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Ginex T, Vázquez J, Estarellas C, Luque FJ. Quantum mechanical-based strategies in drug discovery: Finding the pace to new challenges in drug design. Curr Opin Struct Biol 2024; 87:102870. [PMID: 38914031 DOI: 10.1016/j.sbi.2024.102870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 06/26/2024]
Abstract
The expansion of the chemical space to tangible libraries containing billions of synthesizable molecules opens exciting opportunities for drug discovery, but also challenges the power of computer-aided drug design to prioritize the best candidates. This directly hits quantum mechanics (QM) methods, which provide chemically accurate properties, but subject to small-sized systems. Preserving accuracy while optimizing the computational cost is at the heart of many efforts to develop high-quality, efficient QM-based strategies, reflected in refined algorithms and computational approaches. The design of QM-tailored physics-based force fields and the coupling of QM with machine learning, in conjunction with the computing performance of supercomputing resources, will enhance the ability to use these methods in drug discovery. The challenge is formidable, but we will undoubtedly see impressive advances that will define a new era.
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Affiliation(s)
- Tiziana Ginex
- Pharmacelera, Parc Científic de Barcelona (PCB), Baldiri Reixac 4-8, 08028 Barcelona, Spain
| | - Javier Vázquez
- Pharmacelera, Parc Científic de Barcelona (PCB), Baldiri Reixac 4-8, 08028 Barcelona, Spain; Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Universitat de Barcelona, Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain; Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain
| | - Carolina Estarellas
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Universitat de Barcelona, Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain; Institut de Química Teòrica i Computacional (IQTCUB), 08921 Santa Coloma de Gramenet, Spain
| | - F Javier Luque
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Universitat de Barcelona, Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain; Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain; Institut de Química Teòrica i Computacional (IQTCUB), 08921 Santa Coloma de Gramenet, Spain.
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2
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Andrade-Collantes E, Landeros-Rivera B, Sixto-López Y, Bello-Rios C, Contreras-García J, Tiznado JAG, Pedroza-Torres A, Camacho-Pérez B, Montaño S. Molecular insight into endosulfan degradation by Ese protein from Arthrobacter: Evidence-based structural bioinformatics and quantum mechanical calculations. Proteins 2024; 92:302-313. [PMID: 37864384 DOI: 10.1002/prot.26610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/22/2023] [Accepted: 09/25/2023] [Indexed: 10/22/2023]
Abstract
Endosulfan is an organochlorine insecticide widely used for agricultural pest control. Many nations worldwide have restricted or completely banned it due to its extreme toxicity to fish and aquatic invertebrates. Arthrobacter sp. strain KW has the ability to degrade α, β endosulfan and its intermediate metabolite endosulfate; this degradation is associated with Ese protein, a two-component flavin-dependent monooxygenase (TC-FDM). Employing in silico tools, we obtained the 3D model of Ese protein, and our results suggest that it belongs to the Luciferase Like Monooxygenase family (LLM). Docking studies showed that the residues V59, V315, D316, and T335 interact with α-endosulfan. The residues: V59, T60, V315, D316, and T335 are implicated in the interacting site with β-endosulfan, and the residues: H17, V315, D316, T335, N364, and Q363 participate in the interaction with endosulfate. Topological analysis of the electron density by means of the Quantum Theory of Atoms in Molecules (QTAIM) and the Non-Covalent Interaction (NCI) index reveals that the Ese-ligands complexes are formed mainly by dispersive forces, where Cl atoms have a predominant role. As Ese is a monooxygenase member, we predict the homodimer formation. However, enzymatic studies must be developed to investigate the Ese protein's enzymatic and catalytic activity.
