1
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Sulimov AV, Ilin IS, Tashchilova AS, Kondakova OA, Kutov DC, Sulimov VB. Docking and other computing tools in drug design against SARS-CoV-2. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024; 35:91-136. [PMID: 38353209 DOI: 10.1080/1062936x.2024.2306336] [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: 10/17/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
The use of computer simulation methods has become an indispensable component in identifying drugs against the SARS-CoV-2 coronavirus. There is a huge body of literature on application of molecular modelling to predict inhibitors against target proteins of SARS-CoV-2. To keep our review clear and readable, we limited ourselves primarily to works that use computational methods to find inhibitors and test the predicted compounds experimentally either in target protein assays or in cell culture with live SARS-CoV-2. Some works containing results of experimental discovery of corresponding inhibitors without using computer modelling are included as examples of a success. Also, some computational works without experimental confirmations are also included if they attract our attention either by simulation methods or by databases used. This review collects studies that use various molecular modelling methods: docking, molecular dynamics, quantum mechanics, machine learning, and others. Most of these studies are based on docking, and other methods are used mainly for post-processing to select the best compounds among those found through docking. Simulation methods are presented concisely, information is also provided on databases of organic compounds that can be useful for virtual screening, and the review itself is structured in accordance with coronavirus target proteins.
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Affiliation(s)
- A V Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - I S Ilin
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - A S Tashchilova
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - O A Kondakova
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - D C Kutov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - V B Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
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2
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Szél V, Zsidó BZ, Jeszenői N, Hetényi C. Target-ligand binding affinity from single point enthalpy calculation and elemental composition. Phys Chem Chem Phys 2023; 25:31714-31725. [PMID: 37964670 DOI: 10.1039/d3cp04483a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Reliable target-ligand binding thermodynamics data are essential for successful drug design and molecular engineering projects. Besides experimental methods, a number of theoretical approaches have been introduced for the generation of binding thermodynamics data. However, available approaches often neglect electronic effects or explicit water molecules influencing target-ligand interactions. To handle electronic effects within a reasonable time frame, we introduce a fast calculator QMH-L using a single target-ligand complex structure pre-optimized at the molecular mechanics level. QMH-L is composed of the semi-empirical quantum mechanics calculation of binding enthalpy with predicted explicit water molecules at the complex interface, and a simple descriptor based on the elemental composition of the ligand. QMH-L estimates the target-ligand binding free energy with a root mean square error (RMSE) of 0.94 kcal mol-1. The calculations also provide binding enthalpy values and they were compared with experimental binding thermodynamics data collected from the most reliable isothermal titration calorimetry studies of systems including various protein targets and challenging, large peptide ligands with a molecular weight of up to 2-3 thousand. The single point enthalpy calculations of QMH-L require modest computational resources and are based on short runs with open source and/or free software like Gromacs, Mopac, MobyWat, and Fragmenter. QMH-L can be applied for fast, automated scoring of drug candidates during a virtual screen, enthalpic engineering of new ligands or thermodynamic explanation of complex interactions.
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Affiliation(s)
- Viktor Szél
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Balázs Zoltán Zsidó
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Norbert Jeszenői
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Csaba Hetényi
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
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3
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Zsidó BZ, Bayarsaikhan B, Börzsei R, Szél V, Mohos V, Hetényi C. The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering. Int J Mol Sci 2023; 24:11784. [PMID: 37511543 PMCID: PMC10381018 DOI: 10.3390/ijms241411784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Water is a key actor of various processes of nature and, therefore, molecular engineering has to take the structural and energetic consequences of hydration into account. While the present review focuses on the target-ligand interactions in drug design, with a focus on biomolecules, these methods and applications can be easily adapted to other fields of the molecular engineering of molecular complexes, including solid hydrates. The review starts with the problems and solutions of the determination of water structures. The experimental approaches and theoretical calculations are summarized, including conceptual classifications. The implementations and applications of water models are featured for the calculation of the binding thermodynamics and computational ligand docking. It is concluded that theoretical approaches not only reproduce or complete experimental water structures, but also provide key information on the contribution of individual water molecules and are indispensable tools in molecular engineering.
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Affiliation(s)
- Balázs Zoltán Zsidó
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Bayartsetseg Bayarsaikhan
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Rita Börzsei
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Viktor Szél
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Violetta Mohos
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
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4
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Shiota K, Suma A, Ogawa H, Yamaguchi T, Iida A, Hata T, Matsushita M, Akutsu T, Tateno M. AQDnet: Deep Neural Network for Protein-Ligand Docking Simulation. ACS OMEGA 2023; 8:23925-23935. [PMID: 37426216 PMCID: PMC10324054 DOI: 10.1021/acsomega.3c02411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023]
Abstract
We have developed an innovative system, AI QM Docking Net (AQDnet), which utilizes the three-dimensional structure of protein-ligand complexes to predict binding affinity. This system is novel in two respects: first, it significantly expands the training dataset by generating thousands of diverse ligand configurations for each protein-ligand complex and subsequently determining the binding energy of each configuration through quantum computation. Second, we have devised a method that incorporates the atom-centered symmetry function (ACSF), highly effective in describing molecular energies, for the prediction of protein-ligand interactions. These advancements have enabled us to effectively train a neural network to learn the protein-ligand quantum energy landscape (P-L QEL). Consequently, we have achieved a 92.6% top 1 success rate in the CASF-2016 docking power, placing first among all models assessed in the CASF-2016, thus demonstrating the exceptional docking performance of our model.
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Affiliation(s)
- Koji Shiota
- Innovation
to Implementation Laboratories, Central
Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka 569-1125, Japan
| | - Akira Suma
- Innovation
to Implementation Laboratories, Central
Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka 569-1125, Japan
| | - Hiroyuki Ogawa
- Innovation
to Implementation Laboratories, Central
Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka 569-1125, Japan
| | - Takuya Yamaguchi
- Innovation
to Implementation Laboratories, Central
Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka 569-1125, Japan
| | - Akio Iida
- Innovation
to Implementation Laboratories, Central
Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka 569-1125, Japan
| | - Takahiro Hata
- Innovation
to Implementation Laboratories, Central
Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka 569-1125, Japan
| | - Mutsuyoshi Matsushita
- Innovation
to Implementation Laboratories, Central
Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka 569-1125, Japan
| | - Tatsuya Akutsu
- Bioinformatics
Center, Institute for Chemical Research,
Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masaru Tateno
- Innovation
to Implementation Laboratories, Central
Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka 569-1125, Japan
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5
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Řezáč J, Stewart JJP. How well do semiempirical QM methods describe the structure of proteins? J Chem Phys 2023; 158:044118. [PMID: 36725526 DOI: 10.1063/5.0135091] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Semiempirical quantum-mechanical (QM) computational methods are an increasingly popular tool for the study of biomolecular systems. They were, however, developed and tested mostly on small model molecules. In this work, we explore one topic fundamental to these applications: the ability of the methods to describe the structure of proteins. In a set of 19 proteins for which a crystal structure with very high resolution is available, we analyze the properties of the protein geometries optimized using several semiempirical QM methods including PM6-D3H4, PM7, and GFN2-xTB. Some of the methods provide a very good description of the general structural features of the protein, yielding results better than or comparable to the AMBER ff03 force field. However, PM7 and PM6-D3H4 optimizations introduce artificial close contacts in the structure, which is partially remediated by reparameterization.
