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Rao RM, El Dhaybi I, Cadet F, Etchebest C, Diharce J. The mutual and dynamic role of TSPO and ligands in their binding process: An example with PK-11195. Biochimie 2024:S0300-9084(24)00067-1. [PMID: 38494108 DOI: 10.1016/j.biochi.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/12/2024] [Accepted: 03/15/2024] [Indexed: 03/19/2024]
Abstract
Translocator protein (TSPO) is an 18 kDa transmembrane protein, localized primarily on the outer mitochondrial membrane. It has been found to be involved in various physiological processes and pathophysiological conditions. Though studies on its structure have been performed only recently, there is little information on the nature of dynamics and doubts about some structures referenced in the literature, especially the NMR structure of mouse TSPO. In the present work, we thoroughly study the dynamics of mouse TSPO protein by means of atomistic molecular dynamics simulations, in presence as well as in absence of the diagnostic ligand PKA. We considered two starting structures: the NMR structure and a homology model (HM) generated on the basis of X-ray structures from bacterial TSPO. We examine the conformational landscape in both the modes for both starting points, in presence and absence of the ligand, in order to measure its impact for both structures. The analysis highlights high flexibility of the protein globally, but NMR simulations show a surprisingly flexibility even in the presence of the ligand. Interestingly, this is not the case for HM calculations, to the point that the ligand seems not so stable as in the NMR system and an unbinding event process is partially sampled. All those results tend to show that the NMR structure of mTSPO seems not deficient but is just in another portion of the global conformation space of TSPO.
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Affiliation(s)
- Rajas M Rao
- Data Analytics, Bioinformatics and Structural Biology Division, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India; Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France
| | - Ibaa El Dhaybi
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France
| | - Frédéric Cadet
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France; Laboratory of Excellence GR-Ex, Paris, France; Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715, Saint Denis Messag, France; PEACCEL, Artificial Intelligence Department, Paris, 75013 France
| | - Catherine Etchebest
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France; Laboratory of Excellence GR-Ex, Paris, France
| | - Julien Diharce
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France; Laboratory of Excellence GR-Ex, Paris, France.
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2
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Martins C, Diharce J, Nadaradjane AA, de Brevern AG. Evaluation of the Potential Impact of In Silico Humanization on V HH Dynamics. Int J Mol Sci 2023; 24:14586. [PMID: 37834033 PMCID: PMC10572902 DOI: 10.3390/ijms241914586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 10/15/2023] Open
Abstract
Camelids have the peculiarity of having classical antibodies composed of heavy and light chains as well as single-chain antibodies. They have lost their light chains and one heavy-chain domain. This evolutionary feature means that their terminal heavy-chain domain, VH, called VHH here, has no partner and forms an independent domain. The VHH is small and easy to express alone; it retains thermodynamic and interaction properties. Consequently, VHHs have garnered significant interest from both biotechnological and pharmaceutical perspectives. However, due to their origin in camelids, they cannot be used directly on humans. A humanization step is needed before a possible use. However, changes, even in the constant parts of the antibodies, can lead to a loss of quality. A dedicated tool, Llamanade, has recently been made available to the scientific community. In a previous paper, we already showed the different types of VHH dynamics. Here, we have selected a representative VHH and tested two humanization hypotheses to accurately assess the potential impact of these changes. This example shows that despite the non-negligible change (1/10th of residues) brought about by humanization, the effect is not drastic, and the humanized VHH retains conformational properties quite similar to those of the camelid VHH.