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Affiliation(s)
- Ernesto Andrade-Collantes
- Laboratorio de Modelado Molecular y Bioinformática, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Sinaloa, Ciudad Universitaria s/n, Culiacán, Sinaloa, Mexico
| | - Bruno Landeros-Rivera
- CNRS, Laboratoire de Chimie Théorique, LCT, Sorbonne Université, Paris, France
- Facultad de Química, Departamento de Química Inorgánica y Nuclear, Universidad Nacional Autónoma de México, Circuito exterior S/N, Ciudad Universitaria, Ciudad de México, Mexico
| | - Yudibeth Sixto-López
- Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, Universidad de Granada, Granada, Spain
| | - Ciresthel Bello-Rios
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Guerrero, Mexico
| | | | - José Antonio Garzón Tiznado
- Laboratorio de Modelado Molecular y Bioinformática, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Sinaloa, Ciudad Universitaria s/n, Culiacán, Sinaloa, Mexico
| | - Abraham Pedroza-Torres
- Cátedra CONACyT-Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Beni Camacho-Pérez
- Instituto Tecnológico y de Estudios Superiores de Occidente, Periférico Sur Manuel Gómez Morín, Tlaquepaque, Jalisco, Mexico
| | - Sarita Montaño
- Laboratorio de Modelado Molecular y Bioinformática, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Sinaloa, Ciudad Universitaria s/n, Culiacán, Sinaloa, Mexico
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Wu J, Lv J, Zhao L, Zhao R, Gao T, Xu Q, Liu D, Yu Q, Ma F. Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167028. [PMID: 37704131 DOI: 10.1016/j.scitotenv.2023.167028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/03/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.
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Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Jin Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ruofan Zhao
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Tian Gao
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China
| | - Qi Xu
- PetroChina Fushun Petrochemical Company, Fushun 113000, China
| | - Dongbo Liu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Qiqi Yu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China.
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4
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Hanpaibool C, Ngamwongsatit N, Ounjai P, Yotphan S, Wolschann P, Mulholland AJ, Spencer J, Rungrotmongkol T. Pyrazolones Potentiate Colistin Activity against MCR-1-Producing Resistant Bacteria: Computational and Microbiological Study. ACS OMEGA 2023; 8:8366-8376. [PMID: 36910942 PMCID: PMC9996792 DOI: 10.1021/acsomega.2c07165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The polymyxin colistin is a last line antibiotic for extensively resistant Gram-negative bacteria. Colistin binding to lipid A disrupts the Gram-negative outer membrane, but mobile colistin resistance (mcr) gene family members confer resistance by catalyzing phosphoethanolamine (PEA) transfer onto lipid A, neutralizing its negative charge to reduce colistin interactions. Multiple mcr isoforms have been identified in clinical and environmental isolates, with mcr-1 being the most widespread and mcr-3 being common in South and East Asia. Preliminary screening revealed that treatment with pyrazolones significantly reduced mcr-1, but not mcr-3, mediated colistin resistance. Molecular dynamics (MD) simulations of the catalytic domains of MCR-1 and a homology model of MCR-3, in different protonation states of active site residues H395/H380 and H478/H463, indicate that the MCR-1 active site has greater water accessibility than MCR-3, but that this is less influenced by changes in protonation. MD-optimized structures of MCR-1 and MCR-3 were used in virtual screening of 20 pyrazolone derivatives. Docking of these into the MCR-1/MCR-3 active sites identifies common residues likely to be involved in protein-ligand interactions, specifically the catalytic threonine (MCR-1 T285, MCR-3 T277) site of PEA addition, as well as differential interactions with adjacent amino acids. Minimal inhibitory concentration assays showed that the pyrazolone with the lowest predicted binding energy (ST3f) restores colistin susceptibility of mcr-1, but not mcr-3, expressing Escherichia coli. Thus, simulations indicate differences in the active site structure between MCR-1 and MCR-3 that may give rise to differences in pyrazolone binding and so relate to differential effects upon producer E. coli. This work identifies pyrazolones as able to restore colistin susceptibility of mcr-1-producing bacteria, laying the foundation for further investigations of their activity as phosphoethanolamine transferase inhibitors as well as of their differential activity toward mcr isoforms.
