Computational Exploration of <i>Vitis vinifera</i>-Derived Molecules as SARS-CoV-2 Main Protease Inhibitors: A Quantum Chemical and Molecular Modeling Approach

Owolabi Mutolib Bankole

doi:doi:10.11648/j.ajbio.20231102.12

| Peer-Reviewed

Computational Exploration of Vitis vinifera-Derived Molecules as SARS-CoV-2 Main Protease Inhibitors: A Quantum Chemical and Molecular Modeling Approach

Owolabi Mutolib Bankole

Published in American Journal of BioScience (Volume 11, Issue 2)

Received: 17 May 2023 Accepted: 2 June 2023 Published: 9 June 2023

Views: Downloads:

Download PDF

Share This Article

Twitter
Linked In
Facebook

Abstract

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has unleashed a global health crisis, resulting in an alarming number of cases exceeding 765 million and deaths surpassing 6 million as of March 2023. Consequently, researchers worldwide are dedicating their efforts to exploring potential drug candidates that can serve as effective therapeutic interventions against this devastating virus. Meanwhile, the popularity of herbal medicines is skyrocketing, as individuals increasingly seek alternative remedies to address various health concerns within different healthcare systems around the world. In this study, a multitude of computational tools were employed to meticulously investigate the Vitis Vinifera extracts for their potential as inhibitors of the SARS-CoV-2 Mpro enzyme. These tools encompassed molecular docking, binding energy calculation, ADMET studies as well as quantum chemical calculations. The objective was to identify specific compounds present in Vitis Vinifera extracts that could effectively hinder the activity of the SARS-CoV-2 Mpro enzyme, a crucial target for therapeutic intervention. The rigorous analysis conducted unveiled six compounds that demonstrated significant potential as inhibitors of the SARS-CoV-2 Mpro enzyme: Hyperoside, Gallocatechin gallate, cis-Astringin, peonidin-3-O-glucoside, Fraxin, and cis-Piceid. When compared to the established standard drug Nelfinavir, these compounds exhibited superior binding affinities and slightly improved ADMET properties. Notably, peonidin-3-O-glucoside emerged as an especially promising compound, surpassing the others as well as the standard drug in terms of binding energy, reactivity, and stability. These findings suggest its potential as a potent inhibitor of the SARS-CoV-2 Mpro enzyme. However, it is imperative to emphasize that further validation through in vivo and in vitro studies is indispensable. While the computational results provide valuable insights, their practical application necessitates verifying the efficacy and safety of these compounds.

Published in	American Journal of BioScience (Volume 11, Issue 2)
DOI	10.11648/j.ajbio.20231102.12
Page(s)	46-56
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2023. Published by Science Publishing Group

Keywords

SARS-CoV-2 Mpro, Vitis Vinifera, Molecular Docking, Binding Energy Calculation, Admet, Quantum Chemical Calculations

