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A density functional theory study on silver and bis-silver complexes with lighter tetrylene: are silver and bis-silver carbenes candidates for SARS-CoV-2 inhibition? Insight from molecular docking simulation

Ribavirin and remdesivir have been preclinically reported as potential drugs for the treatment of SARS-CoV-2 infection, while light silver tetrylene complexes (NHE(Ph)–AgCl and (NHE(Ph)–AgCl)(2) with E = C, Si, and Ge) have gained significant interest due to their promising applicability on the cyto...

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Autores principales: Bui, Thanh Q., Phuong Loan, Huynh Thi, Ai My, Tran Thi, Quang, Duong Tuan, Phuong Thuy, Bui Thi, Nhan, Vo Duy, Quy, Phan Tu, Van Tat, Pham, Dao, Duy Quang, Trung, Nguyen Tien, Huynh, Lam K., Ai Nhung, Nguyen Thi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society of Chemistry 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9056359/
https://www.ncbi.nlm.nih.gov/pubmed/35516033
http://dx.doi.org/10.1039/d0ra05159d
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author Bui, Thanh Q.
Phuong Loan, Huynh Thi
Ai My, Tran Thi
Quang, Duong Tuan
Phuong Thuy, Bui Thi
Nhan, Vo Duy
Quy, Phan Tu
Van Tat, Pham
Dao, Duy Quang
Trung, Nguyen Tien
Huynh, Lam K.
Ai Nhung, Nguyen Thi
author_facet Bui, Thanh Q.
Phuong Loan, Huynh Thi
Ai My, Tran Thi
Quang, Duong Tuan
Phuong Thuy, Bui Thi
Nhan, Vo Duy
Quy, Phan Tu
Van Tat, Pham
Dao, Duy Quang
Trung, Nguyen Tien
Huynh, Lam K.
Ai Nhung, Nguyen Thi
author_sort Bui, Thanh Q.
collection PubMed
description Ribavirin and remdesivir have been preclinically reported as potential drugs for the treatment of SARS-CoV-2 infection, while light silver tetrylene complexes (NHE(Ph)–AgCl and (NHE(Ph)–AgCl)(2) with E = C, Si, and Ge) have gained significant interest due to their promising applicability on the cytological scale. Firstly, the structures and bonding states of silver–tetrylene complexes (NHE–Ag) and bis-silver–tetrylene complexes (NHE–Ag-bis) were investigated using density functional theory (DFT) at the BP86 level with the def2-SVP and def2-TZVPP basis sets. Secondly, the inhibitory capabilities of the carbene complexes (NHC–Ag and NHC–Ag-bis) and the two potential drugs (ribavirin and remdesivir) on human-protein ACE2 and SARS-CoV-2 protease PDB6LU7 were evaluated using molecular docking simulation. The carbene ligand NHC bonds in a head-on configuration with AgCl and (AgCl)(2), whereas, the other NHE (E = Si and Ge) tetrylene ligands bond in a side-on mode to the metal fragments. The bond dissociation energy (BDE) of the NHE–Ag bond in the complex families follows the order of NHC–Ag > NHSi–Ag > NHGe–Ag and NHSi–Ag-bis > NHGe–Ag-bis > NHC–Ag-bis. The natural bond orbital analysis implies that the [NHE(Ph)→AgCl] and [(NHE(Ph))(2)→(AgCl)(2)] donations are derived mainly from the σ- and π-contributions of the ligands. The docking results indicate that both the ACE2 and PDB6LU7 proteins are strongly inhibited by silver–carbene NHC–Ag, bis-silver–carbene NHC–Ag-bis, ribavirin, and remdesivir with the docking score energy values varying from −17.5 to −16.5 kcal mol(−1) and −16.9 to −16.6 kcal mol(−1), respectively. The root-mean-square deviation values were recorded to be less than 2 Å in all the calculated systems. Thus, the present study suggests that silver–carbene NHC–Ag and bis-silver–carbene NHC–Ag-bis complexes are potential candidates to inhibit ACE2 and PDB6LU7, and thus potentially conducive to prevent infection caused by the SARS-CoV-2 virus.
