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Zajaček D, Dunárová A, Bucinsky L, Štekláč M. Compromise in Docking Power of Liganded Crystal Structures of M pro SARS-CoV-2 Surpasses 90% Success Rate. J Chem Inf Model 2024; 64:1628-1643. [PMID: 38408033 DOI: 10.1021/acs.jcim.3c01552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Herein, we present the capacity of three different molecular docking programs (AutoDock, AutoDock Vina, and PLANTS) to identify and reproduce the binding modes of ligands present in 247 covalent and 169 noncovalent complex crystal structures of the severe acute respiratory syndrome coronavirus 2 main protease (Mpro). The compromise in docking power is evaluated with respect to their ability to generate poses similar to the crystal structure binding mode (heavy atoms' root-mean-square deviation < 2 Å) and their ability to recognize the native binding mode with an included compensation for the scoring function error. Noncovalently bound inhibitors are best modeled by AutoDock Vina (90.6% success rate in the active site), while the most relevant results for covalently bound inhibitors are produced by PLANTS (93.0%). AutoDock shows acceptable performance for both types of ligands, 81.1 and 76.4% for noncovalent and covalent complexes, respectively. All three programs manifest worse performance when reproducing surface-bound ligands. Comparison with other works illustrates the importance of crystal structure processing (12% of noncovalent and 26% of covalent ligands had to be manually corrected), proper sampling protocol settings, and inclusion of root-mean-square deviation (RMSD)/scoring function error compensations in crystal structure pose identification. Results are analyzed with respect to a clustering scheme of the noncovalently bound ligands and the chemical reaction type of the covalent ligand bound to the Cys145 residue. A comparison of screening power based on the docking scores of noncovalent ligands from the crystal structures with a "Directory of Useful Decoys, Enhanced" set of known decoys (6562 compounds) and ZINC15 in vivo subset (60,394 compounds) is provided. Ligand and protein input files are provided for future benchmarking purposes.
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Affiliation(s)
- Dávid Zajaček
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, SK-81237 Bratislava, Slovakia
| | - Adriána Dunárová
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, SK-81237 Bratislava, Slovakia
| | - Lukas Bucinsky
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, SK-81237 Bratislava, Slovakia
| | - Marek Štekláč
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, SK-81237 Bratislava, Slovakia
- Computing Center, Centre of Operations of the Slovak Academy of Sciences, Dúbravská cesta č. 9, SK-84535 Bratislava, Slovakia
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Štekláč M, Breza M. DFT studies of camptothecins cytotoxicity IV — active and inactive forms of irinotecan. Acta Chimica Slovaca 2023. [DOI: 10.2478/acs-2023-0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Abstract
Structures of irinotecan (CPT-11) in neutral lactone, neutral carboxyl, and anionic carboxylate forms in singlet ground states and of their complexes with Cu(II) in doublet ground states are optimized using B3LYP/6-311G* treatment. Metal ion affinities (MIA), Cu charges and Laplacians of Cu-ligand bond critical points of possible CPT active sites are evaluated. The formation of Cu(II) complexes with the anionic carboxylate ligand leads to the release of CO2 that can cause a decrease in the concentration of the active lactone form due to equilibria between all forms of the drug. MIA values and electron density transfer to Cu increase in the sequence lactone < neutral carboxyl < anionic carboxylate. Both neutral forms of irinotecan exhibit lower MIA values than those of camptothecin, unlike the anionic carboxylate form.
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Šimunková M, Biela M, Štekláč M, Hlinčík A, Klein E, Malček M. Cu(II) complexes of flavonoids in solution: Impact of the Cu(II) ion on the antioxidant and DNA-intercalating properties. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Jablonský M, Štekláč M, Majová V, Gall M, Matúška J, Pitoňák M, Bučinský L. Molecular docking and machine learning affinity prediction of compounds identified upon softwood bark extraction to the main protease of the SARS-CoV-2 virus. Biophys Chem 2022; 288:106854. [PMID: 35810518 PMCID: PMC9233873 DOI: 10.1016/j.bpc.2022.106854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/03/2022] [Accepted: 06/21/2022] [Indexed: 11/15/2022]
Abstract
Molecular docking of 234 unique compounds identified in the softwood bark (W set) is presented with a focus on their inhibition potential to the main protease of the SARS-CoV-2 virus 3CLpro (6WQF). The docking results are compared with the docking results of 866 COVID19-related compounds (S set). Furthermore, machine learning (ML) prediction of docking scores of the W set is presented using the S set trained TensorFlow, XGBoost, and SchNetPack ML approaches. Docking scores are evaluated with the Autodock 4.2.6 software. Four compounds in the W set achieve a docking score below −13 kcal/mol, with (+)-lariciresinol 9′-p-coumarate (CID 11497085) achieving the best docking score (−15 kcal/mol) within the W and S sets. In addition, 50% of W set docking scores are found below −8 kcal/mol and 25% below −10 kcal/mol. Therefore, the compounds identified in the softwood bark, show potential for antiviral activity upon extraction or further derivatization. The W set molecular docking studies are validated by means of molecular dynamics (five best compounds). The solubility (Log S, ESOL) and druglikeness of the best docking compounds in S and W sets are compared to evaluate the pharmacological potential of compounds identified in softwood bark.