References

[1]	Oyagbemi AA, Ajibade TO, Aboua YG, Gbadamosi IT, Adedapo ADA, Aro AO, et al. Potential health benefits of zinc supplementation for the management of COVID-19 pandemic. Journal of Food Biochemistry. 2021; 45 (2): e13604.
[2]	WHO Coronavirus (COVID-19) Dashboard [Internet]. [cited 2023 May 4]. Available from: https://covid19.who.int
[3]	Transmissibility and transmission of respiratory viruses \| Nature Reviews Microbiology [Internet]. [cited 2023 May 4]. Available from: https://www.nature.com/articles/s41579-021-00535-6
[4]	Shi Y, Wang G, Cai X peng, Deng J wen, Zheng L, Zhu H hong, et al. An overview of COVID-19. Journal of Zhejiang University Science B. 2020 May; 21 (5): 343.
[5]	Hoofman J, Secord E. The Effect of COVID-19 on Education. Pediatric Clinics. 2021 Oct 1; 68 (5): 1071–9.
[6]	The Economic Effects of COVID-19 Containment Measures \| SpringerLink [Internet]. [cited 2023 Apr 25]. Available from: https://link.springer.com/article/10.1007/s11079-021-09638-2
[7]	Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure–Activity Relationship Insights and Evolution Perspectives \| Journal of Medicinal Chemistry [Internet]. [cited 2023 May 4]. Available from: https://pubs.acs.org/doi/full/10.1021/acs.jmedchem.2c01005
[8]	Mujwar S, Harwansh RK. In silico bioprospecting of taraxerol as a main protease inhibitor of SARS-CoV-2 to develop therapy against COVID-19. Struct Chem. 2022/05/04 ed. 2022 Apr 28; 1–12.
[9]	Johnson TO, Adegboyega AE, Ojo OA, Yusuf AJ, Iwaloye O, Ugwah-Oguejiofor CJ, et al. A Computational Approach to Elucidate the Interactions of Chemicals From Artemisia annua Targeted Toward SARS-CoV-2 Main Protease Inhibition for COVID-19 Treatment. Front Med (Lausanne). 2022 Jun 15; 9: 907583.
[10]	Akinnusi PA, Olubode SO, Salaudeen WA. Molecular binding studies of anthocyanins with multiple antiviral activities against SARS-CoV-2. Bull Natl Res Cent. 2022 Dec; 46 (1): 102.
[11]	Adebesin AO, Ayodele AO, Omotoso O, Akinnusi PA, Olubode SO. Computational evaluation of bioactive compounds from V. Vinifera as a novel β-catenin inhibitor for cancer treatment. Bull Natl Res Cent. 2022 Dec; 46 (1): 183.
[12]	Olubode SO, Bankole MO, Akinnusi PA, Adanlawo OS, Ojubola KI, Nwankwo DO, et al. Molecular Modeling Studies of Natural Inhibitors of Androgen Signaling in Prostate Cancer. Cancer Inform. 2022 Jan; 21: 117693512211185.
[13]	Bongo GN, Ngbolua KTN, Mbadiko Mutunda C, Inkoto C, Mpiana PT, Gbolo BZ, et al. Phytochemistry and Antiviral activities of some fruit plant species as potential resources for anti-viral agents: A review. 2022 Mar 11; 3: 1–11.
[14]	Olubode S, Bankole O, Akinnusi P, Salaudeen W, Ojubola K, Adanlawo O, et al. Computational study of the inhibitory potential of Gongronema latifolium (benth) leave on farnesyl pyrophosphate synthase, a target enzyme in the treatment of osteoporosis. A molecular modelling approach. Journal of Herbal Drugs. 2022; 13 (2): 10.
[15]	Olubode SO, I Omotuyi O, Fadipe D. Computational Prediction of HCV RNA Polymerase Inhibitors from Alkaloid Library. Lett Appl NanoBioSci. 2021 Sep 7; 11 (3): 3661–71.
[16]	Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, et al. Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes. J Med Chem. 2006 Oct 1; 49 (21): 6177–96.
[17]	Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, et al. PubChem Substance and Compound databases. Nucleic Acids Res. 2016 Jan 4; 44 (D1): D1202–13.
[18]	Release S. LigPrep, Schrödinger, LLC, New York, NY, 2017. New York, NY.
[19]	Bissantz C, Folkers G, Rognan D. Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations. J Med Chem. 2000 Dec 1; 43 (25): 4759–67.