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Affiliation(s)
- Carla Martins
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
| | - Julien Diharce
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
| | - Aravindan Arun Nadaradjane
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
| | - Alexandre G. de Brevern
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
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3
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Aci-Sèche S, Bourg S, Bonnet P, Rebehmed J, de Brevern AG, Diharce J. A perspective on the sharing of docking data. Data Brief 2023; 49:109386. [PMID: 37492229 PMCID: PMC10365938 DOI: 10.1016/j.dib.2023.109386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/17/2023] [Accepted: 07/03/2023] [Indexed: 07/27/2023] Open
Abstract
Computational approaches are nowadays largely applied in drug discovery projects. Among these, molecular docking is the most used for hit identification against a drug target protein. However, many scientists in the field shed light on the lack of availability and reproducibility of the data obtained from such studies to the whole community. Consequently, sustaining and developing the efforts toward a large and fully transparent sharing of those data could be beneficial for all researchers in drug discovery. The purpose of this article is first to propose guidelines and recommendations on the appropriate way to conduct virtual screening experiments and second to depict the current state of sharing molecular docking data. In conclusion, we have explored and proposed several prospects to enhance data sharing from docking experiment that could be developed in the foreseeable future.
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Affiliation(s)
- Samia Aci-Sèche
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 2, 45067, France
| | - Stéphane Bourg
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 2, 45067, France
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 2, 45067, France
| | - Joseph Rebehmed
- Department of Computer Science and Mathematics, Lebanese, American University, Beirut, Lebanon
| | - Alexandre G. de Brevern
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, Biologie Intégrée du Globule Rouge, UMR_S 1134, DSIMB Bioinformatics team, 75014 Paris, France
| | - Julien Diharce
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, Biologie Intégrée du Globule Rouge, UMR_S 1134, DSIMB Bioinformatics team, 75014 Paris, France
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4
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Nadaradjane AA, Diharce J, Rebehmed J, Cadet F, Gardebien F, Gelly JC, Etchebest C, de Brevern AG. Quality assessment of V HH models. J Biomol Struct Dyn 2023; 41:13287-13301. [PMID: 36752327 DOI: 10.1080/07391102.2023.2172613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/19/2023] [Indexed: 02/09/2023]
Abstract
Heavy Chain Only Antibodies are specific to Camelid species. Despite the lack of the light chain variable domain, their heavy chain variable domain (VH) domain, named VHH or nanobody, has promising potential applications in research and therapeutic fields. The structural study of VHH is therefore of great interest. Unfortunately, considering the huge amount of sequences that might be produced, only about one thousand of VHH experimental structures are publicly available in the Protein Data Bank, implying that structural model prediction of VHH is a necessary alternative to obtaining 3D information besides its sequence. The present study aims to assess and compare the quality of predictions from different modelling methodologies. Established comparative & homology modelling approaches to recent Deep Learning-based modelling strategies were applied, i.e. Modeller using single or multiple structural templates, ModWeb, SwissModel (with two evaluation schema), RoseTTAfold, AlphaFold 2 and NanoNet. The prediction accuracy was evaluated using RMSD, TM-score, GDT-TS, GDT-HA and Protein Blocks distance metrics. Besides the global structure assessment, we performed specific analyses of Frameworks and CDRs structures. We observed that AlphaFold 2 and especially NanoNet performed better than the other evaluated softwares. Importantly, we performed molecular dynamics simulations of an experimental structure and a NanoNet predicted model of a VHH in order to compare the global structural flexibility and local conformations using Protein Blocks. Despite rather similar structures, substantial differences in dynamical properties were observed, which underlies the complexity of the task of model evaluation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aravindan Arun Nadaradjane
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
| | - Julien Diharce
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Joseph Rebehmed
- Department of Computer Science and Mathematics, Lebanese, American University, Beirut, Lebanon
| | - Frédéric Cadet
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
- Artificial Intelligence Department, PEACCEL, Paris, France
| | - Fabrice Gardebien
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
| | - Jean-Christophe Gelly
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Catherine Etchebest
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Alexandre G de Brevern
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
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5
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Fogha J, de Brevern AG, Diharce J. Conformational and binding mode assessment of the human IL-3 recognition by its alpha receptor. Proteins 2023. [PMID: 36729088 DOI: 10.1002/prot.26476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/08/2022] [Accepted: 01/30/2023] [Indexed: 02/03/2023]
