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Malaspina LA, Wieduwilt EK, Bergmann J, Kleemiss F, Meyer B, Ruiz-López MF, Pal R, Hupf E, Beckmann J, Piltz RO, Edwards AJ, Grabowsky S, Genoni A. Fast and Accurate Quantum Crystallography: From Small to Large, from Light to Heavy. J Phys Chem Lett 2019; 10:6973-6982. [PMID: 31633355 DOI: 10.1021/acs.jpclett.9b02646] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The coupling of the crystallographic refinement technique Hirshfeld atom refinement (HAR) with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) gives rise to the new quantum-crystallographic method HAR-ELMO. This method is significantly faster than HAR but as accurate and precise, especially concerning the free refinement of hydrogen atoms from X-ray diffraction data, so that the first fully quantum-crystallographic refinement of a protein is presented here. However, the promise of HAR-ELMO exceeds large molecules and protein crystallography. In fact, it also renders possible electron-density investigations of heavy elements in small molecules and facilitates the detection and isolation of systematic errors from physical effects.
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Affiliation(s)
- Lorraine A Malaspina
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Erna K Wieduwilt
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Justin Bergmann
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Florian Kleemiss
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Departement für Chemie und Biochemie , Universität Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Benjamin Meyer
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Manuel F Ruiz-López
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Rumpa Pal
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Emanuel Hupf
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Ross O Piltz
- Australian Nuclear Science and Technology Organisation , Australian Centre for Neutron Scattering , New Illawarra Road , Lucas Heights , NSW 2234 , Australia
| | - Alison J Edwards
- Australian Nuclear Science and Technology Organisation , Australian Centre for Neutron Scattering , New Illawarra Road , Lucas Heights , NSW 2234 , Australia
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Departement für Chemie und Biochemie , Universität Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Alessandro Genoni
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
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Arias-Olivares D, Wieduwilt EK, Contreras-García J, Genoni A. NCI-ELMO: A New Method To Quickly and Accurately Detect Noncovalent Interactions in Biosystems. J Chem Theory Comput 2019; 15:6456-6470. [DOI: 10.1021/acs.jctc.9b00658] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- David Arias-Olivares
- Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andrés Bello, Ave. Republica 275, Santiago, Chile
- Sorbonne Université & CNRS, Laboratoire de Chimie Théorique, UMR CNRS 7616, 4 Place Jussieu, F-75005 Paris, France
| | - Erna K. Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Julia Contreras-García
- Sorbonne Université & CNRS, Laboratoire de Chimie Théorique, UMR CNRS 7616, 4 Place Jussieu, F-75005 Paris, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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Baptista SJ, Silva MMC, Moroni E, Meli M, Colombo G, Dinis TCP, Salvador JAR. Novel PARP-1 Inhibitor Scaffolds Disclosed by a Dynamic Structure-Based Pharmacophore Approach. PLoS One 2017; 12:e0170846. [PMID: 28122037 PMCID: PMC5266331 DOI: 10.1371/journal.pone.0170846] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 01/11/2017] [Indexed: 12/20/2022] Open
Abstract
PARP-1 inhibition has been studied over the last decades for the treatment of various diseases. Despite the fact that several molecules act as PARP-1 inhibitors, a reduced number of compounds are used in clinical practice. To identify new compounds with a discriminatory PARP-1 inhibitory function, explicit-solvent molecular dynamics simulations using different inhibitors bound to the PARP-1 catalytic domain were performed. The representative structures obtained were used to generate structure-based pharmacophores, taking into account the dynamic features of receptor-ligand interactions. Thereafter, a virtual screening of compound databases using the pharmacophore models obtained was performed and the hits retrieved were subjected to molecular docking-based scoring. The drug-like molecules featuring the best ranking were evaluated for their PARP-1 inhibitory activity and IC50 values were calculated for the top scoring docked compounds. Altogether, three new PARP-1 inhibitor chemotypes were identified.