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Affiliation(s)
- J Řezáč
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16000 Prague, Czech Republic
| | - J J P Stewart
- Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, Colorado 80921, USA
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6
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Dutkiewicz Z. Computational methods for calculation of protein-ligand binding affinities in structure-based drug design. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2020-0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Abstract
Drug design is an expensive and time-consuming process. Any method that allows reducing the time the costs of the drug development project can have great practical value for the pharmaceutical industry. In structure-based drug design, affinity prediction methods are of great importance. The majority of methods used to predict binding free energy in protein-ligand complexes use molecular mechanics methods. However, many limitations of these methods in describing interactions exist. An attempt to go beyond these limits is the application of quantum-mechanical description for all or only part of the analyzed system. However, the extensive use of quantum mechanical (QM) approaches in drug discovery is still a demanding challenge. This chapter briefly reviews selected methods used to calculate protein-ligand binding affinity applied in virtual screening (VS), rescoring of docked poses, and lead optimization stage, including QM methods based on molecular simulations.
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Affiliation(s)
- Zbigniew Dutkiewicz
- Department of Chemical Technology of Drugs , Poznan University of Medical Sciences , ul. Grunwaldzka 6 , 60-780 Poznań , Poznan , 60-780, Poland
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7
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Gervasoni S, Spencer J, Hinchliffe P, Pedretti A, Vairoletti F, Mahler G, Mulholland AJ. A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors. Proteins 2022; 90:372-384. [PMID: 34455628 PMCID: PMC8944931 DOI: 10.1002/prot.26227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/09/2021] [Accepted: 08/18/2021] [Indexed: 02/03/2023]
Abstract
Antibiotic resistance is a major threat to global public health. β-lactamases, which catalyze breakdown of β-lactam antibiotics, are a principal cause. Metallo β-lactamases (MBLs) represent a particular challenge because they hydrolyze almost all β-lactams and to date no MBL inhibitor has been approved for clinical use. Molecular simulations can aid drug discovery, for example, predicting inhibitor complexes, but empirical molecular mechanics (MM) methods often perform poorly for metalloproteins. Here we present a multiscale approach to model thiol inhibitor binding to IMP-1, a clinically important MBL containing two catalytic zinc ions, and predict the binding mode of a 2-mercaptomethyl thiazolidine (MMTZ) inhibitor. Inhibitors were first docked into the IMP-1 active site, testing different docking programs and scoring functions on multiple crystal structures. Complexes were then subjected to molecular dynamics (MD) simulations and subsequently refined through QM/MM optimization with a density functional theory (DFT) method, B3LYP/6-31G(d), increasing the accuracy of the method with successive steps. This workflow was tested on two IMP-1:MMTZ complexes, for which it reproduced crystallographically observed binding, and applied to predict the binding mode of a third MMTZ inhibitor for which a complex structure was crystallographically intractable. We also tested a 12-6-4 nonbonded interaction model in MD simulations and optimization with a SCC-DFTB QM/MM approach. The results show the limitations of empirical models for treating these systems and indicate the need for higher level calculations, for example, DFT/MM, for reliable structural predictions. This study demonstrates a reliable computational pipeline that can be applied to inhibitor design for MBLs and other zinc-metalloenzyme systems.
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Affiliation(s)
- Silvia Gervasoni
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | | | - Franco Vairoletti
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República (UdelaR), Avda. General Flores 2124, Montevideo, Uruguay
| | - Graciela Mahler
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República (UdelaR), Avda. General Flores 2124, Montevideo, Uruguay
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8
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Firouzi R, Noohi B. Identification of key stabilizing interactions of amyloid-β oligomers based on fragment molecular orbital calculations on macrocyclic β-hairpin peptides. Proteins 2021; 90:229-238. [PMID: 34387401 DOI: 10.1002/prot.26212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/01/2021] [Accepted: 08/06/2021] [Indexed: 11/10/2022]
Abstract
Analyzing the electronic states and inter-/intra-molecular interactions of amyloid oligomers expand our understanding of the molecular basis of Alzheimer's disease and other amyloid diseases. In the current study, several high-resolution crystal structures of oligomeric assemblies of Aβ-derived peptides have been studied by the ab initio fragment molecular orbital (FMO) method. The FMO method provides comprehensive details of the molecular interactions between the residues of the amyloid oligomers at the quantum mechanical level. Based on the calculations, two sequential aromatic residues (F19 and F20) and negatively charged E22 on the central region of Aβ have been identified as key residues in oligomer stabilization and potential interesting pharmacophores for preventing oligomer formation.
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Affiliation(s)
- Rohoullah Firouzi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | - Bahare Noohi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
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9
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Ehlert S, Stahn M, Spicher S, Grimme S. Robust and Efficient Implicit Solvation Model for Fast Semiempirical Methods. J Chem Theory Comput 2021; 17:4250-4261. [PMID: 34185531 DOI: 10.1021/acs.jctc.1c00471] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We present a robust and efficient method to implicitly account for solvation effects in modern semiempirical quantum mechanics and force fields. A computationally efficient yet accurate solvation model based on the analytical linearized Poisson-Boltzmann (ALPB) model is parameterized for the extended tight binding (xTB) and density functional tight binding (DFTB) methods as well as for the recently proposed GFN-FF general force field. The proposed methods perform well over a broad range of systems and applications, from conformational energies over transition-metal complexes to large supramolecular association reactions of charged species. For hydration free energies of small molecules, GFN1-xTB(ALPB) is reaching the accuracy of sophisticated explicitly solvated approaches, with a mean absolute deviation of only 1.4 kcal/mol compared to the experiment. Logarithmic octanol-water partition coefficients (log Kow) are computed with a mean absolute deviation of about 0.65 using GFN2-xTB(ALPB) compared to experimental values indicating a consistent description of differential solvent effects. Overall, more than twenty solvents for each of the six semiempirical methods are parameterized and tested. They are readily available in the xtb and dftb+ programs for diverse computational applications.
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Affiliation(s)
- Sebastian Ehlert
- Mulliken Center of Theoretical Chemistry, University of Bonn, Bonn 53115, Germany
| | - Marcel Stahn
- Mulliken Center of Theoretical Chemistry, University of Bonn, Bonn 53115, Germany
| | - Sebastian Spicher
- Mulliken Center of Theoretical Chemistry, University of Bonn, Bonn 53115, Germany
| | - Stefan Grimme
- Mulliken Center of Theoretical Chemistry, University of Bonn, Bonn 53115, Germany
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10
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Sulimov VB, Kutov DC, Taschilova AS, Ilin IS, Tyrtyshnikov EE, Sulimov AV. Docking Paradigm in Drug Design. Curr Top Med Chem 2021; 21:507-546. [PMID: 33292135 DOI: 10.2174/1568026620666201207095626] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/28/2020] [Accepted: 10/16/2020] [Indexed: 11/22/2022]
Abstract
Docking is in demand for the rational computer aided structure based drug design. A review of docking methods and programs is presented. Different types of docking programs are described. They include docking of non-covalent small ligands, protein-protein docking, supercomputer docking, quantum docking, the new generation of docking programs and the application of docking for covalent inhibitors discovery. Taking into account the threat of COVID-19, we present here a short review of docking applications to the discovery of inhibitors of SARS-CoV and SARS-CoV-2 target proteins, including our own result of the search for inhibitors of SARS-CoV-2 main protease using docking and quantum chemical post-processing. The conclusion is made that docking is extremely important in the fight against COVID-19 during the process of development of antivirus drugs having a direct action on SARS-CoV-2 target proteins.
