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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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Sulimov A, Ilin I, Kutov D, Shikhaliev K, Shcherbakov D, Pyankov O, Stolpovskaya N, Medvedeva S, Sulimov V. New Chemicals Suppressing SARS-CoV-2 Replication in Cell Culture. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27175732. [PMID: 36080498 PMCID: PMC9457583 DOI: 10.3390/molecules27175732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 01/18/2023]
Abstract
Candidates to being inhibitors of the main protease (Mpro) of SARS-CoV-2 were selected from the database of Voronezh State University using molecular modeling. The database contained approximately 19,000 compounds represented by more than 41,000 ligand conformers. These ligands were docked into Mpro using the SOL docking program. For one thousand ligands with best values of the SOL score, the protein–ligand binding enthalpy was calculated by the PM7 quantum-chemical method with the COSMO solvent model. Using the SOL score and the calculated protein–ligand binding enthalpies, eighteen compounds were selected for the experiments. Several of these inhibitors suppressed the replication of the coronavirus in cell culture, and we used the best three among them in the search for chemical analogs. Selection among analogs using the same procedure followed by experiments led to identification of seven inhibitors of the SARS-CoV-2 replication in cell culture with EC50 values at the micromolar level. The identified inhibitors belong to three chemical classes. The three inhibitors, 4,4-dimethyldithioquinoline derivatives, inhibit SARS-CoV-2 replication in Vero E6 cell culture just as effectively as the best published non-covalent inhibitors, and show low cytotoxicity. These results open up a possibility to develop antiviral drugs against the SARS-CoV-2 coronavirus.
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Affiliation(s)
- Alexey Sulimov
- Dimonta Ltd., 15 Nagornaya Str., Bldg 8, 117186 Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Leninskie Gory, 1, Building 4, 119234 Moscow, Russia
| | - Ivan Ilin
- Dimonta Ltd., 15 Nagornaya Str., Bldg 8, 117186 Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Leninskie Gory, 1, Building 4, 119234 Moscow, Russia
| | - Danil Kutov
- Dimonta Ltd., 15 Nagornaya Str., Bldg 8, 117186 Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Leninskie Gory, 1, Building 4, 119234 Moscow, Russia
- Correspondence: (D.K.); (V.S.)
| | - Khidmet Shikhaliev
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya Sq., 394018 Voronezh, Russia
| | - Dmitriy Shcherbakov
- State Research Centre of Virology and Biotechnology “Vector”, 630559 Koltsovo, Russia
| | - Oleg Pyankov
- State Research Centre of Virology and Biotechnology “Vector”, 630559 Koltsovo, Russia
| | - Nadezhda Stolpovskaya
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya Sq., 394018 Voronezh, Russia
| | - Svetlana Medvedeva
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya Sq., 394018 Voronezh, Russia
| | - Vladimir Sulimov
- Dimonta Ltd., 15 Nagornaya Str., Bldg 8, 117186 Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Leninskie Gory, 1, Building 4, 119234 Moscow, Russia
- Correspondence: (D.K.); (V.S.)
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Sulimov A, Kutov D, Ilin I, Sulimov V. Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:274. [PMID: 35055291 PMCID: PMC8781293 DOI: 10.3390/nano12020274] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 01/14/2023]
Abstract
The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the energy of the protein-ligand complex calculated by the quantum-chemical method. In quantum quasi-docking, firstly, we look for a wide spectrum of low-energy minima, calculated using the MMFF94 force field, and secondly, we recalculate the energies of all these minima using the quantum-chemical method, and among these recalculated energies we determine the lowest energy and the corresponding ligand position. Both PM6-D3H4X and PM7 are novel methods that describe well-dispersion interactions, hydrogen and halogen bonds. The PM6-D3H4X and PM7 methods are used with the COSMO implicit solvent model as it is implemented in the MOPAC program. The comparison is made for 25 high quality protein-ligand complexes. Firstly, the docking positioning accuracies have been compared, and we demonstrated that PM7+COSMO provides better positioning accuracy than PM6-D3H4X. Secondly, we found that PM7+COSMO demonstrates a much higher correlation between the calculated and measured protein-ligand binding enthalpies than PM6-D3H4X. For future quantum docking PM7+COSMO is preferable, but the COSMO model must be improved.
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Affiliation(s)
- Alexey Sulimov
- Dimonta, Ltd., 117186 Moscow, Russia; (A.S.); (I.I.)
- Research Computer Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Danil Kutov
- Dimonta, Ltd., 117186 Moscow, Russia; (A.S.); (I.I.)
- Research Computer Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Ivan Ilin
- Dimonta, Ltd., 117186 Moscow, Russia; (A.S.); (I.I.)