[20]	Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, et al. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. J Chem Theory Comput. 2016 Jan 12; 12 (1): 281–96.
[21]	Glide Docking, Autodock, Binding Free Energy and Drug-Likeness Studies for Prediction of Potential Inhibitors of Cyclin-Dependent Kinase 14 Protein in Wnt Signaling Pathway. Biointerface Res Appl Chem. 2021 Jun 18; 12 (2): 2473–88.
[22]	Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017 May 12; 7 (1): 42717.
[23]	Banerjee P, Eckert AO, Schrey AK, Preissner R. ProTox-II: a webserver for the prediction of toxicity of chemicals. Nucleic Acids Research. 2018 Jul 2; 46 (W1): W257–63.
[24]	Jacobson MP, Friesner RA, Xiang Z, Honig B. On the Role of the Crystal Environment in Determining Protein Side-chain Conformations. Journal of Molecular Biology. 2002 Jul; 320 (3): 597–608.
[25]	Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences - Bochevarov - 2013 - International Journal of Quantum Chemistry - Wiley Online Library [Internet]. [cited 2023 May 4]. Available from: https://onlinelibrary.wiley.com/doi/full/10.1002/qua.24481
[26]	K Inyang O, I Omotuyi O, J Ogunleye A, O Eniafe G, Adewumi B, S Metibemu D. Molecular Interaction and Inhibitory Potential of Polyphenol on DNA Repair Pathway in Small Cell Lung Cancer: A Computational Study. JAPLR [Internet]. 2017 Oct 25 [cited 2022 Jun 24]; 6 (3). Available from: https://medcraveonline.com/JAPLR/molecular-interaction-and-inhibitory-potential-of-polyphenol-on-dna-repair-pathway-in-small-cell-lung-cancer-a-computational-study.html
[27]	Akinnusi PA, Olubode SO, Alade AA, Ahmed SA, Ayekolu SF, Ogunlade TM, et al. A molecular modeling approach for structure-based virtual screening and identification of novel anti-hypercholesterolemic agents from Grape. Informatics in Medicine Unlocked. 2022; 32: 101065.
[28]	Ray AK, Sen Gupta PS, Panda SK, Biswal S, Bhattacharya U, Rana MK. Repurposing of FDA-approved drugs as potential inhibitors of the SARS-CoV-2 main protease: Molecular insights into improved therapeutic discovery. Computers in Biology and Medicine. 2022 Mar 1; 142: 105183.
[29]	Avti P, Chauhan A, Shekhar N, Prajapat M, Sarma P, Kaur H, et al. Computational basis of SARS-CoV 2 main protease inhibition: an insight from molecular dynamics simulation based findings. Journal of Biomolecular Structure and Dynamics. 2022 Nov 26; 40 (19): 8894–904.
[30]	Akinnusi PA, Olubode SO, Adebesin AO, Osadipe TJ, Nwankwo DO, Adebisi AD, et al. Structure-based scoring of anthocyanins and molecular modeling of PfLDH, PfDHODH, and PfDHFR reveal novel potential P. falciparum inhibitors. Informatics in Medicine Unlocked. 2023 Jan 1; 38: 101206.
[31]	Akinnusi PA, Olubode SO, Adebesin AO, Nana TA, Shodehinde SA. Discovery of Promising Inhibitors of Epidermal Growth Factor Receptor (EGFR), Human Epidermal Growth Factor Receptor 2 (HER2), Estrogen Receptor (ER), and Phosphatidylinositol-3-kinase a (PI3Ka) for Personalized Breast Cancer Treatment. Cancer Inform. 2022 Jan; 21: 117693512211278.
[32]	Omoboyowa DA, Balogun TA, Saibu OA, Chukwudozie OS, Alausa A, Olubode SO, et al. Structure-based discovery of selective CYP17A1 inhibitors for Castration-resistant prostate cancer treatment. Biology Methods and Protocols. 2022 Jan 10; 7 (1): bpab026.
[33]	Lipinski CA. Lead- and drug-like compounds: the rule-of-five revolution. Drug Discovery Today: Technologies. 2004 Dec; 1 (4): 337–41.
[34]	Optometric Management - April 2022 [Internet]. Optometric Management. [cited 2023 May 4]. Available from: https://www.optometricmanagement.com/newsletters/nutritional-insights-for-clinical-practice/april-2022