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Affiliation(s)
- Vladimir B Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Danil C Kutov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Anna S Taschilova
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Ivan S Ilin
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Eugene E Tyrtyshnikov
- Institute of Numerical Mathematics of Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey V Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
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11
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Sulimov AV, Ilin IS, Kutov DC, Stolpovskaya NV, Shikhaliev KS, Sulimov VB. Supercomputing, Docking and Quantum Mechanics in Quest for Inhibitors of Papain-like Protease of SARS-CoV-2. LOBACHEVSKII JOURNAL OF MATHEMATICS 2021; 42. [PMCID: PMC8351772 DOI: 10.1134/s1995080221070222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Lomonosov-2 supercomputer is used to search for new organic compounds that can suppress the replication of the SARS-CoV-2 coronavirus. The latter is responsible for the COVID-19 pandemic. Docking and a quantum-chemical semiempirical atomistic modeling method are used to find inhibitors of the SARS-CoV-2 papain-like protease, which is one of the key coronavirus enzymes responsible for its replication. The atomistic model of the papain-like protease of this coronavirus is based on the high-resolution structure deposited in the Protein Data Bank. The SOL docking program has been used for virtual screening of more than \documentclass[12pt]{minimal}
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\begin{document}$$40000$$\end{document} low molecular weight molecules (ligands). Ligands with the highest protein-ligand binding energy, selected using the docking results, were subjected to quantum-chemical calculations. The latters are performed by the PM7 semiempirical method with the COSMO implicit solvent model using the MOPAC program. The enthalpy of protein-ligand binding is calculated for the best position of the ligand in the protein. \documentclass[12pt]{minimal}
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\begin{document}$$19$$\end{document} ligands were selected for experimental in vitro testing as candidates for papain-like protease inhibitors base on docking and quantum-chemical results. In case of experimental confirmation, these compounds may become the basis for direct-acting antiviral drugs for the SARS-CoV-2 coronavirus.
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Affiliation(s)
- A. V. Sulimov
- Research Computing Center of Lomonosov Moscow State University, 119234 Moscow, Russia
- Moscow Center of Fundamental and Applied Mathematics, 119234 Moscow, Russia
| | - I. S. Ilin
- Research Computing Center of Lomonosov Moscow State University, 119234 Moscow, Russia
- Moscow Center of Fundamental and Applied Mathematics, 119234 Moscow, Russia
| | - D. C. Kutov
- Research Computing Center of Lomonosov Moscow State University, 119234 Moscow, Russia
- Moscow Center of Fundamental and Applied Mathematics, 119234 Moscow, Russia
| | - N. V. Stolpovskaya
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 394006 Voronezh, Russia
| | - Kh. S. Shikhaliev
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 394006 Voronezh, Russia
| | - V. B. Sulimov
- Research Computing Center of Lomonosov Moscow State University, 119234 Moscow, Russia
- Moscow Center of Fundamental and Applied Mathematics, 119234 Moscow, Russia
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12
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Willow SY, Xie B, Lawrence J, Eisenberg RS, Minh DDL. On the polarization of ligands by proteins. Phys Chem Chem Phys 2020; 22:12044-12057. [PMID: 32421120 DOI: 10.1039/d0cp00376j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence binding, the magnitude of this effect has not been studied in many systems. Here, we use a quantum mechanics/molecular mechanics (QM/MM) approach, in which the ligand is the QM region, to compute the ligand polarization energy of 286 protein-ligand complexes from the PDBBind Core Set (release 2016). Calculations were performed both with and without implicit solvent based on the domain decomposition Conductor-like Screening Model. We observe that the ligand polarization energy is linearly correlated with the magnitude of the electric field acting on the ligand, the magnitude of the induced dipole moment, and the classical polarization energy. The influence of protein and cation charges on the ligand polarization diminishes with the distance and is below 2 kcal mol-1 at 9 Å and 1 kcal mol-1 at 12 Å. Compared to these embedding field charges, implicit solvent has a relatively minor effect on ligand polarization. Considering both polarization and solvation appears essential to computing negative binding energies in some crystallographic complexes. Solvation, but not polarization, is essential for achieving moderate correlation with experimental binding free energies.
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Affiliation(s)
- Soohaeng Yoo Willow
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, USA.
| | - Bing Xie
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, USA.
| | - Jason Lawrence
- Department of Computer Science, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - Robert S Eisenberg
- Department of Applied Mathematics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - David D L Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, USA.
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13
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Manukyan AK. Structural aspects and activation mechanism of human secretory group IIA phospholipase. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:511-531. [DOI: 10.1007/s00249-020-01458-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 11/30/2022]
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14
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González-Paz L, Paz JL, Vera-Villalobos J, Alvarado YJ. Compuestos Fitoquímicos Dirigidos al Bloqueo de la Polimerasa Viral del SARS-CoV-2 Causante del COVID-19: un Análisis Comparativo de Funciones de Puntuación para Acoplamientos con Interés Biomédico. REVISTA POLITÉCNICA 2020. [DOI: 10.33333/rp.vol46n1.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
La pandemia mundial del COVID-19 causada por el SARS-CoV-2 ha hecho necesario buscar alternativas de tratamiento. La OMS ha recomendado el fármaco aprobado por la FDA Remdesivir dirigido a la RNA polimerasa viral. Adicionalmente, se han evaluado computacionalmente compuestos naturales con propiedades antivirales. Sin embargo, estos estudios se centran en el uso de la función de puntuación del algoritmo AutoDock Vina (ADV) para predecir los candidatos. Aquí proponemos evaluar los fitoquímicos Piperina_ID_638024, EPGG_ID_65064, Curcumina_ID_969516, y Capsaicina_ID_1548943 frente a la RNA polimerasa del SARS-CoV-2 (PDB_ID_6NUR), usando Remdesivir_ID_121304016 como control, mediante análisis computacional, comparativo y multivariado de las funciones de puntuación ADV, PLANTS, MolDock, Rerank y DockT considerando la solubilidad de ligandos e hidrofobicidad de las cavidades implicadas en las interacciones, para aumentar la precisión en la predicción de los mejores acoplamientos de los compuestos naturales frente al COVID-19. Encontramos que 4/5 de las funciones de puntuación exceptuando ADV predijeron el acoplamiento termodinámicamente más favorable con Piperina, superando a Remdesivir. También observamos que las calificaciones de PLANTS, ADV y DockT se afectan por la solubilidad del ligando e hidrofobicidad de cavidades. Bajo las condiciones de este estudio concluimos que los algoritmos MolDock y Rerank son más adecuados para el cribado rápido y la reorganización de acoplamientos, cuando se trabaje con ligandos solubles (Rp = 0.70 para ambos), indistintamente de su polaridad, y dirigidos a cavidades hidrofóbicas de la RNA polimerasa del SARS-CoV-2 (Rp = 0.95 y Rp = 0.90, respectivamente), especialmente para los enfoques computacionales en el contexto de la investigación de fármacos frente al COVID-19.
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15
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Pecina A, Eyrilmez SM, Köprülüoğlu C, Miriyala VM, Lepšík M, Fanfrlík J, Řezáč J, Hobza P. SQM/COSMO Scoring Function: Reliable Quantum-Mechanical Tool for Sampling and Ranking in Structure-Based Drug Design. Chempluschem 2020; 85:2362-2371. [PMID: 32609421 DOI: 10.1002/cplu.202000120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/27/2020] [Indexed: 12/17/2022]
Abstract
Quantum mechanical (QM) methods have been gaining importance in structure-based drug design where a reliable description of protein-ligand interactions is of utmost significance. However, strategies i. e. QM/MM, fragmentation or semiempirical (SQM) methods had to be pursued to overcome the unfavorable scaling of QM methods. Various SQM-based approaches have significantly contributed to the accuracy of docking and improvement of lead compounds. Parametrizations of SQM and implicit solvent methods in our laboratory have been instrumental to obtain a reliable SQM-based scoring function. The experience gained in its application for activity ranking of ligands binding to tens of protein targets resulted in setting up a faster SQM/COSMO scoring approach, which outperforms standard scoring methods in native pose identification for two dozen protein targets with ten thousand poses. Recently, SQM/COSMO was effectively applied in a proof-of-concept study of enrichment in virtual screening. Due to its superior performance, feasibility and chemical generality, we propose the SQM/COSMO approach as an efficient tool in structure-based drug design.
