Repurposing antibiotics as potent multi-drug candidates for SARS-CoV-2 delta and omicron variants : molecular docking and dynamics
There is a daunting public health emergency due to the emergence and rapid global spread of the new omicron variants of SARS-CoV-2. The variants differ in many characteristics, such as transmissibility, antigenicity and the immune system of the human hosts' shifting responses. This change in characteristics raises concern, as it leads to unknown consequences and also raises doubts about the efficacy of the currently available vaccines. As of March 2022, there are five variants of SARS-CoV-2 disseminating: the alpha, the beta, the gamma, the delta and the omicron variant. The omicron variant has more than 30 mutations on the spike protein, which is used by the virus to enter the host cell and is also used as a target for the vaccines. In this work, we studied the possible anti-COVID-19 effect of two molecules by molecular docking using Autodock Vina and molecular dynamic simulations using Gromacs 2020 software. We docked amoxicillin and clavulanate to the main protease (Mpro), the RNA-dependent RNA polymerase (RdRp) and the spike protein receptor-binding domain (SRBD) of the wild type with the two variants (delta and omicron) of SARS-CoV-2. The docking results show that the ligands bound tightly with the SRBD of the omicron variant, while the dynamic simulation revealed the ability of amoxicillin to bind to the SRBD of both variants' delta and omicron. The high number of mutations that occurred in both variants increases the affinity of amoxicillin towards them.Communicated by Ramaswamy H. Sarma.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2023 |
|---|---|
| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:41 |
|---|---|
| Enthalten in: |
Journal of biomolecular structure & dynamics - 41(2023), 20 vom: 18. Dez., Seite 10377-10387 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Serseg, Talia [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
804826J2HU |
|---|
| Anmerkungen: |
Date Completed 10.11.2023 Date Revised 13.11.2023 published: Print-Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1080/07391102.2022.2157876 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM350527334 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM350527334 | ||
| 003 | DE-627 | ||
| 005 | 20231226045213.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231226s2023 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1080/07391102.2022.2157876 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1168.xml |
| 035 | |a (DE-627)NLM350527334 | ||
| 035 | |a (NLM)36541102 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Serseg, Talia |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Repurposing antibiotics as potent multi-drug candidates for SARS-CoV-2 delta and omicron variants |b molecular docking and dynamics |
| 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 10.11.2023 | ||
| 500 | |a Date Revised 13.11.2023 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a There is a daunting public health emergency due to the emergence and rapid global spread of the new omicron variants of SARS-CoV-2. The variants differ in many characteristics, such as transmissibility, antigenicity and the immune system of the human hosts' shifting responses. This change in characteristics raises concern, as it leads to unknown consequences and also raises doubts about the efficacy of the currently available vaccines. As of March 2022, there are five variants of SARS-CoV-2 disseminating: the alpha, the beta, the gamma, the delta and the omicron variant. The omicron variant has more than 30 mutations on the spike protein, which is used by the virus to enter the host cell and is also used as a target for the vaccines. In this work, we studied the possible anti-COVID-19 effect of two molecules by molecular docking using Autodock Vina and molecular dynamic simulations using Gromacs 2020 software. We docked amoxicillin and clavulanate to the main protease (Mpro), the RNA-dependent RNA polymerase (RdRp) and the spike protein receptor-binding domain (SRBD) of the wild type with the two variants (delta and omicron) of SARS-CoV-2. The docking results show that the ligands bound tightly with the SRBD of the omicron variant, while the dynamic simulation revealed the ability of amoxicillin to bind to the SRBD of both variants' delta and omicron. The high number of mutations that occurred in both variants increases the affinity of amoxicillin towards them.Communicated by Ramaswamy H. Sarma | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Amoxicillin | |
| 650 | 4 | |a Mpro | |
| 650 | 4 | |a RdRp | |
| 650 | 4 | |a SARS-CoV-2 | |
| 650 | 4 | |a SRBD | |
| 650 | 4 | |a clavulanate | |
| 650 | 4 | |a docking | |
| 650 | 4 | |a dynamics | |
| 650 | 7 | |a Anti-Bacterial Agents |2 NLM | |
| 650 | 7 | |a Spike Glycoprotein, Coronavirus |2 NLM | |
| 650 | 7 | |a Amoxicillin |2 NLM | |
| 650 | 7 | |a 804826J2HU |2 NLM | |
| 650 | 7 | |a Vaccines |2 NLM | |
| 650 | 7 | |a spike protein, SARS-CoV-2 |2 NLM | |
| 700 | 1 | |a Linani, Abderahmane |e verfasserin |4 aut | |
| 700 | 1 | |a Benarous, Khedidja |e verfasserin |4 aut | |
| 700 | 1 | |a Goumri-Said, Souraya |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Journal of biomolecular structure & dynamics |d 1985 |g 41(2023), 20 vom: 18. Dez., Seite 10377-10387 |w (DE-627)NLM012639974 |x 1538-0254 |7 nnns |
| 773 | 1 | 8 | |g volume:41 |g year:2023 |g number:20 |g day:18 |g month:12 |g pages:10377-10387 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1080/07391102.2022.2157876 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 41 |j 2023 |e 20 |b 18 |c 12 |h 10377-10387 | ||