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Affiliation(s)
- Salete J. Baptista
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Maria M. C. Silva
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Elisabetta Moroni
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
| | - Massimiliano Meli
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
- * E-mail: (GC); (JARS)
| | - Teresa C. P. Dinis
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Jorge A. R. Salvador
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- * E-mail: (GC); (JARS)
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Wang J, Shu M, Wen X, Wang Y, Wang Y, Hu Y, Lin Z. Discovery of vascular endothelial growth factor receptor tyrosine kinase inhibitors by quantitative structure–activity relationships, molecular dynamics simulation and free energy calculation. RSC Adv 2016. [DOI: 10.1039/c6ra03743g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Employing the combined strategy to understand the features of KDR–ligands complexes, and provide a basis for rational design of inhibitors.
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Affiliation(s)
- Juan Wang
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
- Key Laboratory of Biorheological Science and Technology (Ministry of Education)
| | - Mao Shu
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Xiaorong Wen
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Yuanliang Wang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education)
- Research Center of Bioinspired Material Science and Engineering
- Bioengineering College
- Chongqing University
- Chongqing 400044
| | - Yuanqiang Wang
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Yong Hu
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Zhihua Lin
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
- College of Chemistry and Chemical Engineering
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Morra G, Genoni A, Colombo G. Mechanisms of Differential Allosteric Modulation in Homologous Proteins: Insights from the Analysis of Internal Dynamics and Energetics of PDZ Domains. J Chem Theory Comput 2015; 10:5677-89. [PMID: 26583250 DOI: 10.1021/ct500326g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Allostery is a general phenomenon in proteins whereby a perturbation at one site reverberates into a functional change at another one, through modulation of its conformational dynamics. Herein, we address the problem of how the molecular signal encoded by a ligand is differentially transmitted through the structures of two homologous PDZ proteins: PDZ2, which responds to binding with structural and dynamical changes in regions distal from the ligand site, and PDZ3, which is characterized by less-intense dynamical variations. We use novel methods of analysis of MD simulations in the unbound and bound states to investigate the determinants of the differential allosteric behavior of the two proteins. The analysis of the correlations between the redistribution of stabilization energy and local fluctuation patterns highlights the nucleus of residues responsible for the stabilization of the 3D fold, the stability core, as the substructure that defines the difference in the allosteric response: in PDZ2, it undergoes a consistent dynamic and energetic reorganization, whereas in PDZ3, it remains largely unperturbed. Specifically, we observe for PDZ2 a significant anticorrelation between the motions of distal loops and residues of the stability core and differences in the correlation patterns between the bound and unbound states. Such variation is not observed in PDZ3, indicating that its energetics and internal dynamics are less affected by the presence/absence of the ligand. Finally, we propose a model with a direct link between the modulation of the structural, energetic and dynamic properties of a protein, and its allosteric response to a perturbation.
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Affiliation(s)
- Giulia Morra
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche Via Mario Bianco 9, 20131 Milano, Italy
| | - Alessandro Genoni
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche Via Mario Bianco 9, 20131 Milano, Italy.,CNRS, Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France.,Université de Lorraine, Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche Via Mario Bianco 9, 20131 Milano, Italy
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Moroni E, Morra G, Colombo G. Molecular dynamics simulations of hsp90 with an eye to inhibitor design. Pharmaceuticals (Basel) 2012; 5:944-62. [PMID: 24280699 PMCID: PMC3816644 DOI: 10.3390/ph5090944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 08/28/2012] [Accepted: 08/31/2012] [Indexed: 01/21/2023] Open
Abstract
Proteins carry out their functions through interactions with different partners. Dynamic conformational switching among different structural sub-states favors the adaptation to the shapes of the different partners. Such conformational changes can be determined by diverse biochemical factors, such as ligand-binding. Atomic level investigations of the mechanisms that underlie functional dynamics may provide new opportunities for the discovery of leads that target disease-related proteins. In this review, we report our views and approaches on the development of novel and accurate physical-chemistry-based models for the characterization of the salient aspects of the ligand-regulated dynamics of Hsp90, and on the exploitation of such new knowledge for the rational discovery of inhibitors of the chaperone.
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Affiliation(s)
- Elisabetta Moroni
- Institute of Molecular Recognition Chemistry, CNR, via Mario Bianco 9, 20131 Milano, Italy.
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