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Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Saltuk M Eyrilmez
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
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16
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Bitencourt-Ferreira G, de Azevedo WF. Molecular Dynamics Simulations with NAMD2. Methods Mol Biol 2020; 2053:109-124. [PMID: 31452102 DOI: 10.1007/978-1-4939-9752-7_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
X-ray diffraction crystallography is the primary technique to determine the three-dimensional structures of biomolecules. Although a robust method, X-ray crystallography is not able to access the dynamical behavior of macromolecules. To do so, we have to carry out molecular dynamics simulations taking as an initial system the three-dimensional structure obtained from experimental techniques or generated using homology modeling. In this chapter, we describe in detail a tutorial to carry out molecular dynamics simulations using the program NAMD2. We chose as a molecular system to simulate the structure of human cyclin-dependent kinase 2.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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17
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Wang Z, Wang X, Li Y, Lei T, Wang E, Li D, Kang Y, Zhu F, Hou T. farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods. Bioinformatics 2020; 35:1777-1779. [PMID: 30329012 DOI: 10.1093/bioinformatics/bty879] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/20/2018] [Accepted: 10/15/2018] [Indexed: 12/31/2022] Open
Abstract
SUMMARY Protein-protein interactions (PPIs) have been regarded as an attractive emerging class of therapeutic targets for the development of new treatments. Computational approaches, especially molecular docking, have been extensively employed to predict the binding structures of PPI-inhibitors or discover novel small molecule PPI inhibitors. However, due to the relatively 'undruggable' features of PPI interfaces, accurate predictions of the binding structures for ligands towards PPI targets are quite challenging for most docking algorithms. Here, we constructed a non-redundant pose ranking benchmark dataset for small-molecule PPI inhibitors, which contains 900 binding poses for 184 protein-ligand complexes. Then, we evaluated the performance of MM/PB(GB)SA approaches to identify the correct binding poses for PPI inhibitors, including two Prime MM/GBSA procedures from the Schrödinger suite and seven different MM/PB(GB)SA procedures from the Amber package. Our results showed that MM/PBSA outperformed the Glide SP scoring function (success rate of 58.6%) and MM/GBSA in most cases, especially the PB3 procedure which could achieve an overall success rate of ∼74%. Moreover, the GB6 procedure (success rate of 68.9%) performed much better than the other MM/GBSA procedures, highlighting the excellent potential of the GBNSR6 implicit solvation model for pose ranking. Finally, we developed the webserver of Fast Amber Rescoring for PPI Inhibitors (farPPI), which offers a freely available service to rescore the docking poses for PPI inhibitors by using the MM/PB(GB)SA methods. AVAILABILITY AND IMPLEMENTATION farPPI web server is freely available at http://cadd.zju.edu.cn/farppi/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhe Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xuwen Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu, China
| | - Tailong Lei
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ercheng Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang, China
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18
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Bagheri S, Behnejad H, Firouzi R, Karimi-Jafari MH. Using the Semiempirical Quantum Mechanics in Improving the Molecular Docking: A Case Study with CDK2. Mol Inform 2020; 39:e2000036. [PMID: 32485047 DOI: 10.1002/minf.202000036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 05/28/2020] [Indexed: 11/12/2022]
Abstract
In this study, we use some modified semiempirical quantum mechanics (SQM) methods for improving the molecular docking process. To this end, the three popular SQM Hamiltonians, PM6, PM6-D3H4X, and PM7 are employed for geometry optimization of some binding modes of ligands docked into the human cyclin-dependent kinase 2 (CDK2) by two widely used docking tools, AutoDock and AutoDock Vina. The results were analyzed with two different evaluation metrics: the symmetry-corrected heavy-atom RMSD and the fraction of recovered ligand-protein contacts. It is shown that the evaluation of the fraction of recovered contacts is more useful to measure the similarity between two structures when interacting with a protein. It was also found that AutoDock is more successful than AutoDock Vina in producing the correct ligand poses (RMSD≤2.0 Å) and ranking of the poses. It is also demonstrated that the ligand optimization at the SQM level improves the docking results and the SQM structures have a significantly better fit to the observed crystal structures. Finally, the SQM optimizations reduce the number of close contacts in the docking poses and successfully remove most of the clash or bad contacts between ligand and protein.
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Affiliation(s)
- Saleh Bagheri
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Hassan Behnejad
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Rohoullah Firouzi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
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19
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Zhu Z, Xu Z, Zhu W. Interaction Nature and Computational Methods for Halogen Bonding: A Perspective. J Chem Inf Model 2020; 60:2683-2696. [DOI: 10.1021/acs.jcim.0c00032] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
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20
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Cavasotto CN, Aucar MG. High-Throughput Docking Using Quantum Mechanical Scoring. Front Chem 2020; 8:246. [PMID: 32373579 PMCID: PMC7186494 DOI: 10.3389/fchem.2020.00246] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 03/16/2020] [Indexed: 11/13/2022] Open
Abstract
Today high-throughput docking is one of the most commonly used computational tools in drug lead discovery. While there has been an impressive methodological improvement in docking accuracy, docking scoring still remains an open challenge. Most docking programs are rooted in classical molecular mechanics. However, to better characterize protein-ligand interactions, the use of a more accurate quantum mechanical (QM) description would be necessary. In this work, we introduce a QM-based docking scoring function for high-throughput docking and evaluate it on 10 protein systems belonging to diverse protein families, and with different binding site characteristics. Outstanding results were obtained, with our QM scoring function displaying much higher enrichment (screening power) than a traditional docking method. It is acknowledged that developments in quantum mechanics theory, algorithms and computer hardware throughout the upcoming years will allow semi-empirical (or low-cost) quantum mechanical methods to slowly replace force-field calculations. It is thus urgently needed to develop and validate novel quantum mechanical-based scoring functions for high-throughput docking toward more accurate methods for the identification and optimization of modulators of pharmaceutically relevant targets.
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Affiliation(s)
- Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Pilar, Argentina.,Facultad de Ciencias Biomédicas and Facultad de Ingeniería, Universidad Austral, Pilar, Argentina.,Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Argentina
| | - M Gabriela Aucar
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Pilar, Argentina
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21
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Optimization of norbornyl‐based carbocyclic nucleoside analogs as cyclin‐dependent kinase 2 inhibitors. J Mol Recognit 2020; 33:e2842. [DOI: 10.1002/jmr.2842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/26/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023]
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22
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Kříž K, Řezáč J. Benchmarking of Semiempirical Quantum-Mechanical Methods on Systems Relevant to Computer-Aided Drug Design. J Chem Inf Model 2020; 60:1453-1460. [PMID: 32062970 DOI: 10.1021/acs.jcim.9b01171] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The semiempirical quantum mechanical (SQM) methods used in drug design are commonly parametrized and tested on data sets of systems that may not be representative models for drug-biomolecule interactions in terms of both size and chemical composition. This is addressed here with a new benchmark data set, PLF547, derived from protein-ligand complexes, consisting of complexes of ligands with protein fragments (such as amino-acid side chains), with interaction energies based on MP2-F12 and DLPNO-CCSD(T) calculations. From these, composite benchmark interaction energies are also built for complexes of the ligand with the complete active site of the protein (PLA15 data set). These data sets are used to test multiple SQM methods with corrections for noncovalent interactions; the role of the solvation model in the calculations is tested as well.
