used. This implementation has access to the wide variety of QM methods avai...

We propose that peptides are highly versatile platforms for the precise design of supramolecular metal architectures, and particularly, for the controlled assembly of helicates. In this context, we show that the bacteriophage T4 Fibritin foldon (T4Ff) can been engineered on its N-terminus with metal-chelating 2,2′-bipyridine units that stereoselect...