Abstract
Protein-protein interactions (PPIs) are attractive targets as they are critical in a variety of biological processes and pathologies. As an illustration, the interleukin 3 (IL-3) and its α subunit receptor (IL-3Rα) are two proteins belonging to the cytokine or receptor βc family and are involved in several disorders like inflammatory diseases or hematological malignancies. This PPI exhibits a low binding affinity and a complex formed by a mutant form of IL-3 (superkine) and IL-3Rα have emerged from the literature, with an increase of the affinity. Therefore, in this study, we performed molecular dynamics simulations and binding energy calculation in order to evaluate protein dynamics and to characterize the main interactions between IL-3 and IL-3Rα, considering both wild-type and mutant. First, in the case of IL-3Rα/IL-3 wild-type complex, IL-3Rα can adopt three different conformations essentially driven by NTD domain, including the open and closed conformations, previously observed in crystal structures. Additionally, our results reveal a third conformation that has a distinct interaction profile that the others. Interestingly, these conformational changes are attenuated in IL-3Rα/IL-3 mutant complex. Then, we highlighted the contribution of different residues which interact principally with IL-3 or IL-3Rα conserved region. As for the mutated residue at position 135 of IL-3, other residues such as IL-3 E138, IL-3 D40, IL-3Rα Y279, IL-3Rα K235, or IL-3Rα R277 seem important for a low or a high binding affinity. Altogether these findings yield new information that could be exploited in a drug discovery process.
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Affiliation(s)
- Jade Fogha
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, Biologie Intégrée du Globule Rouge, UMR_S 1134, DSIMB, Paris, France
| | - Alexandre G de Brevern
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, Biologie Intégrée du Globule Rouge, UMR_S 1134, DSIMB, Paris, France
| | - Julien Diharce
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, Biologie Intégrée du Globule Rouge, UMR_S 1134, DSIMB, Paris, France
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6
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Ziada S, Diharce J, Raimbaud E, Aci-Sèche S, Ducrot P, Bonnet P. Estimation of Drug-Target Residence Time by Targeted Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:5536-5549. [PMID: 36350238 DOI: 10.1021/acs.jcim.2c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Drug-target residence time has emerged as a key selection factor in drug discovery since the binding duration of a drug molecule to its protein target can significantly impact its in vivo efficacy. The challenge in studying the residence time, in early drug discovery stages, lies in how to cost-effectively determine the residence time for the systematic assessment of compounds. Currently, there is still a lack of computational protocols to quickly estimate such a measure, particularly for large and flexible protein targets and drugs. Here, we report an efficient computational protocol, based on targeted molecular dynamics, to rank drug candidates by their residence time and to obtain insights into ligand-target dissociation mechanisms. The method was assessed on a dataset of 10 arylpyrazole inhibitors of CDK8, a large, flexible, and clinically important target, for which the experimental residence time of the inhibitors ranges from minutes to hours. The compounds were correctly ranked according to their estimated residence time scores compared to their experimental values. The analysis of protein-ligand interactions along the dissociation trajectories highlighted the favorable contribution of hydrophobic contacts to residence time and revealed key residues that strongly affect compound residence time.
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Affiliation(s)
- Sonia Ziada
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 245067, France
| | - Julien Diharce
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 245067, France
| | - Eric Raimbaud
- Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine78290, France
| | - Samia Aci-Sèche
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 245067, France
| | - Pierre Ducrot
- Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine78290, France
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 245067, France
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7
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Miret-Casals L, Van De Putte S, Aerssens D, Diharce J, Bonnet P, Madder A. Equipping Coiled-Coil Peptide Dimers With Furan Warheads Reveals Novel Cross-Link Partners. Front Chem 2022; 9:799706. [PMID: 35252125 PMCID: PMC8888431 DOI: 10.3389/fchem.2021.799706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/27/2021] [Indexed: 11/24/2022] Open
Abstract
Using a coiled-coil peptide dimer as a model system to explore furan reactivity, we describe novel cross-link partners of furan warheads for site-specific cross-linking. We demonstrate that replacement of weak interhelical ionic contacts with a furan moiety and its potential cross-link partner affords covalently connected coiled-coil motifs upon furan activation. We describe for the first time the reaction of the activated furan warhead with cysteine and tyrosine, besides the previously reported lysine, thus enhancing the versatility of the furan cross-link methodology by the possibility to target different amino acids. The present in vitro validation of “furan-armed” α-helices provides further grounds for exploiting furan technology in the development of furan-modified ligands/proteins to target proteins in a covalent way through various amino acid side chains.