[35]	Recent Advances in the Prediction of Pharmacokinetics Properties in Drug Design Studies: A Review - Pantaleão - 2022 - ChemMedChem - Wiley Online Library [Internet]. [cited 2023 May 4]. Available from: https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/cmdc.202100542
[36]	Wilson CG, Aarons L, Augustijns P, Brouwers J, Darwich AS, De Waal T, et al. Integration of advanced methods and models to study drug absorption and related processes: An UNGAP perspective. European Journal of Pharmaceutical Sciences. 2022 May 1; 172: 106100.
[37]	Teleanu RI, Preda MD, Niculescu AG, Vladâcenco O, Radu CI, Grumezescu AM, et al. Current Strategies to Enhance Delivery of Drugs across the Blood–Brain Barrier. Pharmaceutics. 2022 May; 14 (5): 987.
[38]	Zwickl CM, Graham JC, Jolly RA, Bassan A, Ahlberg E, Amberg A, et al. Principles and procedures for assessment of acute toxicity incorporating in silico methods. Computational Toxicology. 2022 Nov 1; 24: 100237.
[39]	Noureddine O, Issaoui N, Medimagh M, Al-Dossary O, Marouani H. Quantum chemical studies on molecular structure, AIM, ELF, RDG and antiviral activities of hybrid hydroxychloroquine in the treatment of COVID-19: Molecular docking and DFT calculations. Journal of King Saud University - Science. 2021 Mar 1; 33 (2): 101334.
[40]	Silva R, Santos J, Figueroa-Villar J. On the Limits of Highest-Occupied Molecular Orbital Driven Reactions: The Frontier Effective-for-Reaction Molecular Orbital Concept. The journal of physical chemistry A. 2006 Feb 1; 110: 1031–40.
[41]	Louis E, San-Fabián E, Díaz-García MA, Chiappe G, Vergés JA. Are Electron Affinity and Ionization Potential Intrinsic Parameters to Predict the Electron or Hole Acceptor Character of Amorphous Molecular Materials? J Phys Chem Lett. 2017 Jun 1; 8 (11): 2445–9.
[42]	Mumit MA, Pal TK, Alam MA, Islam MAAAA, Paul S, Sheikh MC. DFT studies on vibrational and electronic spectra, HOMO–LUMO, MEP, HOMA, NBO and molecular docking analysis of benzyl-3-N-(2, 4, 5-trimethoxyphenylmethylene) hydrazinecarbodithioate. J Mol Struct. 2020 Nov 15; 1220: 128715.
[43]	Mohapatra R, Mohapatra P, Azam M, Sarangi A, Abdalla M, Perekhoda L, et al. Computational studies on potential new anti-Covid-19 agents with a multi-target mode of action. Journal of King Saud University - Science. 2022 May 10; 34.
[44]	Huang Y, Rong C, Zhang R, Liu S. Evaluating frontier orbital energy and HOMO/LUMO gap with descriptors from density functional reactivity theory. Journal of Molecular Modeling. 2017 Jan 1; 23.
[45]	Sens L, Oliveira A, Mascarello A, Brighente II, Yunes R, Nunes R. Synthesis, Antioxidant Activity, Acetylcholinesterase Inhibition and Quantum Studies of Thiosemicarbazones. Journal of the Brazilian Chemical Society. 2017 Jan 1; 29.
[46]	Pegu D, Deb J, Van Alsenoy C, Sarkar U. Theoretical Investigation of Electronic, Vibrational and Nonlinear Optical Properties of 4-fluoro-4-hydroxybenzophenone. Spectroscopy Letters. 2017 Mar 22; 50.
[47]	El-Shamy NT, Alkaoud AM, Hussein RK, Ibrahim MA, Alhamzani AG, Abou-Krisha MM. DFT, ADMET and Molecular Docking Investigations for the Antimicrobial Activity of 6, 6′-Diamino-1, 1′, 3, 3′-tetramethyl-5, 5′-(4-chlorobenzylidene) bis[pyrimidine-2, 4 (1H, 3H)-dione]. Molecules. 2022 Jan 18; 27 (3): 620.
[48]	Miar M, Shiroudi A, Pourshamsian K, Oliaey AR, Hatamjafari F. Theoretical investigations on the HOMO–LUMO gap and global reactivity descriptor studies, natural bond orbital, and nucleus-independent chemical shifts analyses of 3-phenylbenzo[d] thiazole-2 (3H)-imine and its para-substituted derivatives: Solvent and substituent effects. Journal of Chemical Research. 2021 Jan 1; 45 (1–2): 147–58.

