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Gupta Y, Savytskyi OV, Coban M, Venugopal A, Pleqi V, Weber CA, Chitale R, Durvasula R, Hopkins C, Kempaiah P, Caulfield TR. Protein structure-based in-silico approaches to drug discovery: Guide to COVID-19 therapeutics. Mol Aspects Med 2023; 91:101151. [PMID: 36371228 PMCID: PMC9613808 DOI: 10.1016/j.mam.2022.101151] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
With more than 5 million fatalities and close to 300 million reported cases, COVID-19 is the first documented pandemic due to a coronavirus that continues to be a major health challenge. Despite being rapid, uncontrollable, and highly infectious in its spread, it also created incentives for technology development and redefined public health needs and research agendas to fast-track innovations to be translated. Breakthroughs in computational biology peaked during the pandemic with renewed attention to making all cutting-edge technology deliver agents to combat the disease. The demand to develop effective treatments yielded surprising collaborations from previously segregated fields of science and technology. The long-standing pharmaceutical industry's aversion to repurposing existing drugs due to a lack of exponential financial gain was overrun by the health crisis and pressures created by front-line researchers and providers. Effective vaccine development even at an unprecedented pace took more than a year to develop and commence trials. Now the emergence of variants and waning protections during the booster shots is resulting in breakthrough infections that continue to strain health care systems. As of now, every protein of SARS-CoV-2 has been structurally characterized and related host pathways have been extensively mapped out. The research community has addressed the druggability of a multitude of possible targets. This has been made possible due to existing technology for virtual computer-assisted drug development as well as new tools and technologies such as artificial intelligence to deliver new leads. Here in this article, we are discussing advances in the drug discovery field related to target-based drug discovery and exploring the implications of known target-specific agents on COVID-19 therapeutic management. The current scenario calls for more personalized medicine efforts and stratifying patient populations early on for their need for different combinations of prognosis-specific therapeutics. We intend to highlight target hotspots and their potential agents, with the ultimate goal of using rational design of new therapeutics to not only end this pandemic but also uncover a generalizable platform for use in future pandemics.
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Affiliation(s)
- Yash Gupta
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Oleksandr V Savytskyi
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; In Vivo Biosystems, Eugene, OR, USA
| | - Matt Coban
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Vasili Pleqi
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Caleb A Weber
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Rohit Chitale
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA; The Council on Strategic Risks, 1025 Connecticut Ave NW, Washington, DC, USA
| | - Ravi Durvasula
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | | | - Prakasha Kempaiah
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of QHS Computational Biology, Mayo Clinic, Jacksonville, FL, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA; Department of Neurosurgery, Mayo Clinic, Jacksonville, FL, USA.
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Volynets GP, Pletnova LV, Sapelkin VM, Savytskyi OV, Yarmoluk SM. A computational analysis of the binding free energies of apoptosis signal-regulating kinase 1 inhibitors from different chemotypes. Molecular Simulation 2021. [DOI: 10.1080/08927022.2021.1922686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Galyna P. Volynets
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv, Ukraine
- Scientific Services Company Otava Ltd., Kyiv, Ukraine
| | - Larysa V. Pletnova
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv, Ukraine
| | - Vladislav M. Sapelkin
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv, Ukraine
| | - Oleksandr V. Savytskyi
- Department of Protein Engineering and Bioinformatics, Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv, Ukraine
| | - Sergiy M. Yarmoluk
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv, Ukraine