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Affiliation(s)
- Kristian Kříž
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 40 Praha 2, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
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23
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Sulimov VB, Kutov DC, Sulimov AV. Advances in Docking. Curr Med Chem 2020; 26:7555-7580. [PMID: 30182836 DOI: 10.2174/0929867325666180904115000] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Design of small molecules which are able to bind to the protein responsible for a disease is the key step of the entire process of the new medicine discovery. Atomistic computer modeling can significantly improve effectiveness of such design. The accurate calculation of the free energy of binding a small molecule (a ligand) to the target protein is the most important problem of such modeling. Docking is one of the most popular molecular modeling methods for finding ligand binding poses in the target protein and calculating the protein-ligand binding energy. This energy is used for finding the most active compounds for the given target protein. This short review aims to give a concise description of distinctive features of docking programs focusing on computation methods and approximations influencing their accuracy. METHODS This review is based on the peer-reviewed research literature including author's own publications. The main features of several representative docking programs are briefly described focusing on their characteristics influencing docking accuracy: force fields, energy calculations, solvent models, algorithms of the best ligand pose search, global and local optimizations, ligand and target protein flexibility, and the simplifications made for the docking accelerating. Apart from other recent reviews focused mainly on the performance of different docking programs, in this work, an attempt is made to extract the most important functional characteristics defining the docking accuracy. Also a roadmap for increasing the docking accuracy is proposed. This is based on the new generation of docking programs which have been realized recently. These programs and respective new global optimization algorithms are described shortly. RESULTS Several popular conventional docking programs are considered. Their search of the best ligand pose is based explicitly or implicitly on the global optimization problem. Several algorithms are used to solve this problem, and among them, the heuristic genetic algorithm is distinguished by its popularity and an elaborate design. All conventional docking programs for their acceleration use the preliminary calculated grids of protein-ligand interaction potentials or preferable points of protein and ligand conjugation. These approaches and commonly used fitting parameters restrict strongly the docking accuracy. Solvent is considered in exceedingly simplified approaches in the course of the global optimization and the search for the best ligand poses. More accurate approaches on the base of implicit solvent models are used frequently for more careful binding energy calculations after docking. The new generation of docking programs are developed recently. They find the spectrum of low energy minima of a protein-ligand complex including the global minimum. These programs should be more accurate because they do not use a preliminary calculated grid of protein-ligand interaction potentials and other simplifications, the energy of any conformation of the molecular system is calculated in the frame of a given force field and there are no fitting parameters. A new docking algorithm is developed and fulfilled specially for the new docking programs. This algorithm allows docking a flexible ligand into a flexible protein with several dozen mobile atoms on the base of the global energy minimum search. Such docking results in improving the accuracy of ligand positioning in the docking process. The adequate choice of the method of molecular energy calculations also results in the better docking positioning accuracy. An advancement in the application of quantum chemistry methods to docking and scoring is revealed. CONCLUSION The findings of this review confirm the great demand in docking programs for discovery of new medicine substances with the help of molecular modeling. New trends in docking programs design are revealed. These trends are focused on the increase of the docking accuracy at the expense of more accurate molecular energy calculations without any fitting parameters, including quantum-chemical methods and implicit solvent models, and by using new global optimization algorithms which make it possible to treat flexibility of ligands and mobility of protein atoms simultaneously. Finally, it is shown that all the necessary prerequisites for increasing the docking accuracy can be accomplished in practice.
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Affiliation(s)
- Vladimir B Sulimov
- Dimonta, Ltd., Nagornaya Street 15, Building 8, 117186 Moscow, Russian Federation.,Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, 119991 Moscow, Russian Federation
| | - Danil C Kutov
- Dimonta, Ltd., Nagornaya Street 15, Building 8, 117186 Moscow, Russian Federation.,Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, 119991 Moscow, Russian Federation
| | - Alexey V Sulimov
- Dimonta, Ltd., Nagornaya Street 15, Building 8, 117186 Moscow, Russian Federation.,Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, 119991 Moscow, Russian Federation
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24
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Cavasotto CN. Binding Free Energy Calculation Using Quantum Mechanics Aimed for Drug Lead Optimization. Methods Mol Biol 2020; 2114:257-268. [PMID: 32016898 DOI: 10.1007/978-1-0716-0282-9_16] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The routine use of in silico tools is already established in drug lead design. Besides the use of molecular docking methods to screen large chemical libraries and thus prioritize compounds for purchase or synthesis, more accurate calculations of protein-ligand binding free energy has shown the potential to guide lead optimization, thus saving time and resources. Theoretical developments and advances in computing power have allowed quantum mechanical-based methods applied to calculations on biomacromolecules to be increasingly explored and used, with the purpose of providing a more accurate description of protein-ligand interactions and an enhanced level of accuracy in the calculation of binding affinities. It should be noted that the quantum mechanical formulation includes, in principle, all contributions to the energy, considering terms usually neglected in molecular mechanics force fields, such as electronic polarization, metal coordination, and covalent binding; moreover, quantum mechanical approaches are systematically improvable. By treating all elements and interactions on equal footing, and avoiding the need of system-dependent parameterizations, they provide a greater degree of transferability. In this review, we illustrate the increasing relevance of quantum mechanical methods for binding free energy calculation in the context of structure-based drug lead optimization, showing representative applications of the different approaches available.
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Affiliation(s)
- Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina. .,Austral Institute for Applied Artificial Intelligence, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina. .,Facultad de Ciencias Biomédicas, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina. .,Facultad de Ingeniería, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
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25
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Abstract
Computational methods are a powerful and consolidated tool in the early stage of the drug lead discovery process. Among these techniques, high-throughput molecular docking has proved to be extremely useful in identifying novel bioactive compounds within large chemical libraries. In the docking procedure, the predominant binding mode of each small molecule within a target binding site is assessed, and a docking score reflective of the likelihood of binding is assigned to them. These methods also shed light on how a given hit could be modified in order to improve protein-ligand interactions and are thus able to guide lead optimization. The possibility of reducing time and cost compared to experimental approaches made this technology highly appealing. Due to methodological developments and the increase of computational power, the application of quantum mechanical methods to study macromolecular systems has gained substantial attention in the last decade. A quantum mechanical description of the interactions involved in molecular association of biomolecules may lead to better accuracy compared to molecular mechanics, since there are many physical phenomena that cannot be correctly described within a classical framework, such as covalent bond formation, polarization effects, charge transfer, bond rearrangements, halogen bonding, and others, that require electrons to be explicitly accounted for. Considering the fact that quantum mechanics-based approaches in biomolecular simulation constitute an active and important field of research, we highlight in this work the recent developments of quantum mechanical-based molecular docking and high-throughput docking.