Cite This Article

Plain Text BibTeX RIS

APA Style

Owolabi Mutolib Bankole. (2023). Computational Exploration of Vitis vinifera-Derived Molecules as SARS-CoV-2 Main Protease Inhibitors: A Quantum Chemical and Molecular Modeling Approach. American Journal of BioScience, 11(2), 46-56. https://doi.org/10.11648/j.ajbio.20231102.12

Copy | Download

ACS Style

Owolabi Mutolib Bankole. Computational Exploration of Vitis vinifera-Derived Molecules as SARS-CoV-2 Main Protease Inhibitors: A Quantum Chemical and Molecular Modeling Approach. Am. J. BioScience 2023, 11(2), 46-56. doi: 10.11648/j.ajbio.20231102.12

Copy | Download

AMA Style

Owolabi Mutolib Bankole. Computational Exploration of Vitis vinifera-Derived Molecules as SARS-CoV-2 Main Protease Inhibitors: A Quantum Chemical and Molecular Modeling Approach. Am J BioScience. 2023;11(2):46-56. doi: 10.11648/j.ajbio.20231102.12

Copy | Download

@article{10.11648/j.ajbio.20231102.12,
  author = {Owolabi Mutolib Bankole},
  title = {Computational Exploration of Vitis vinifera-Derived Molecules as SARS-CoV-2 Main Protease Inhibitors: A Quantum Chemical and Molecular Modeling Approach},
  journal = {American Journal of BioScience},
  volume = {11},
  number = {2},
  pages = {46-56},
  doi = {10.11648/j.ajbio.20231102.12},
  url = {https://doi.org/10.11648/j.ajbio.20231102.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajbio.20231102.12},
  abstract = {The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has unleashed a global health crisis, resulting in an alarming number of cases exceeding 765 million and deaths surpassing 6 million as of March 2023. Consequently, researchers worldwide are dedicating their efforts to exploring potential drug candidates that can serve as effective therapeutic interventions against this devastating virus. Meanwhile, the popularity of herbal medicines is skyrocketing, as individuals increasingly seek alternative remedies to address various health concerns within different healthcare systems around the world. In this study, a multitude of computational tools were employed to meticulously investigate the Vitis Vinifera extracts for their potential as inhibitors of the SARS-CoV-2 Mpro enzyme. These tools encompassed molecular docking, binding energy calculation, ADMET studies as well as quantum chemical calculations. The objective was to identify specific compounds present in Vitis Vinifera extracts that could effectively hinder the activity of the SARS-CoV-2 Mpro enzyme, a crucial target for therapeutic intervention. The rigorous analysis conducted unveiled six compounds that demonstrated significant potential as inhibitors of the SARS-CoV-2 Mpro enzyme: Hyperoside, Gallocatechin gallate, cis-Astringin, peonidin-3-O-glucoside, Fraxin, and cis-Piceid. When compared to the established standard drug Nelfinavir, these compounds exhibited superior binding affinities and slightly improved ADMET properties. Notably, peonidin-3-O-glucoside emerged as an especially promising compound, surpassing the others as well as the standard drug in terms of binding energy, reactivity, and stability. These findings suggest its potential as a potent inhibitor of the SARS-CoV-2 Mpro enzyme. However, it is imperative to emphasize that further validation through in vivo and in vitro studies is indispensable. While the computational results provide valuable insights, their practical application necessitates verifying the efficacy and safety of these compounds.},
 year = {2023}
}