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Affiliation(s)
- Laia Miret-Casals
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Faculty of Science, Ghent University, Ghent, Belgium
- *Correspondence: Laia Miret-Casals, ; Annemieke Madder,
| | - Sander Van De Putte
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Faculty of Science, Ghent University, Ghent, Belgium
| | - Dorien Aerssens
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Faculty of Science, Ghent University, Ghent, Belgium
| | - Julien Diharce
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, Orléans, France
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, Orléans, France
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Faculty of Science, Ghent University, Ghent, Belgium
- *Correspondence: Laia Miret-Casals, ; Annemieke Madder,
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8
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Diharce J, Bignon E, Fiorucci S, Antonczak S. Exploring Dihydroflavonol-4-Reductase Reactivity and Selectivity by QM/MM-MD Simulations. Chembiochem 2021; 23:e202100553. [PMID: 34859558 DOI: 10.1002/cbic.202100553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/29/2021] [Indexed: 11/12/2022]
Abstract
Flavonoids are secondary metabolites ubiquitously found in plants. Their antioxidant properties make them highly interesting natural compounds for use in pharmacology. Therefore, unravelling the mechanisms of flavonoid biosynthesis is an important challenge. Among all the enzymes involved in this biosynthetic pathway, dihydroflavonol-4-reductase (DFR) plays a key role in the production of anthocyanins and proanthocyanidins. Here, we provide new information on the mechanism of action of this enzyme by using QM/MM-MD simulations applied to both dihydroquercetin (DHQ) and dihydrokaempferol (DHK) substrates. The consideration of these very similar compounds shed light on the major role played by the enzyme on the stabilization of the transition state but also on the activation of the substrate before the reaction through near-attack conformer effects.
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Affiliation(s)
- Julien Diharce
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France.,Université de Paris, INSERM, Biologie Intégrée du Globule Rouge, UMR_S1134, 75015, Paris, France.,Laboratoire d'Excellence GR-Ex, 75015, Paris, France
| | - Emmanuelle Bignon
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
| | - Sébastien Fiorucci
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
| | - Serge Antonczak
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
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9
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Fogha J, Bayry J, Diharce J, de Brevern AG. Structural and evolutionary exploration of the IL-3 family and its alpha subunit receptors. Amino Acids 2021; 53:1211-1227. [PMID: 34196789 DOI: 10.1007/s00726-021-03026-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/21/2021] [Indexed: 12/14/2022]
Abstract
Interleukin-3 (IL-3) is a cytokine belonging to the family of common β (βc) and is involved in various biological systems. Its activity is mediated by the interaction with its receptor (IL-3R), a heterodimer composed of two distinct subunits: IL-3Rα and βc. IL-3 and its receptor, especially IL-3Rα, play a crucial role in pathologies like inflammatory diseases and therefore are interesting therapeutic targets. Here, we have performed an analysis of these proteins and their interaction based on structural and evolutionary information. We highlighted that IL-3 and IL-3Rα structural architectures are conserved across evolution and shared with other proteins belonging to the same βc family interleukin-5 (IL-5) and granulocyte-macrophage colony-stimulating factor (GM-CSF). The IL-3Rα/IL-3 interaction is mediated by a large interface in which most residues are surprisingly not conserved during evolution and across family members. In spite of this high variability, we suggested small regions constituted by few residues conserved during the evolution in both proteins that could be important for the binding affinity.