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Affiliation(s)
- M Gabriela Aucar
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina
| | - Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
- Austral Institute for Applied Artificial Intelligence, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
- Facultad de Ciencias Biomédicas, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
- Facultad de Ingeniería, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
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26
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Eyrilmez SM, Köprülüoğlu C, Řezáč J, Hobza P. Impressive Enrichment of Semiempirical Quantum Mechanics-Based Scoring Function: HSP90 Protein with 4541 Inhibitors and Decoys. Chemphyschem 2019; 20:2759-2766. [PMID: 31460692 DOI: 10.1002/cphc.201900628] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/21/2019] [Indexed: 12/11/2022]
Abstract
This paper describes the excellent performance of a newly developed scoring function (SF), based on the semiempirical QM (SQM) PM6-D3H4X method combined with the conductor-like screening implicit solvent model (COSMO). The SQM/COSMO, Amber/GB and nine widely used SFs have been evaluated in terms of ranking power on the HSP90 protein with 72 biologically active compounds and 4469 structurally similar decoys. Among conventional SFs, the highest early and overall enrichment measured by EF1 and AUC% obtained using single-scoring-function ranking has been found for Glide SP and Gold-ASP SFs, respectively (7, 75 % and 3, 76 %). The performance of other standard SFs has not been satisfactory, mostly even decreasing below random values. The SQM/COSMO SF, where P-L structures were optimised at the advanced Amber level, has resulted in a dramatic enrichment increase (47, 98 %), almost reaching the best possible receiver operator characteristic (ROC) curve. The best SQM frame thus inserts about seven times more active compounds into the selected dataset than the best standard SF.
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Affiliation(s)
- Saltuk M Eyrilmez
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, CzechRepublic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, CzechRepublic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, CzechRepublic
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27
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Costa PJ, Nunes R, Vila-Viçosa D. Halogen bonding in halocarbon-protein complexes and computational tools for rational drug design. Expert Opin Drug Discov 2019; 14:805-820. [PMID: 31131651 DOI: 10.1080/17460441.2019.1619692] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introduction: Halogens have a prominent role in drug design. Often used as a mean to improve ADME properties, they are also becoming a tool in protein-ligand recognition given their ability to form a non-covalent interaction, termed halogen bond, where halogens act as electrophilic species interacting with electron-rich partners. Rational drug design of halogen-bonding lead molecules requires an accurate description of halocarbon-protein complexes by computational tools though not all methods are able to tackle this non-covalent interaction. Areas covered: The authors present a review of computational methodologies that can be used to properly describe halogen bonds in the context of protein-ligand complexes, providing also insights on how these methods can be used in the context of computer-aided drug design. Expert opinion: Although in the last few years many computational tools, ranging from fast screening methods to the more expensive QM calculations, have been developed to tackle the halogen bonding phenomenon, they are not yet standard in the literature. This will eventually change as official software distributions are including support for halogen bonding in their methods. Tackling desolvation of halogenated species seems to be a good strategy to improve the accuracy of computational methods, that will be more commonly used prior to laboratory work in the future.
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Affiliation(s)
- Paulo J Costa
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| | - Rafael Nunes
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| | - Diogo Vila-Viçosa
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
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28
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Kříž K, Řezáč J. Reparametrization of the COSMO Solvent Model for Semiempirical Methods PM6 and PM7. J Chem Inf Model 2019; 59:229-235. [DOI: 10.1021/acs.jcim.8b00681] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Kristian Kříž
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 40 Prague 2, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
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29
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Bitencourt-Ferreira G, Veit-Acosta M, de Azevedo WF. Van der Waals Potential in Protein Complexes. Methods Mol Biol 2019; 2053:79-91. [PMID: 31452100 DOI: 10.1007/978-1-4939-9752-7_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Van der Waals forces are determinants of the formation of protein-ligand complexes. Physical models based on the Lennard-Jones potential can estimate van der Waals interactions with considerable accuracy and with a computational complexity that allows its application to molecular docking simulations and virtual screening of large databases of small organic molecules. Several empirical scoring functions used to evaluate protein-ligand interactions approximate van der Waals interactions with the Lennard-Jones potential. In this chapter, we present the main concepts necessary to understand van der Waals interactions relevant to molecular recognition of a ligand by the binding pocket of a protein target. We describe the Lennard-Jones potential and its application to calculate potential energy for an ensemble of structures to highlight the main features related to the importance of this interaction for binding affinity.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Martina Veit-Acosta
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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30
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Interface Interactions of the Bowman-Birk Inhibitor BTCI in a Ternary Complex with Trypsin and Chymotrypsin Evaluated by Semiempirical Quantum Mechanical Calculations. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800754] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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31
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32
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A new approach for the acceleration of large-scale serial quantum chemical calculations of docking complexes. Russ Chem Bull 2018. [DOI: 10.1007/s11172-018-2186-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Cavasotto CN, Adler NS, Aucar MG. Quantum Chemical Approaches in Structure-Based Virtual Screening and Lead Optimization. Front Chem 2018; 6:188. [PMID: 29896472 PMCID: PMC5986912 DOI: 10.3389/fchem.2018.00188] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/09/2018] [Indexed: 12/05/2022] Open
Abstract
Today computational chemistry is a consolidated tool in drug lead discovery endeavors. Due to methodological developments and to the enormous advance in computer hardware, methods based on quantum mechanics (QM) have gained great attention in the last 10 years, and calculations on biomacromolecules are becoming increasingly explored, aiming to provide better accuracy in the description of protein-ligand interactions and the prediction of binding affinities. In principle, the QM formulation includes all contributions to the energy, accounting for terms usually missing in molecular mechanics force-fields, such as electronic polarization effects, metal coordination, and covalent binding; moreover, QM methods are systematically improvable, and provide a greater degree of transferability. In this mini-review we present recent applications of explicit QM-based methods in small-molecule docking and scoring, and in the calculation of binding free-energy in protein-ligand systems. Although the routine use of QM-based approaches in an industrial drug lead discovery setting remains a formidable challenging task, it is likely they will increasingly become active players within the drug discovery pipeline.
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Affiliation(s)
- Claudio N. Cavasotto
- Laboratory of Computational Chemistry and Drug Design, Instituto de Investigación en Biomedicina de Buenos Aires, CONICET, Partner Institute of the Max Planck Society, Buenos Aires, Argentina
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34
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Miriyala VM, Řezáč J. Testing Semiempirical Quantum Mechanical Methods on a Data Set of Interaction Energies Mapping Repulsive Contacts in Organic Molecules. J Phys Chem A 2018; 122:2801-2808. [PMID: 29473742 DOI: 10.1021/acs.jpca.8b00260] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Semiempirical quantum mechanical (QM) methods with corrections for noncovalent interactions provide a favorable combination of accuracy and computational efficiency that makes them a useful tool for a study of large molecular systems. It was, however, noted that the accuracy of these methods deteriorates at intermolecular distances shorter than equilibrium. In this work, we explore this issue systematically using a newly developed data set of benchmark interaction energies named R160×6. This data set maps repulsive contacts in organic molecules, and it consists of 160 model complexes for which six points along the dissociation curve are provided. Testing a wide range of semiempirical QM methods against the CCSD(T)/CBS benchmark revealed that most methods, and all the dispersion-corrected ones, underestimate the repulsion systematically. The worst cases are usually hydrogen-hydrogen contacts. The best results were obtained with PM6-D3H4 and DFTB3-D3H4, as these methods already contain a correction for the H-H repulsion, but the errors are still about twice as large as in equilibrium geometries.