Copy | Download

TY  - JOUR
T1  - Computational Exploration of Vitis vinifera-Derived Molecules as SARS-CoV-2 Main Protease Inhibitors: A Quantum Chemical and Molecular Modeling Approach
AU  - Owolabi Mutolib Bankole
Y1  - 2023/06/09
PY  - 2023
N1  - https://doi.org/10.11648/j.ajbio.20231102.12
DO  - 10.11648/j.ajbio.20231102.12
T2  - American Journal of BioScience
JF  - American Journal of BioScience
JO  - American Journal of BioScience
SP  - 46
EP  - 56
PB  - Science Publishing Group
SN  - 2330-0167
UR  - https://doi.org/10.11648/j.ajbio.20231102.12
AB  - The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has unleashed a global health crisis, resulting in an alarming number of cases exceeding 765 million and deaths surpassing 6 million as of March 2023. Consequently, researchers worldwide are dedicating their efforts to exploring potential drug candidates that can serve as effective therapeutic interventions against this devastating virus. Meanwhile, the popularity of herbal medicines is skyrocketing, as individuals increasingly seek alternative remedies to address various health concerns within different healthcare systems around the world. In this study, a multitude of computational tools were employed to meticulously investigate the Vitis Vinifera extracts for their potential as inhibitors of the SARS-CoV-2 Mpro enzyme. These tools encompassed molecular docking, binding energy calculation, ADMET studies as well as quantum chemical calculations. The objective was to identify specific compounds present in Vitis Vinifera extracts that could effectively hinder the activity of the SARS-CoV-2 Mpro enzyme, a crucial target for therapeutic intervention. The rigorous analysis conducted unveiled six compounds that demonstrated significant potential as inhibitors of the SARS-CoV-2 Mpro enzyme: Hyperoside, Gallocatechin gallate, cis-Astringin, peonidin-3-O-glucoside, Fraxin, and cis-Piceid. When compared to the established standard drug Nelfinavir, these compounds exhibited superior binding affinities and slightly improved ADMET properties. Notably, peonidin-3-O-glucoside emerged as an especially promising compound, surpassing the others as well as the standard drug in terms of binding energy, reactivity, and stability. These findings suggest its potential as a potent inhibitor of the SARS-CoV-2 Mpro enzyme. However, it is imperative to emphasize that further validation through in vivo and in vitro studies is indispensable. While the computational results provide valuable insights, their practical application necessitates verifying the efficacy and safety of these compounds.
VL  - 11
IS  - 2
ER  -

Copy | Download

Author Information

Owolabi Mutolib Bankole

Department of Chemical Sciences, Adekunle Ajasin University, Akungba, Nigeria

Download PDF

Sections

Plain Text BibTeX RIS

APA Style

Owolabi Mutolib Bankole. (2023). Computational Exploration of Vitis vinifera-Derived Molecules as SARS-CoV-2 Main Protease Inhibitors: A Quantum Chemical and Molecular Modeling Approach. American Journal of BioScience, 11(2), 46-56. https://doi.org/10.11648/j.ajbio.20231102.12

Copy | Download

ACS Style

Owolabi Mutolib Bankole. Computational Exploration of Vitis vinifera-Derived Molecules as SARS-CoV-2 Main Protease Inhibitors: A Quantum Chemical and Molecular Modeling Approach. Am. J. BioScience 2023, 11(2), 46-56. doi: 10.11648/j.ajbio.20231102.12

Copy | Download

AMA Style

Owolabi Mutolib Bankole. Computational Exploration of Vitis vinifera-Derived Molecules as SARS-CoV-2 Main Protease Inhibitors: A Quantum Chemical and Molecular Modeling Approach. Am J BioScience. 2023;11(2):46-56. doi: 10.11648/j.ajbio.20231102.12

