Computational studies on the interaction of Omicron subvariants (BA.1, BA.2, and BA.3) with ACE2 and polyphenols
© 2023 John Wiley & Sons Ltd..
INTRODUCTION: The SARS-CoV-2 Omicron variant BA.2 is spreading widely across the globe. The World Health Organization (WHO) designated BA.2 as a variant of concern due to its high transmission rate and pathogenicity. To elucidate the structural changes caused by mutations, we conducted a comparative analysis of BA.2 with variants BA.1 and BA.3.
OBJECTIVE: In the present study, we aimed to investigate the interactions of the spike glycoprotein receptor-binding domain (SGp RBD) of Omicron variants BA.1, BA.2, and BA.3 with the human receptor hACE2. Further, a library of 233 polyphenols was screened by molecular docking with the SGp RBDs of Omicron variants BA.1, BA.2, and BA.3.
METHODS: Protein-protein and protein-ligand molecular docking simulations were performed with AutoDock Vina and the ClusPro 2.0 server, respectively. The protein-ligand interactions were evaluated by BIOVIA Discovery Studio and ChimeraX 1.4. The molecular dynamics simulations for 100 ns were performed using GROMACS 2021.
RESULTS: Compared to other variants of concern, the structural changes in Omicron caused by mutations at key positions improved its ability to cause infection. Despite multiple mutations, many important polyphenols bind effectively at the RBDs of Omicron variants, with the required pharmacokinetic and ADME features and obeying the Lipinski rule.
CONCLUSION: Even though Omicron variants have multiple mutations and their transmission rate is relatively high, the computed binding affinities of lead polyphenols like epigallocatechin-3-O-gallate (EGCG) and luteolin-7-O-glucuronide (L7G) indicate that traditional medicines and proper immunity booster diets may be useful in the long-term fight against SARS-CoV-2.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2023 |
|---|---|
| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:34 |
|---|---|
| Enthalten in: |
Phytochemical analysis : PCA - 34(2023), 7 vom: 27. Okt., Seite 800-815 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Vardhan, Seshu [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
ACE2 protein, human |
|---|
| Anmerkungen: |
Date Completed 06.11.2023 Date Revised 06.11.2023 published: Print-Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1002/pca.3204 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM351175423 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM351175423 | ||
| 003 | DE-627 | ||
| 005 | 20231226050722.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231226s2023 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1002/pca.3204 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1170.xml |
| 035 | |a (DE-627)NLM351175423 | ||
| 035 | |a (NLM)36606391 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Vardhan, Seshu |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Computational studies on the interaction of Omicron subvariants (BA.1, BA.2, and BA.3) with ACE2 and polyphenols |
| 264 | 1 | |c 2023 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 06.11.2023 | ||
| 500 | |a Date Revised 06.11.2023 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2023 John Wiley & Sons Ltd. | ||
| 520 | |a INTRODUCTION: The SARS-CoV-2 Omicron variant BA.2 is spreading widely across the globe. The World Health Organization (WHO) designated BA.2 as a variant of concern due to its high transmission rate and pathogenicity. To elucidate the structural changes caused by mutations, we conducted a comparative analysis of BA.2 with variants BA.1 and BA.3 | ||
| 520 | |a OBJECTIVE: In the present study, we aimed to investigate the interactions of the spike glycoprotein receptor-binding domain (SGp RBD) of Omicron variants BA.1, BA.2, and BA.3 with the human receptor hACE2. Further, a library of 233 polyphenols was screened by molecular docking with the SGp RBDs of Omicron variants BA.1, BA.2, and BA.3 | ||
| 520 | |a METHODS: Protein-protein and protein-ligand molecular docking simulations were performed with AutoDock Vina and the ClusPro 2.0 server, respectively. The protein-ligand interactions were evaluated by BIOVIA Discovery Studio and ChimeraX 1.4. The molecular dynamics simulations for 100 ns were performed using GROMACS 2021 | ||
| 520 | |a RESULTS: Compared to other variants of concern, the structural changes in Omicron caused by mutations at key positions improved its ability to cause infection. Despite multiple mutations, many important polyphenols bind effectively at the RBDs of Omicron variants, with the required pharmacokinetic and ADME features and obeying the Lipinski rule | ||
| 520 | |a CONCLUSION: Even though Omicron variants have multiple mutations and their transmission rate is relatively high, the computed binding affinities of lead polyphenols like epigallocatechin-3-O-gallate (EGCG) and luteolin-7-O-glucuronide (L7G) indicate that traditional medicines and proper immunity booster diets may be useful in the long-term fight against SARS-CoV-2 | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Omicron | |
| 650 | 4 | |a dynamics simulations | |
| 650 | 4 | |a molecular docking | |
| 650 | 4 | |a polyphenols | |
| 650 | 7 | |a Angiotensin-Converting Enzyme 2 |2 NLM | |
| 650 | 7 | |a EC 3.4.17.23 |2 NLM | |
| 650 | 7 | |a Ligands |2 NLM | |
| 650 | 7 | |a ACE2 protein, human |2 NLM | |
| 650 | 7 | |a EC 3.4.17.23 |2 NLM | |
| 650 | 7 | |a Polyphenols |2 NLM | |
| 700 | 1 | |a Sahoo, Suban K |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Phytochemical analysis : PCA |d 1997 |g 34(2023), 7 vom: 27. Okt., Seite 800-815 |w (DE-627)NLM091553571 |x 1099-1565 |7 nnns |
| 773 | 1 | 8 | |g volume:34 |g year:2023 |g number:7 |g day:27 |g month:10 |g pages:800-815 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1002/pca.3204 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 34 |j 2023 |e 7 |b 27 |c 10 |h 800-815 | ||