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Affiliation(s)
- V M Miriyala
- Department of Computational Chemistry , Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo Náměstí 542/2 , 16610 Prague , Czech Republic
| | - J Řezáč
- Department of Computational Chemistry , Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo Náměstí 542/2 , 16610 Prague , Czech Republic
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35
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Pecina A, Brynda J, Vrzal L, Gnanasekaran R, Hořejší M, Eyrilmez SM, Řezáč J, Lepšík M, Řezáčová P, Hobza P, Majer P, Veverka V, Fanfrlík J. Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II-Inhibitor Complexes. Chemphyschem 2018; 19:873-879. [PMID: 29316128 DOI: 10.1002/cphc.201701104] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Indexed: 11/11/2022]
Abstract
Accurate prediction of protein-ligand binding affinities is essential for hit-to-lead optimization and virtual screening. The reliability of scoring functions can be improved by including quantum effects. Here, we demonstrate the ranking power of the semiempirical quantum mechanics (SQM)/implicit solvent (COSMO) scoring function by using a challenging set of 10 inhibitors binding to carbonic anhydrase II through Zn2+ in the active site. This new dataset consists of the high-resolution (1.1-1.4 Å) crystal structures and experimentally determined inhibitory constant (Ki ) values. It allows for evaluation of the common approximations, such as representing the solvent implicitly or by using a single target conformation combined with a set of ligand docking poses. SQM/COSMO attained a good correlation of R2 of 0.56-0.77 with the experimental inhibitory activities, benefiting from careful handling of both noncovalent interactions (e.g. charge transfer) and solvation. This proof-of-concept study of SQM/COSMO ranking for metalloprotein-ligand systems demonstrates its potential for hit-to-lead applications.
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Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Lukáš Vrzal
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Ramachandran Gnanasekaran
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Current address: Department of Chemistry, Pondicherry University, Puducherry, 605014, India
| | - Magdalena Hořejší
- Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Saltuk M Eyrilmez
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Palacký University, 77146, Olomouc, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
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36
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New generation of docking programs: Supercomputer validation of force fields and quantum-chemical methods for docking. J Mol Graph Model 2017; 78:139-147. [DOI: 10.1016/j.jmgm.2017.10.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 11/19/2022]
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37
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Řezáč J. Empirical Self-Consistent Correction for the Description of Hydrogen Bonds in DFTB3. J Chem Theory Comput 2017; 13:4804-4817. [DOI: 10.1021/acs.jctc.7b00629] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Řezáč
- Institute of Organic Chemistry
and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
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38
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Ajani H, Pecina A, Eyrilmez SM, Fanfrlík J, Haldar S, Řezáč J, Hobza P, Lepšík M. Superior Performance of the SQM/COSMO Scoring Functions in Native Pose Recognition of Diverse Protein-Ligand Complexes in Cognate Docking. ACS OMEGA 2017; 2:4022-4029. [PMID: 30023710 PMCID: PMC6044937 DOI: 10.1021/acsomega.7b00503] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/18/2017] [Indexed: 06/08/2023]
Abstract
General and reliable description of structures and energetics in protein-ligand (PL) binding using the docking/scoring methodology has until now been elusive. We address this urgent deficiency of scoring functions (SFs) by the systematic development of corrected semiempirical quantum mechanical (SQM) methods, which correctly describe all types of noncovalent interactions and are fast enough to treat systems of thousands of atoms. Two most accurate SQM methods, PM6-D3H4X and SCC-DFTB3-D3H4X, are coupled with the conductor-like screening model (COSMO) implicit solvation model in so-called "SQM/COSMO" SFs and have shown unique recognition of native ligand poses in cognate docking in four challenging PL systems, including metalloprotein. Here, we apply the two SQM/COSMO SFs to 17 diverse PL complexes and compare their performance with four widely used classical SFs (Glide XP, AutoDock4, AutoDock Vina, and UCSF Dock). We observe superior performance of the SQM/COSMO SFs and identify challenging systems. This method, due to its generality, comparability across the chemical space, and lack of need for any system-specific parameters, gives promise of becoming, after comprehensive large-scale testing in the near future, a useful computational tool in structure-based drug design and serving as a reference method for the development of other SFs.
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Affiliation(s)
- Haresh Ajani
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Department
of Physical Chemistry, Palacký University, tř. 17. listopadu 1192/12, 77146 Olomouc, Czech Republic
| | - Adam Pecina
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Saltuk M. Eyrilmez
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Department
of Physical Chemistry, Palacký University, tř. 17. listopadu 1192/12, 77146 Olomouc, Czech Republic
| | - Jindřich Fanfrlík
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Susanta Haldar
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Jan Řezáč
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Pavel Hobza
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Department
of Physical Chemistry, Regional Centre of Advanced Technologies and
Materials, Palacký University, 77146 Olomouc, Czech Republic
| | - Martin Lepšík
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
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39
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Sulimov AV, Zheltkov DA, Oferkin IV, Kutov DC, Katkova EV, Tyrtyshnikov EE, Sulimov VB. Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms. Comput Struct Biotechnol J 2017; 15:275-285. [PMID: 28377797 PMCID: PMC5367798 DOI: 10.1016/j.csbj.2017.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/28/2017] [Indexed: 11/28/2022] Open
Abstract
We present the novel docking algorithm based on the Tensor Train decomposition and the TT-Cross global optimization. The algorithm is applied to the docking problem with flexible ligand and moveable protein atoms. The energy of the protein-ligand complex is calculated in the frame of the MMFF94 force field in vacuum. The grid of precalculated energy potentials of probe ligand atoms in the field of the target protein atoms is not used. The energy of the protein-ligand complex for any given configuration is computed directly with the MMFF94 force field without any fitting parameters. The conformation space of the system coordinates is formed by translations and rotations of the ligand as a whole, by the ligand torsions and also by Cartesian coordinates of the selected target protein atoms. Mobility of protein and ligand atoms is taken into account in the docking process simultaneously and equally. The algorithm is realized in the novel parallel docking SOL-P program and results of its performance for a set of 30 protein-ligand complexes are presented. Dependence of the docking positioning accuracy is investigated as a function of parameters of the docking algorithm and the number of protein moveable atoms. It is shown that mobility of the protein atoms improves docking positioning accuracy. The SOL-P program is able to perform docking of a flexible ligand into the active site of the target protein with several dozens of protein moveable atoms: the native crystallized ligand pose is correctly found as the global energy minimum in the search space with 157 dimensions using 4700 CPU ∗ h at the Lomonosov supercomputer.
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Affiliation(s)
- Alexey V Sulimov
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia; Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg. 4, Moscow 119992, Russia
| | - Dmitry A Zheltkov
- Faculty of Computational Mathematics and Cybernetics of Lomonosov Moscow State University, Leninskie Gory 1, Bldg. 52, Moscow 119992, Russia
| | - Igor V Oferkin
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia
| | - Danil C Kutov
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia; Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg. 4, Moscow 119992, Russia
| | - Ekaterina V Katkova
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia; Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg. 4, Moscow 119992, Russia
| | - Eugene E Tyrtyshnikov
- Faculty of Computational Mathematics and Cybernetics of Lomonosov Moscow State University, Leninskie Gory 1, Bldg. 52, Moscow 119992, Russia; Institute of Numerical Mathematics of Russian Academy of Sciences, Gubkin Street 8, Moscow, 119333, Russia
| | - Vladimir B Sulimov
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia; Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg. 4, Moscow 119992, Russia
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40
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Bani-Yaseen AD. Computational molecular perspectives on the interaction of propranolol with β-cyclodextrin in solution: Towards the drug-receptor mechanism of interaction. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.12.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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41
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Pecina A, Haldar S, Fanfrlík J, Meier R, Řezáč J, Lepšík M, Hobza P. SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein–Ligand Poses. J Chem Inf Model 2017; 57:127-132. [DOI: 10.1021/acs.jcim.6b00513] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Adam Pecina
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Susanta Haldar
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - René Meier
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Jan Řezáč
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Martin Lepšík
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Hobza
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Palacký University, 77146 Olomouc, Czech Republic
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42
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Sulimov AV, Kutov DC, Katkova EV, Sulimov VB. Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7. Adv Bioinformatics 2017; 2017:7167691. [PMID: 28191015 PMCID: PMC5278191 DOI: 10.1155/2017/7167691] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/19/2016] [Accepted: 12/22/2016] [Indexed: 12/11/2022] Open
Abstract
Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.