Copy | Download

@article{10.11648/j.ajbio.20231102.12,
  author = {Owolabi Mutolib Bankole},
  title = {Computational Exploration of Vitis vinifera-Derived Molecules as SARS-CoV-2 Main Protease Inhibitors: A Quantum Chemical and Molecular Modeling Approach},
  journal = {American Journal of BioScience},
  volume = {11},
  number = {2},
  pages = {46-56},
  doi = {10.11648/j.ajbio.20231102.12},
  url = {https://doi.org/10.11648/j.ajbio.20231102.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajbio.20231102.12},
  abstract = {The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has unleashed a global health crisis, resulting in an alarming number of cases exceeding 765 million and deaths surpassing 6 million as of March 2023. Consequently, researchers worldwide are dedicating their efforts to exploring potential drug candidates that can serve as effective therapeutic interventions against this devastating virus. Meanwhile, the popularity of herbal medicines is skyrocketing, as individuals increasingly seek alternative remedies to address various health concerns within different healthcare systems around the world. In this study, a multitude of computational tools were employed to meticulously investigate the Vitis Vinifera extracts for their potential as inhibitors of the SARS-CoV-2 Mpro enzyme. These tools encompassed molecular docking, binding energy calculation, ADMET studies as well as quantum chemical calculations. The objective was to identify specific compounds present in Vitis Vinifera extracts that could effectively hinder the activity of the SARS-CoV-2 Mpro enzyme, a crucial target for therapeutic intervention. The rigorous analysis conducted unveiled six compounds that demonstrated significant potential as inhibitors of the SARS-CoV-2 Mpro enzyme: Hyperoside, Gallocatechin gallate, cis-Astringin, peonidin-3-O-glucoside, Fraxin, and cis-Piceid. When compared to the established standard drug Nelfinavir, these compounds exhibited superior binding affinities and slightly improved ADMET properties. Notably, peonidin-3-O-glucoside emerged as an especially promising compound, surpassing the others as well as the standard drug in terms of binding energy, reactivity, and stability. These findings suggest its potential as a potent inhibitor of the SARS-CoV-2 Mpro enzyme. However, it is imperative to emphasize that further validation through in vivo and in vitro studies is indispensable. While the computational results provide valuable insights, their practical application necessitates verifying the efficacy and safety of these compounds.},
 year = {2023}
}

Copy | Download

TY  - JOUR
T1  - Computational Exploration of Vitis vinifera-Derived Molecules as SARS-CoV-2 Main Protease Inhibitors: A Quantum Chemical and Molecular Modeling Approach
AU  - Owolabi Mutolib Bankole
Y1  - 2023/06/09
PY  - 2023
N1  - https://doi.org/10.11648/j.ajbio.20231102.12
DO  - 10.11648/j.ajbio.20231102.12
T2  - American Journal of BioScience
JF  - American Journal of BioScience
JO  - American Journal of BioScience
SP  - 46
EP  - 56
PB  - Science Publishing Group
SN  - 2330-0167
UR  - https://doi.org/10.11648/j.ajbio.20231102.12
AB  - The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has unleashed a global health crisis, resulting in an alarming number of cases exceeding 765 million and deaths surpassing 6 million as of March 2023. Consequently, researchers worldwide are dedicating their efforts to exploring potential drug candidates that can serve as effective therapeutic interventions against this devastating virus. Meanwhile, the popularity of herbal medicines is skyrocketing, as individuals increasingly seek alternative remedies to address various health concerns within different healthcare systems around the world. In this study, a multitude of computational tools were employed to meticulously investigate the Vitis Vinifera extracts for their potential as inhibitors of the SARS-CoV-2 Mpro enzyme. These tools encompassed molecular docking, binding energy calculation, ADMET studies as well as quantum chemical calculations. The objective was to identify specific compounds present in Vitis Vinifera extracts that could effectively hinder the activity of the SARS-CoV-2 Mpro enzyme, a crucial target for therapeutic intervention. The rigorous analysis conducted unveiled six compounds that demonstrated significant potential as inhibitors of the SARS-CoV-2 Mpro enzyme: Hyperoside, Gallocatechin gallate, cis-Astringin, peonidin-3-O-glucoside, Fraxin, and cis-Piceid. When compared to the established standard drug Nelfinavir, these compounds exhibited superior binding affinities and slightly improved ADMET properties. Notably, peonidin-3-O-glucoside emerged as an especially promising compound, surpassing the others as well as the standard drug in terms of binding energy, reactivity, and stability. These findings suggest its potential as a potent inhibitor of the SARS-CoV-2 Mpro enzyme. However, it is imperative to emphasize that further validation through in vivo and in vitro studies is indispensable. While the computational results provide valuable insights, their practical application necessitates verifying the efficacy and safety of these compounds.
VL  - 11
IS  - 2
ER  -

Copy | Download