- Research Computer Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Vladimir Sulimov
- Dimonta, Ltd., 117186 Moscow, Russia; (A.S.); (I.I.)
- Research Computer Center, Lomonosov Moscow State University, 119992 Moscow, Russia
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Sulimov AV, Shikhaliev KS, Pyankov OV, Shcherbakov DN, Chirkova VY, Ilin IS, Kutov DC, Tashchilova AS, Krysin MY, Krylskiy DV, Stolpovskaya NV, Volosnikova EA, Belenkaya SV, Sulimov VB. [Development of antiviral drugs based on inhibitors of the SARS-COV-2 main protease]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2021; 67:259-267. [PMID: 34142533 DOI: 10.18097/pbmc20216703259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Docking and quantum-chemical methods have been used for screening of drug-like compounds from the own database of the Voronezh State University to find inhibitors the SARS-CoV-2 main protease, an important enzyme of the coronavirus responsible for the COVID-19 pandemic. Using the SOL program more than 42000 3D molecular structures were docked into the active site of the main protease, and more than 1000 ligands with most negative values of the SOL score were selected for further processing. For all these top ligands, the protein-ligand binding enthalpy has been calculated using the PM7 semiempirical quantum-chemical method with the COSMO implicit solvent model. 20 ligands with the most negative SOL scores and the most negative binding enthalpies have been selected for further experimental testing. The latter has been made by measurements of the inhibitory activity against the main protease and suppression of SARS-CoV-2 replication in a cell culture. The inhibitory activity \of the compounds was determined using a synthetic fluorescently labeled peptide substrate including the proteolysis site of the main protease. The antiviral activity was tested against SARS-CoV-2 virus in the Vero cell culture. Eight compounds showed inhibitory activity against the main protease of SARS-CoV-2 in the submicromolar and micromolar ranges of the IC50 values. Three compounds suppressed coronavirus replication in the cell culture at the micromolar range of EC50 values and had low cytotoxicity. The found chemically diverse inhibitors can be used for optimization in order to obtain a leader compound, the basis of new direct-acting antiviral drugs against the SARS-CoV-2 coronavirus.
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Affiliation(s)
- A V Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russia; Dimonta Ltd., Moscow, Russia
| | | | - O V Pyankov
- State Research Centre of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - D N Shcherbakov
- State Research Centre of Virology and Biotechnology "Vector", Koltsovo, Russia; Altai State University, Barnaul, Russia
| | | | - I S Ilin
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russia; Dimonta Ltd., Moscow, Russia
| | - D C Kutov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russia; Dimonta Ltd., Moscow, Russia
| | - A S Tashchilova
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russia; Dimonta Ltd., Moscow, Russia
| | | | | | | | - E A Volosnikova
- State Research Centre of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - S V Belenkaya
- State Research Centre of Virology and Biotechnology "Vector", Koltsovo, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - V B Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russia; Dimonta Ltd., Moscow, Russia
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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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Abstract
Molecular Docking is used to positioning the computer-generated 3D structure of small
ligands into a receptor structure in a variety of orientations, conformations and positions. This
method is useful in drug discovery and medicinal chemistry providing insights into molecular
recognition. Docking has become an integral part of Computer-Aided Drug Design and Discovery
(CADDD). Traditional docking methods suffer from limitations of semi-flexible or static treatment
of targets and ligand. Over the last decade, advances in the field of computational, proteomics and
genomics have also led to the development of different docking methods which incorporate
protein-ligand flexibility and their different binding conformations. Receptor flexibility accounts
for more accurate binding pose predictions and a more rational depiction of protein binding
interactions with the ligand. Protein flexibility has been included by generating protein ensembles
or by dynamic docking methods. Dynamic docking considers solvation, entropic effects and also
fully explores the drug-receptor binding and recognition from both energetic and mechanistic point
of view. Though in the fast-paced drug discovery program, dynamic docking is computationally
expensive but is being progressively used for screening of large compound libraries to identify the
potential drugs. In this review, a quick introduction is presented to the available docking methods
and their application and limitations in drug discovery.
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Affiliation(s)
- Ritu Jakhar
- Center for Bioinformatics, Maharshi Dayanand University, Rohtak, India
| | - Mehak Dangi
- Center for Bioinformatics, Maharshi Dayanand University, Rohtak, India
| | - Alka Khichi
- Center for Bioinformatics, Maharshi Dayanand University, Rohtak, India
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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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Sulimov V, Ilin I, Kutov D, Sulimov A. Development of docking programs for Lomonosov supercomputer. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2019. [DOI: 10.18596/jotcsa.634130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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