Conserved in 186 Countries The RBD Fraction of SARS CoV-2 S-Protein With in-Silico T500S Mutation Strongly Blocks ACE2 Rejecting The Viral Spike; A Molecular-Docking Analysis.
Abstract SARS CoV-2 developed a global pandemic with millions of infections/deaths. The role of blocker/inhibitor of ACE2 and viral-spikes Receptor-Binding-Domain RBD-blockers has been reported. In the current study, conserved RBD portions or cuts from 186 countries were screened and compared with WUHAN-Hu-1 wild-type by CLUSTAL X2 and Structural alignment analyses using Pymol. The RBD of ACE2 bound nCOV2 crystal-structure (2.68 Å) 6VYB1 was analyzed by PyMol and compared with RBD-Cut docking by Haddock and Patch Dock. Extensive structural study/trial to introduce point/double/triple mutations in the following locations (Y489S/Y453S/T500S/T500Y)/ (Y489S,Y453S/Y489S,T500S/Y489S,T500Y/Y453S,T500S/Y453S,T500Y)/ (Y489S,Y453S,T500S/ Y489S,Y453S,T500Y) of CUT4 were tested with Swiss Model Expacy. Blind docking of mutated CUTs to ACE2 (6VW1) by Haddock and Hawkdock was performed and complete rejection of nCOV2 was optimized through its re-docking trial and using pre-docked ACE2. Further, competitive-docking was performed and its binding analyses were done by PRODIGY. Present results suggest that compared to the wild-spike, CUT4 showed extra LYS31-PHE490 and GLN42-GLN498 bonding and lack of TYR41-THR500 interaction (in wild H-bond: 2.639Å) with ACE2 RBD, which can potentially but compete with the wild-spike. Whereas mutated CUT4 strongly binds with the ACE2 RBD, promoting TYR41-T500S (H-bond: 2.0Å and 1.8Å)/T500Y (H-bond: 2.6Å) interaction and complete inhibition of ACE2 RBD-nCOV2 S-protein binding. Mutant combinations T500S, Y489S,T500S and Y489S,Y453S,T500Y were found to be the most potent blocker of ACE2. It is hypothesized that Cut4 mutant is kinetically more favoured for ACE2-RBD binding and even reject whole glycosylated nCoV2 in all format of experiments; pre-dock, post-dock, and competitive-docking. Studies are necessary in this regard..
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Preprint| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
ResearchSquare.com - (2021) vom: 17. März Zur Gesamtaufnahme - year:2021 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
Banerjee, Amrita [VerfasserIn] |
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| Links: |
Volltext [kostenfrei] |
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| doi: |
10.21203/rs.3.rs-258960/v1 |
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XRA033723796 |
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| 245 | 1 | 0 | |a Conserved in 186 Countries The RBD Fraction of SARS CoV-2 S-Protein With in-Silico T500S Mutation Strongly Blocks ACE2 Rejecting The Viral Spike; A Molecular-Docking Analysis. |
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| 520 | |a Abstract SARS CoV-2 developed a global pandemic with millions of infections/deaths. The role of blocker/inhibitor of ACE2 and viral-spikes Receptor-Binding-Domain RBD-blockers has been reported. In the current study, conserved RBD portions or cuts from 186 countries were screened and compared with WUHAN-Hu-1 wild-type by CLUSTAL X2 and Structural alignment analyses using Pymol. The RBD of ACE2 bound nCOV2 crystal-structure (2.68 Å) 6VYB1 was analyzed by PyMol and compared with RBD-Cut docking by Haddock and Patch Dock. Extensive structural study/trial to introduce point/double/triple mutations in the following locations (Y489S/Y453S/T500S/T500Y)/ (Y489S,Y453S/Y489S,T500S/Y489S,T500Y/Y453S,T500S/Y453S,T500Y)/ (Y489S,Y453S,T500S/ Y489S,Y453S,T500Y) of CUT4 were tested with Swiss Model Expacy. Blind docking of mutated CUTs to ACE2 (6VW1) by Haddock and Hawkdock was performed and complete rejection of nCOV2 was optimized through its re-docking trial and using pre-docked ACE2. Further, competitive-docking was performed and its binding analyses were done by PRODIGY. Present results suggest that compared to the wild-spike, CUT4 showed extra LYS31-PHE490 and GLN42-GLN498 bonding and lack of TYR41-THR500 interaction (in wild H-bond: 2.639Å) with ACE2 RBD, which can potentially but compete with the wild-spike. Whereas mutated CUT4 strongly binds with the ACE2 RBD, promoting TYR41-T500S (H-bond: 2.0Å and 1.8Å)/T500Y (H-bond: 2.6Å) interaction and complete inhibition of ACE2 RBD-nCOV2 S-protein binding. Mutant combinations T500S, Y489S,T500S and Y489S,Y453S,T500Y were found to be the most potent blocker of ACE2. It is hypothesized that Cut4 mutant is kinetically more favoured for ACE2-RBD binding and even reject whole glycosylated nCoV2 in all format of experiments; pre-dock, post-dock, and competitive-docking. Studies are necessary in this regard. | ||
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