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Affiliation(s)
- Jade Fogha
- UMR_S 1134, DSIMB, Université de Paris, Inserm, Biologie Intégrée du Globule Rouge, 75739, Paris, France
- Institut National de La Transfusion Sanguine (INTS), 75739, Paris, France
- Laboratoire D'Excellence GR-Ex, 75739, Paris, France
| | - Jagadeesh Bayry
- Centre de Recherche Des Cordeliers, Institut National de La Santé Et de La Recherche Médicale, Sorbonne Université, Université de Paris, 75006, Paris, France
- Indian Institute of Technology Palakkad, Kozhippara, Palakkad, 678 557, India
| | - Julien Diharce
- UMR_S 1134, DSIMB, Université de Paris, Inserm, Biologie Intégrée du Globule Rouge, 75739, Paris, France.
- Institut National de La Transfusion Sanguine (INTS), 75739, Paris, France.
- Laboratoire D'Excellence GR-Ex, 75739, Paris, France.
| | - Alexandre G de Brevern
- UMR_S 1134, DSIMB, Université de Paris, Inserm, Biologie Intégrée du Globule Rouge, 75739, Paris, France.
- Institut National de La Transfusion Sanguine (INTS), 75739, Paris, France.
- Laboratoire D'Excellence GR-Ex, 75739, Paris, France.
- UMR_S 1134, DSIMB, Université de La Réunion, Inserm, Biologie Intégrée du Globule Rouge, La Réunion, 97744, Saint-Denis, France.
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10
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Rao R, Diharce J, Dugué B, Ostuni MA, Cadet F, Etchebest C. Versatile Dimerisation Process of Translocator Protein (TSPO) Revealed by an Extensive Sampling Based on a Coarse-Grained Dynamics Study. J Chem Inf Model 2020; 60:3944-3957. [DOI: 10.1021/acs.jcim.0c00246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rajas Rao
- Université de Paris, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, F-75015, Paris, France
- Laboratoire d’Excellence GR-Ex, 75015 Paris, France
- Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, Faculté des Sciences & Technologies Saint-Denis, F-97715 St. Denis, France
| | - Julien Diharce
- Université de Paris, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, F-75015, Paris, France
- Laboratoire d’Excellence GR-Ex, 75015 Paris, France
- Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, Faculté des Sciences & Technologies Saint-Denis, F-97715 St. Denis, France
| | - Bérénice Dugué
- Université de Paris, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, F-75015, Paris, France
- Laboratoire d’Excellence GR-Ex, 75015 Paris, France
- Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, Faculté des Sciences & Technologies Saint-Denis, F-97715 St. Denis, France
| | - Mariano A. Ostuni
- Université de Paris, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, F-75015, Paris, France
- Laboratoire d’Excellence GR-Ex, 75015 Paris, France
| | - Frédéric Cadet
- Université de Paris, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, F-75015, Paris, France
- Laboratoire d’Excellence GR-Ex, 75015 Paris, France
- Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, Faculté des Sciences & Technologies Saint-Denis, F-97715 St. Denis, France
- PEACCEL, Artificial Intelligence Department, 6 Square Albin Cachot, Box 42, 75013 Paris, France
| | - Catherine Etchebest
- Université de Paris, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, F-75015, Paris, France
- Laboratoire d’Excellence GR-Ex, 75015 Paris, France
- Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, Faculté des Sciences & Technologies Saint-Denis, F-97715 St. Denis, France
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11
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Fogha J, Diharce J, Obled A, Aci-Sèche S, Bonnet P. Computational Analysis of Crystallization Additives for the Identification of New Allosteric Sites. ACS Omega 2020; 5:2114-2122. [PMID: 32064372 PMCID: PMC7016913 DOI: 10.1021/acsomega.9b02697] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/21/2019] [Indexed: 06/10/2023]
Abstract
Allosteric effect can modulate the biological activity of a protein. Thus, the discovery of new allosteric sites is very attractive for designing new modulators or inhibitors. Here, we propose an innovative way to identify allosteric sites, based on crystallization additives (CA), used to stabilize proteins during the crystallization process. Density and clustering analyses of CA, applied on protein kinase and nuclear receptor families, revealed that CA are not randomly distributed around protein structures, but they tend to aggregate near common sites. All orthosteric and allosteric cavities described in the literature are retrieved from the analysis of CA distribution. In addition, new sites were identified, which could be associated to putative allosteric sites. We proposed an efficient and easy way to use the structural information of CA to identify allosteric sites. This method could assist medicinal chemists for the design of new allosteric compounds targeting cavities of new drug targets.