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Kravchuk VO, Savytskyi OV, Odynets KO, Mykuliak VV, Kornelyuk AI. Computational modeling and molecular dynamics simulations of mammalian cytoplasmic tyrosyl-tRNA synthetase and its complexes with substrates. J Biomol Struct Dyn 2016; 35:2772-2788. [PMID: 27615678 DOI: 10.1080/07391102.2016.1235512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Cytoplasmic tyrosyl-tRNA synthetase (TyrRS) is one of the key enzymes of protein biosynthesis. TyrRSs of pathogenic organisms have gained attention as potential targets for drug development. Identifying structural differences between various TyrRSs will facilitate the development of specific inhibitors for the TyrRSs of pathogenic organisms. However, there is a deficiency in structural data for mammalian cytoplasmic TyrRS in complexes with substrates. In this work, we constructed spatial structure of full-length Bos taurus TyrRS (BtTyrRS) and its complexes with substrates using the set of computational modeling techniques. Special attention was paid to BtTyrRS complexes with substrates [L-tyrosine, K+ and ATP:Mg2+] and intermediate products [tyrosyl-adenylate (Tyr-AMP), K+ and PPi:Mg2+] with the different catalytic loop conformations. In order to analyze their dynamical properties, we performed 100 ns of molecular dynamics (MD) simulations. MD simulations revealed new structural data concerning the tyrosine activation reaction in mammalian TyrRS. Formation of strong interaction between Lys154 and γ-phosphate suggests the additional role of CP1 insertion as an important factor for ATP binding. The presence of a potassium-binding pocket within the active site of mammalian TyrRS compensates the absence of the second lysine in the KMSKS motif. Our data provide new details concerning a role of K+ ions at different stages of the first step of the tyrosylation reaction, including the coordination of substrates and involvement in the PPi releasing. The results of this work suggest that differences between ATP-binding sites of mammalian and bacterial TyrRSs are meaningful and could be exploited in the drug design.
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Affiliation(s)
- Vladyslav O Kravchuk
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.,b Department of Biotechnology , National Aviation University , 1, Kosmonavta Komarova Str., Kyiv , 03058 , Ukraine
| | - Oleksandr V Savytskyi
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine
| | - Konstantin O Odynets
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine
| | - Vasyl V Mykuliak
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.,c Institute of High Technologies , Taras Shevchenko National University of Kyiv , 64, Volodymyrs'ka Str., Kyiv , 01601 , Ukraine
| | - Alexander I Kornelyuk
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.,c Institute of High Technologies , Taras Shevchenko National University of Kyiv , 64, Volodymyrs'ka Str., Kyiv , 01601 , Ukraine
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Savytskyi OV, Kornelyuk AI. [COMPUTATIONAL MODELING OF MOLECULAR DYNAMICS OF G41R MUTANT FORM OF HUMAN TYROSYL-tRNA SYNTHETASE, ASSOSIATED WITH CHARCOT-MARIE-TOOTH NEUROPATHY]. Ukr Biochem J 2016; 87:142-53. [PMID: 27025069 DOI: 10.15407/ubj87.06.142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The computational structural models of human tyrosyl-tRNA synthetase and its mutant form G41R (Charcot-Marie-Tooth associated) were constructed, while their whole structural coordinates are still unknown. Grid-services of MolDynGrid Virtual Laboratory and Ukrainian National Grid-infrastructure were used for molecular dynamics (MD) simulations. The analyses of trajectories of MD simulations have shown the β-sheet formation in region Lys147 - Glu157 between H9 and H10 helices (CP1 insertion of Rossman fold) for G41R mutant.
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Savytskyi OV, Yesylevskyy SO, Kornelyuk AI. Asymmetric structure and domain binding interfaces of human tyrosyl-tRNA synthetase studied by molecular dynamics simulations. J Mol Recognit 2013; 26:113-20. [DOI: 10.1002/jmr.2259] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 11/20/2012] [Accepted: 12/10/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Oleksandr V. Savytskyi
- Institute of Molecular Biology and Genetics; National Academy of Sciences of Ukraine; Akademika Zabolotnogo Str., 150; Kyiv-03680; Ukraine
| | - Semen O. Yesylevskyy
- Institute of Physics; National Academy of Sciences of Ukraine; Prospect Nauki, 46; Kyiv-03039; Ukraine
| | - Alexander I. Kornelyuk
- Institute of Molecular Biology and Genetics; National Academy of Sciences of Ukraine; Akademika Zabolotnogo Str., 150; Kyiv-03680; Ukraine
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