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spelling pubmed-90563592022-05-04 A density functional theory study on silver and bis-silver complexes with lighter tetrylene: are silver and bis-silver carbenes candidates for SARS-CoV-2 inhibition? Insight from molecular docking simulation Bui, Thanh Q. Phuong Loan, Huynh Thi Ai My, Tran Thi Quang, Duong Tuan Phuong Thuy, Bui Thi Nhan, Vo Duy Quy, Phan Tu Van Tat, Pham Dao, Duy Quang Trung, Nguyen Tien Huynh, Lam K. Ai Nhung, Nguyen Thi RSC Adv Chemistry Ribavirin and remdesivir have been preclinically reported as potential drugs for the treatment of SARS-CoV-2 infection, while light silver tetrylene complexes (NHE(Ph)–AgCl and (NHE(Ph)–AgCl)(2) with E = C, Si, and Ge) have gained significant interest due to their promising applicability on the cytological scale. Firstly, the structures and bonding states of silver–tetrylene complexes (NHE–Ag) and bis-silver–tetrylene complexes (NHE–Ag-bis) were investigated using density functional theory (DFT) at the BP86 level with the def2-SVP and def2-TZVPP basis sets. Secondly, the inhibitory capabilities of the carbene complexes (NHC–Ag and NHC–Ag-bis) and the two potential drugs (ribavirin and remdesivir) on human-protein ACE2 and SARS-CoV-2 protease PDB6LU7 were evaluated using molecular docking simulation. The carbene ligand NHC bonds in a head-on configuration with AgCl and (AgCl)(2), whereas, the other NHE (E = Si and Ge) tetrylene ligands bond in a side-on mode to the metal fragments. The bond dissociation energy (BDE) of the NHE–Ag bond in the complex families follows the order of NHC–Ag > NHSi–Ag > NHGe–Ag and NHSi–Ag-bis > NHGe–Ag-bis > NHC–Ag-bis. The natural bond orbital analysis implies that the [NHE(Ph)→AgCl] and [(NHE(Ph))(2)→(AgCl)(2)] donations are derived mainly from the σ- and π-contributions of the ligands. The docking results indicate that both the ACE2 and PDB6LU7 proteins are strongly inhibited by silver–carbene NHC–Ag, bis-silver–carbene NHC–Ag-bis, ribavirin, and remdesivir with the docking score energy values varying from −17.5 to −16.5 kcal mol(−1) and −16.9 to −16.6 kcal mol(−1), respectively. The root-mean-square deviation values were recorded to be less than 2 Å in all the calculated systems. Thus, the present study suggests that silver–carbene NHC–Ag and bis-silver–carbene NHC–Ag-bis complexes are potential candidates to inhibit ACE2 and PDB6LU7, and thus potentially conducive to prevent infection caused by the SARS-CoV-2 virus. The Royal Society of Chemistry 2020-08-21 /pmc/articles/PMC9056359/ /pubmed/35516033 http://dx.doi.org/10.1039/d0ra05159d Text en This journal is © The Royal Society of Chemistry https://creativecommons.org/licenses/by-nc/3.0/
spellingShingle Chemistry
Bui, Thanh Q.
Phuong Loan, Huynh Thi
Ai My, Tran Thi
Quang, Duong Tuan
Phuong Thuy, Bui Thi
Nhan, Vo Duy
Quy, Phan Tu
Van Tat, Pham
Dao, Duy Quang
Trung, Nguyen Tien
Huynh, Lam K.
Ai Nhung, Nguyen Thi
A density functional theory study on silver and bis-silver complexes with lighter tetrylene: are silver and bis-silver carbenes candidates for SARS-CoV-2 inhibition? Insight from molecular docking simulation
title A density functional theory study on silver and bis-silver complexes with lighter tetrylene: are silver and bis-silver carbenes candidates for SARS-CoV-2 inhibition? Insight from molecular docking simulation
title_full A density functional theory study on silver and bis-silver complexes with lighter tetrylene: are silver and bis-silver carbenes candidates for SARS-CoV-2 inhibition? Insight from molecular docking simulation
title_fullStr A density functional theory study on silver and bis-silver complexes with lighter tetrylene: are silver and bis-silver carbenes candidates for SARS-CoV-2 inhibition? Insight from molecular docking simulation
title_full_unstemmed A density functional theory study on silver and bis-silver complexes with lighter tetrylene: are silver and bis-silver carbenes candidates for SARS-CoV-2 inhibition? Insight from molecular docking simulation
title_short A density functional theory study on silver and bis-silver complexes with lighter tetrylene: are silver and bis-silver carbenes candidates for SARS-CoV-2 inhibition? Insight from molecular docking simulation
title_sort density functional theory study on silver and bis-silver complexes with lighter tetrylene: are silver and bis-silver carbenes candidates for sars-cov-2 inhibition? insight from molecular docking simulation
topic Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9056359/
https://www.ncbi.nlm.nih.gov/pubmed/35516033
http://dx.doi.org/10.1039/d0ra05159d
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