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12
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Sirbu D, Diharce J, Martinić I, Chopin N, Eliseeva SV, Guillaumet G, Petoud S, Bonnet P, Suzenet F. An original class of small sized molecules as versatile fluorescent probes for cellular imaging. Chem Commun (Camb) 2019; 55:7776-7779. [PMID: 31210218 DOI: 10.1039/c9cc03765a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An unusual class, compact in size, of fluorescent probes based on pyridazino-1,3a,6a-triazapentalene scaffolds exhibits promising fluorescent properties (quantum yield values up to 73%, large Stokes shifts, emission wavelengths located in the green-yellow range, excellent solubility) with good photostability suitable for optical imaging applications.
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Affiliation(s)
- Doina Sirbu
- Institut de Chimie Organique et Analytique - ICOA UMR7311, rue de Chartres, 45100 Orléans, France.
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13
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Couly F, Harari M, Dubouilh-Benard C, Bailly L, Petit E, Diharce J, Bonnet P, Meijer L, Fruit C, Besson T. Development of Kinase Inhibitors via Metal-Catalyzed C⁻H Arylation of 8-Alkyl-thiazolo[5,4- f]-quinazolin-9-ones Designed by Fragment-Growing Studies. Molecules 2018; 23:E2181. [PMID: 30158487 PMCID: PMC6225322 DOI: 10.3390/molecules23092181] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 12/14/2022] Open
Abstract
Efficient metal catalyzed C⁻H arylation of 8-alkyl-thiazolo[5,4-f]-quinazolin-9-ones was explored for SAR studies. Application of this powerful chemical tool at the last stage of the synthesis of kinase inhibitors allowed the synthesis of arrays of molecules inspired by fragment-growing studies generated by molecular modeling calculations. Among the potentially active compounds designed through this strategy, FC162 (4c) exhibits nanomolar IC50 values against some kinases, and is the best candidate for the development as a DYRK kinase inhibitor.
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Affiliation(s)
- Florence Couly
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA UMR 6014, 76000 Rouen, France.
| | - Marine Harari
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA UMR 6014, 76000 Rouen, France.
| | | | - Laetitia Bailly
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA UMR 6014, 76000 Rouen, France.
| | - Emilie Petit
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA UMR 6014, 76000 Rouen, France.
| | - Julien Diharce
- Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans, UMR CNRS, 7311 BP 6759, 45067 Orléans CEDEX 2, France.
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans, UMR CNRS, 7311 BP 6759, 45067 Orléans CEDEX 2, France.
| | - Laurent Meijer
- ManRos Therapeutics, Perharidy Peninsula, 29680 Roscoff, France.
| | - Corinne Fruit
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA UMR 6014, 76000 Rouen, France.
| | - Thierry Besson
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA UMR 6014, 76000 Rouen, France.