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Affiliation(s)
- Michal Jablonský
- Institute of Natural and Synthetic Polymers, Department of Wood, Pulp and Paper, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, Bratislava SK-812 37, Slovakia.
| | - Marek Štekláč
- Institute of Physical Chemistry and Chemical Physics, Department of Physical Chemistry, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, Bratislava SK-812 37, Slovakia
| | - Veronika Majová
- Institute of Natural and Synthetic Polymers, Department of Wood, Pulp and Paper, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, Bratislava SK-812 37, Slovakia
| | - Marián Gall
- Institute of Information Engineering, Automation and Mathematics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, SK-81237 Bratislava, Slovak Republic; Computing Center, Centre of Operations of the Slovak Academy of Sciences, Dúbravská cesta c. 9, SK-84535 Bratislava, Slovak Republic
| | - Ján Matúška
- Institute of Physical Chemistry and Chemical Physics, Department of Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, Bratislava SK-812 37, Slovakia
| | - Michal Pitoňák
- Computing Center, Centre of Operations of the Slovak Academy of Sciences, Dúbravská cesta c. 9, SK-84535 Bratislava, Slovak Republic; Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, SK-84215 Bratislava, Slovak Republic
| | - Lukáš Bučinský
- Institute of Physical Chemistry and Chemical Physics, Department of Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, Bratislava SK-812 37, Slovakia.
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Bucinsky L, Bortňák D, Gall M, Matúška J, Milata V, Pitoňák M, Štekláč M, Végh D, Zajaček D. Machine learning prediction of 3CLpro SARS-CoV-2 docking scores. Comput Biol Chem 2022; 98:107656. [PMID: 35288359 PMCID: PMC8881816 DOI: 10.1016/j.compbiolchem.2022.107656] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/14/2022]
Abstract
Molecular docking results of two training sets containing 866 and 8,696 compounds were used to train three different machine learning (ML) approaches. Neural network approaches according to Keras and TensorFlow libraries and the gradient boosted decision trees approach of XGBoost were used with DScribe’s Smooth Overlap of Atomic Positions molecular descriptors. In addition, neural networks using the SchNetPack library and descriptors were used. The ML performance was tested on three different sets, including compounds for future organic synthesis. The final evaluation of the ML predicted docking scores was based on the ZINC in vivo set, from which 1,200 compounds were randomly selected with respect to their size. The results obtained showed a consistent ML prediction capability of docking scores, and even though compounds with more than 60 atoms were found slightly overestimated they remain valid for a subsequent evaluation of their drug repurposing suitability.
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Štekláč M, Zajaček D, Bučinský L. 3CL pro and PL pro affinity, a docking study to fight COVID19 based on 900 compounds from PubChem and literature. Are there new drugs to be found? J Mol Struct 2021; 1245:130968. [PMID: 34219808 PMCID: PMC8238401 DOI: 10.1016/j.molstruc.2021.130968] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/16/2022]
Abstract
The spread of a novel coronavirus SARS-CoV-2 and a resulting COVID19 disease in late 2019 has transformed into a worldwide pandemic and has effectively brought the world to a halt. Proteases 3CLpro and PLpro, responsible for proteolysis of new virions, represent vital inhibition targets for the COVID19 treatment. Herein, we report an in silico docking study of more than 860 COVID19-related compounds from the PubChem database. Molecular dynamic simulations were carried out to validate the conformation stability of compound-ligand complexes with best docking scores. The MM-PBSA approach was employed to calculate binding free energies. The comparison with ca. 50 previously reported potential SARS-CoV-2's proteases inhibitors show a number of new compounds with excellent binding affinities. Anti-inflammatory drugs Montelukast, Ebastine and Solumedrol, the anti-migraine drug Vazegepant or the anti-MRSA pro-drug TAK-599, among many others, all show remarkable affinities to 3CLpro and with known side effects present candidates for immediate clinical trials. This study reports thorough docking scores summary of COVID19-related compounds found in the PubChem database and illustrates the asset of computational screening methods in search for possible drug-like candidates. Several yet-untested compounds show affinities on par with reported inhibitors and warrant further attention. Furthermore, the submitted work provides readers with ADME data, ZINC and PubChem IDs, as well as docking scores of all studied compounds for further comparisons.
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Affiliation(s)
- Marek Štekláč
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak Technical University, Bratislava SK-81237, Slovakia
| | - Dávid Zajaček
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak Technical University, Bratislava SK-81237, Slovakia
| | - Lukáš Bučinský
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak Technical University, Bratislava SK-81237, Slovakia
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Affiliation(s)
- Marek Štekláč
- Department of Physical Chemistry Faculty of Chemical and Food Technology Slovak Technical University, SK- 81237 Bratislava Slovakia
| | - Martin Breza
- Department of Physical Chemistry Faculty of Chemical and Food Technology Slovak Technical University, SK- 81237 Bratislava Slovakia
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Štekláč M, Breza M. On the relation between oxidation states and d-electron populations of the 1st row transition metal complexes I. Tetrachloro complexes. Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Šimunková M, Štekláč M, Malček M. Spectroscopic, computational and molecular docking study of Cu( ii) complexes with flavonoids: from cupric ion binding to DNA intercalation. NEW J CHEM 2021. [DOI: 10.1039/d1nj01960k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Copper(ii) complexes with flavonoids as perspective therapeutic agents with DNA as a target molecule.
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Affiliation(s)
- Miriama Šimunková
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology
- Slovak University of Technology in Bratislava, Radlinského 9, SK-812 37
- Bratislava
- Slovak Republic
| | - Marek Štekláč
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology
- Slovak University of Technology in Bratislava, Radlinského 9, SK-812 37
- Bratislava
- Slovak Republic
| | - Michal Malček
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology
- Slovak University of Technology in Bratislava, Radlinského 9, SK-812 37
- Bratislava
- Slovak Republic
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