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Affiliation(s)
- Chonnikan Hanpaibool
- Center
of Excellence in Biocatalyst and Sustainable Biotechnology, Department
of Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Natharin Ngamwongsatit
- Department
of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
- Laboratory
of Bacteria, Veterinary Diagnostic Center, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Puey Ounjai
- Department
of Biology, Faculty of Science, Mahidol
University, Bangkok 10400, Thailand
- Center
of Excellence on Environmental Health and Toxicology, Office of Higher
Education Commission, Ministry of Education, Bangkok 10400, Thailand
| | - Sirilata Yotphan
- Center of
Excellence for Innovation in Chemistry (PERCH-CIC), Department of
Chemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Peter Wolschann
- Institute
of Theoretical Chemistry, University of
Vienna, Vienna 1090, Austria
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - James Spencer
- School
of Cellular and Molecular Medicine, University
of Bristol, Bristol BS8 1TD, U.K.
| | - Thanyada Rungrotmongkol
- Center
of Excellence in Biocatalyst and Sustainable Biotechnology, Department
of Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
- Program
in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10400, Thailand
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5
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Wang K. GPDOCK: highly accurate docking strategy for metalloproteins based on geometric probability. Brief Bioinform 2023; 24:6987821. [PMID: 36642411 DOI: 10.1093/bib/bbac620] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/09/2022] [Accepted: 12/17/2022] [Indexed: 01/17/2023] Open
Abstract
Accurately predicting the interaction modes for metalloproteins remains extremely challenging in structure-based drug design and mechanism analysis of enzymatic catalysis due to the complexity of metal coordination in metalloproteins. Here, we report a docking method for metalloproteins based on geometric probability (GPDOCK) with unprecedented accuracy. The docking tests of 10 common metal ions with 9360 metalloprotein-ligand complexes demonstrate that GPDOCK has an accuracy of 94.3% in predicting binding pose. What is more, it can accurately realize the docking of metalloproteins with ligand when one or two water molecules are engaged in the metal ion coordination. Since GPDOCK only depends on the three-dimensional structure of metalloprotein and ligand, structure-based machine learning model is employed for the scoring of binding poses, which significantly improves computational efficiency. The proposed docking strategy can be an effective and efficient tool for drug design and further study of binding mechanism of metalloproteins. The manual of GPDOCK and the code for the logistical regression model used to re-rank the docking results are available at https://github.com/wangkai-zhku/GPDOCK.git.
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Affiliation(s)
- Kai Wang
- School of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, P. R. China.,Abinitio Technology Company, Ltd, Guangzhou 510640, P. R. China
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Yang Z, Twidale RM, Gervasoni S, Suardíaz R, Colenso CK, Lang EJM, Spencer J, Mulholland AJ. Multiscale Workflow for Modeling Ligand Complexes of Zinc Metalloproteins. J Chem Inf Model 2021; 61:5658-5672. [PMID: 34748329 DOI: 10.1021/acs.jcim.1c01109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Zinc metalloproteins are ubiquitous, with protein zinc centers of structural and functional importance, involved in interactions with ligands and substrates and often of pharmacological interest. Biomolecular simulations are increasingly prominent in investigations of protein structure, dynamics, ligand interactions, and catalysis, but zinc poses a particular challenge, in part because of its versatile, flexible coordination. A computational workflow generating reliable models of ligand complexes of biological zinc centers would find broad application. Here, we evaluate the ability of alternative treatments, using (nonbonded) molecular mechanics (MM) and quantum mechanics/molecular mechanics (QM/MM) at semiempirical (DFTB3) and density functional theory (DFT) levels of theory, to describe the zinc centers of ligand complexes of six metalloenzyme systems differing in coordination geometries, zinc stoichiometries (mono- and dinuclear), and the nature of interacting groups (specifically the presence of zinc-sulfur interactions). MM molecular dynamics (MD) simulations can overfavor octahedral geometries, introducing additional water molecules to the zinc coordination shell, but this can be rectified by subsequent semiempirical (DFTB3) QM/MM MD simulations. B3LYP/MM geometry optimization further improved the accuracy of the description of coordination distances, with the overall effectiveness of the approach depending upon factors, including the presence of zinc-sulfur interactions that are less well described by semiempirical methods. We describe a workflow comprising QM/MM MD using DFTB3 followed by QM/MM geometry optimization using DFT (e.g., B3LYP) that well describes our set of zinc metalloenzyme complexes and is likely to be suitable for creating accurate models of zinc protein complexes when structural information is more limited.
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Affiliation(s)
- Zongfan Yang
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K.,School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, U.K
| | - Rebecca M Twidale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K
| | - Silvia Gervasoni
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K.,Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli, 25, I-20133 Milano, Italy
| | - Reynier Suardíaz
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K
| | - Charlotte K Colenso
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K.,School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, U.K
| | - Eric J M Lang
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K
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