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14
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Chaikuad A, Diharce J, Schröder M, Foucourt A, Leblond B, Casagrande AS, Désiré L, Bonnet P, Knapp S, Besson T. An Unusual Binding Model of the Methyl 9-Anilinothiazolo[5,4-f] quinazoline-2-carbimidates (EHT 1610 and EHT 5372) Confers High Selectivity for Dual-Specificity Tyrosine Phosphorylation-Regulated Kinases. J Med Chem 2016; 59:10315-10321. [DOI: 10.1021/acs.jmedchem.6b01083] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Apirat Chaikuad
- Target
Discovery Institute (TDI), and Structural Genomics Consortium (SGC), University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, U.K
| | - Julien Diharce
- Institut
de Chimie Organique et Analytique, UMR CNRS-Université d’Orléans
7311, Université d’Orléans, BP 6759, Orléans 45067 Cedex 2, France
| | - Martin Schröder
- Institute
of Pharmaceutical Chemistry and Buchman Institute for Life Sciences, Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Alicia Foucourt
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA UMR 6014, 76000 Rouen, France
| | | | | | | | - Pascal Bonnet
- Institut
de Chimie Organique et Analytique, UMR CNRS-Université d’Orléans
7311, Université d’Orléans, BP 6759, Orléans 45067 Cedex 2, France
| | - Stefan Knapp
- Target
Discovery Institute (TDI), and Structural Genomics Consortium (SGC), University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, U.K
- Institute
of Pharmaceutical Chemistry and Buchman Institute for Life Sciences, Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Thierry Besson
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA UMR 6014, 76000 Rouen, France
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15
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Diharce J, Golebiowski J, Fiorucci S, Antonczak S. Fine-tuning of microsolvation and hydrogen bond interaction regulates substrate channelling in the course of flavonoid biosynthesis. Phys Chem Chem Phys 2016; 18:10337-45. [PMID: 27027108 DOI: 10.1039/c5cp05059f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the course of metabolite formation, some multienzymatic edifices, the so-called metabolon, are formed and lead to a more efficient production of these natural compounds. One of the major features of these enzyme complexes is the facilitation of direct transfer of the metabolite between enzyme active sites by substrate channelling. Biophysical insights into substrate channelling remain scarce because the transient nature of these macromolecular complexes prevents the observation of high resolution structures. Here, using molecular modelling, we describe the substrate channelling of a flavonoid compound between DFR (dihydroflavonol-4-reductase) and LAR (leucoanthocyanidin reductase). The simulation presents crucial details concerning the kinetic, thermodynamic, and structural aspects of this diffusion. The formation of the DFR-LAR complex leads to the opening of the DFR active site giving rise to a facilitated diffusion, in about 1 μs, of the DFR product towards LAR cavity. The theoretically observed substrate channelling is supported experimentally by the fact that this metabolite, i.e. the product of the DFR enzyme, is not stable in the media. Moreover, along this path, the influence of the solvent is crucial. The metabolite remains close to the surface of the complex avoiding full solvation. In addition, when the dynamic behaviour of the system leads to a loss of interaction between the metabolite and the enzymes, water molecules through bridging H-bonds prevent the former from escaping to the bulk.
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Affiliation(s)
- Julien Diharce
- Institut de Chimie de Nice, UMR-CNRS 7272, Faculté des Sciences, Université de Nice-Sophia Antipolis, 28 Avenue Valrose, 06108 Nice Cedex 2, France.
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16
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Topin J, Diharce J, Fiorucci S, Antonczak S, Golebiowski J. O2 Migration Rates in [NiFe] Hydrogenases. A Joint Approach Combining Free-Energy Calculations and Kinetic Modeling. J Phys Chem B 2014; 118:676-81. [DOI: 10.1021/jp4093964] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jérémie Topin
- Institut de Chimie de Nice, UMR 7272, Université de Nice-Sophia Antipolis, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Julien Diharce
- Institut de Chimie de Nice, UMR 7272, Université de Nice-Sophia Antipolis, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Sébastien Fiorucci
- Institut de Chimie de Nice, UMR 7272, Université de Nice-Sophia Antipolis, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Serge Antonczak
- Institut de Chimie de Nice, UMR 7272, Université de Nice-Sophia Antipolis, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Jérôme Golebiowski
- Institut de Chimie de Nice, UMR 7272, Université de Nice-Sophia Antipolis, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
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