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Affiliation(s)
- A. V. Sulimov
- Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia
- Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia
| | - D. C. Kutov
- Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia
- Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia
| | - E. V. Katkova
- Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia
- Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia
| | - V. B. Sulimov
- Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia
- Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia
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43
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Hylsová M, Carbain B, Fanfrlík J, Musilová L, Haldar S, Köprülüoğlu C, Ajani H, Brahmkshatriya PS, Jorda R, Kryštof V, Hobza P, Echalier A, Paruch K, Lepšík M. Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines. Eur J Med Chem 2016; 126:1118-1128. [PMID: 28039837 DOI: 10.1016/j.ejmech.2016.12.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 12/17/2022]
Abstract
We present comprehensive testing of solvent representation in quantum mechanics (QM)-based scoring of protein-ligand affinities. To this aim, we prepared 21 new inhibitors of cyclin-dependent kinase 2 (CDK2) with the pyrazolo[1,5-a]pyrimidine core, whose activities spanned three orders of magnitude. The crystal structure of a potent inhibitor bound to the active CDK2/cyclin A complex revealed that the biphenyl substituent at position 5 of the pyrazolo[1,5-a]pyrimidine scaffold was located in a previously unexplored pocket and that six water molecules resided in the active site. Using molecular dynamics, protein-ligand interactions and active-site water H-bond networks as well as thermodynamics were probed. Thereafter, all the inhibitors were scored by the QM approach utilizing the COSMO implicit solvent model. Such a standard treatment failed to produce a correlation with the experiment (R2 = 0.49). However, the addition of the active-site waters resulted in significant improvement (R2 = 0.68). The activities of the compounds could thus be interpreted by taking into account their specific noncovalent interactions with CDK2 and the active-site waters. In summary, using a combination of several experimental and theoretical approaches we demonstrate that the inclusion of explicit solvent effects enhance QM/COSMO scoring to produce a reliable structure-activity relationship with physical insights. More generally, this approach is envisioned to contribute to increased accuracy of the computational design of novel inhibitors.
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Affiliation(s)
- Michaela Hylsová
- Department of Chemistry, CZ Openscreen, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Benoit Carbain
- Department of Chemistry, CZ Openscreen, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Lenka Musilová
- Department of Chemistry, CZ Openscreen, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Susanta Haldar
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic
| | - Haresh Ajani
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic
| | - Pathik S Brahmkshatriya
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Radek Jorda
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Institute of Experimental Botany, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Institute of Experimental Botany, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic
| | - Aude Echalier
- Centre de Biochimie Structurale, CNRS UMR 5048 - UM - INSERM U 1054, 29 rue de Navacelles, 34090 Montpellier, France
| | - Kamil Paruch
- Department of Chemistry, CZ Openscreen, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic.
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.
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Marianski M, Supady A, Ingram T, Schneider M, Baldauf C. Assessing the Accuracy of Across-the-Scale Methods for Predicting Carbohydrate Conformational Energies for the Examples of Glucose and α-Maltose. J Chem Theory Comput 2016; 12:6157-6168. [DOI: 10.1021/acs.jctc.6b00876] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mateusz Marianski
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Adriana Supady
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Teresa Ingram
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Markus Schneider
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
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Stewart JJP. A method for predicting individual residue contributions to enzyme specificity and binding-site energies, and its application to MTH1. J Mol Model 2016; 22:259. [PMID: 27714533 PMCID: PMC5054044 DOI: 10.1007/s00894-016-3119-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/08/2016] [Indexed: 12/20/2022]
Abstract
A new method for predicting the energy contributions to substrate binding and to specificity has been developed. Conventional global optimization methods do not permit the subtle effects responsible for these properties to be modeled with sufficient precision to allow confidence to be placed in the results, but by making simple alterations to the model, the precisions of the various energies involved can be improved from about ±2 kcal mol−1 to ±0.1 kcal mol−1. This technique was applied to the oxidized nucleotide pyrophosphohydrolase enzyme MTH1. MTH1 is unusual in that the binding and reaction sites are well separated—an advantage from a computational chemistry perspective, as it allows the energetics involved in docking to be modeled without the need to consider any issues relating to reaction mechanisms. In this study, two types of energy terms were investigated: the noncovalent interactions between the binding site and the substrate, and those responsible for discriminating between the oxidized nucleotide 8-oxo-dGTP and the normal dGTP. Both of these were investigated using the semiempirical method PM7 in the program MOPAC. The contributions of the individual residues to both the binding energy and the specificity of MTH1 were calculated by simulating the effect of mutations. Where comparisons were possible, all calculated results were in agreement with experimental observations. This technique provides fresh insight into the binding mechanism that enzymes use for discriminating between possible substrates.
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Affiliation(s)
- James J P Stewart
- Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, CO, 80921, USA.
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Wang Z, Sun H, Yao X, Li D, Xu L, Li Y, Tian S, Hou T. Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power. Phys Chem Chem Phys 2016; 18:12964-75. [PMID: 27108770 DOI: 10.1039/c6cp01555g] [Citation(s) in RCA: 549] [Impact Index Per Article: 68.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
As one of the most popular computational approaches in modern structure-based drug design, molecular docking can be used not only to identify the correct conformation of a ligand within the target binding pocket but also to estimate the strength of the interaction between a target and a ligand. Nowadays, as a variety of docking programs are available for the scientific community, a comprehensive understanding of the advantages and limitations of each docking program is fundamentally important to conduct more reasonable docking studies and docking-based virtual screening. In the present study, based on an extensive dataset of 2002 protein-ligand complexes from the PDBbind database (version 2014), the performance of ten docking programs, including five commercial programs (LigandFit, Glide, GOLD, MOE Dock, and Surflex-Dock) and five academic programs (AutoDock, AutoDock Vina, LeDock, rDock, and UCSF DOCK), was systematically evaluated by examining the accuracies of binding pose prediction (sampling power) and binding affinity estimation (scoring power). Our results showed that GOLD and LeDock had the best sampling power (GOLD: 59.8% accuracy for the top scored poses; LeDock: 80.8% accuracy for the best poses) and AutoDock Vina had the best scoring power (rp/rs of 0.564/0.580 and 0.569/0.584 for the top scored poses and best poses), suggesting that the commercial programs did not show the expected better performance than the academic ones. Overall, the ligand binding poses could be identified in most cases by the evaluated docking programs but the ranks of the binding affinities for the entire dataset could not be well predicted by most docking programs. However, for some types of protein families, relatively high linear correlations between docking scores and experimental binding affinities could be achieved. To our knowledge, this study has been the most extensive evaluation of popular molecular docking programs in the last five years. It is expected that our work can offer useful information for the successful application of these docking tools to different requirements and targets.
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Affiliation(s)
- Zhe Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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Affiliation(s)
- Michal H. Kolář
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Institute
of Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations
(IAS-5), Forschungszentrum Jülich GmbH, 52428 Jülich, Federal Republic of Germany
| | - Pavel Hobza
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Department
of Physical Chemistry, Regional Centre of Advanced Technologies and
Materials, Palacky University, 771 46 Olomouc, Czech Republic
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