Comparative molecular docking and simulation analysis of molnupiravir and remdesivir with SARS-CoV-2 RNA dependent RNA polymerase (RdRp)

doi:10.6026/97320630017932

. 2021 Nov 30;17(11):932-939.

doi: 10.6026/97320630017932. eCollection 2021.

Comparative molecular docking and simulation analysis of molnupiravir and remdesivir with SARS-CoV-2 RNA dependent RNA polymerase (RdRp)

Shashank M Patil¹, K R Maruthi², Shrisha Naik Bajpe², V M Vyshali³, S Sushmitha³, Chagalamari Akhila⁴, Ramith Ramu¹

Affiliations

¹ Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru-570015, Karnataka, India.
² Department of Biotechnology, Sri Dharmasthala Manjunatheshwara College (Autonomous), Ujire-574240, Karnataka, India.
³ Department of Biotechnology, BMS College for Women, Basavangudi, Bengaluru-560004, Karnataka, India.
⁴ Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru-570015, Karnataka, India.

PMID: 35655903
PMCID: PMC9148593
DOI: 10.6026/97320630017932

Comparative molecular docking and simulation analysis of molnupiravir and remdesivir with SARS-CoV-2 RNA dependent RNA polymerase (RdRp)

Shashank M Patil et al. Bioinformation. 2021.

. 2021 Nov 30;17(11):932-939.

doi: 10.6026/97320630017932. eCollection 2021.

Authors

Shashank M Patil¹, K R Maruthi², Shrisha Naik Bajpe², V M Vyshali³, S Sushmitha³, Chagalamari Akhila⁴, Ramith Ramu¹

Affiliations

¹ Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru-570015, Karnataka, India.
² Department of Biotechnology, Sri Dharmasthala Manjunatheshwara College (Autonomous), Ujire-574240, Karnataka, India.
³ Department of Biotechnology, BMS College for Women, Basavangudi, Bengaluru-560004, Karnataka, India.
⁴ Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru-570015, Karnataka, India.

PMID: 35655903
PMCID: PMC9148593
DOI: 10.6026/97320630017932

Abstract

Treatment of SARS-CoV-2 targeting its RNA dependent RNA polymerase (RdRp) is of current interest. Remdesivir has been approved for the treatment of COVID-19 around the world. However, the drug has been linked with pharmacological limitations like adverse effects and reduced efficiency. Nevertheless, recent advancements have depicted molnupiravir as an effective therapeutic agent to target the SARS-CoV-2 RdRp. The drug has cleared both in vitro and in vivo screening. It is in phase-III clinical trial. Nonetheless, there are no data on themolecular binding interaction of molnupiravir with RdRp. Therefore, it is of interest to report the binding interaction of molnupiravir using molecular docking. It is also of interest to show its stability during interaction using molecular dynamics and binding free energy calculations along with drug likeliness and pharmacokinetic properties in comparison with remdesivir.

Keywords: Molnupiravir; RdRp; Remdesivir; SARS-CoV-2; binding free energy calculations; druglikeliness; in silico experiments; molecular docking; molecular dynamics; pharmacokinetic properties.

PubMed Disclaimer

Conflict of interest statement

No conflicts of interest associated with this work.

Cited by

Inhibitory Effect of Polyphenols from the Whole Green Jackfruit Flour against α-Glucosidase, α-Amylase, Aldose Reductase and Glycation at Multiple Stages and Their Interaction: Inhibition Kinetics and Molecular Simulations.
Maradesha T, Patil SM, Al-Mutairi KA, Ramu R, Madhunapantula SV, Alqadi T. Maradesha T, et al. Molecules. 2022 Mar 14;27(6):1888. doi: 10.3390/molecules27061888. Molecules. 2022. PMID: 35335251 Free PMC article.
Antidiabetic Activity of Potential Probiotics Limosilactobacillus spp., Levilactobacillus spp., and Lacticaseibacillus spp. Isolated from Fermented Sugarcane Juice: A Comprehensive In Vitro and In Silico Study.
Kumari V B C, Huligere SS, Alotaibi G, Al Mouslem AK, Bahauddin AA, Shivanandappa TB, Ramu R. Kumari V B C, et al. Nutrients. 2023 Apr 13;15(8):1882. doi: 10.3390/nu15081882. Nutrients. 2023. PMID: 37111101 Free PMC article.
Fermented sugarcane juice-derived probiotic Levilactobacillus brevis RAMULAB54 enhances lipid metabolism and glucose homeostasis through PPAR-γ activation.
Kumari VBC, Ramu R, Huligere SS, Patil SM, Nayakvadi S, Bijoor S, Manjappara UV, Ahmed MZ, Wong LS. Kumari VBC, et al. Front Microbiol. 2025 Jan 29;15:1502751. doi: 10.3389/fmicb.2024.1502751. eCollection 2024. Front Microbiol. 2025. PMID: 39943964 Free PMC article.
Discovery of novel benzophenone integrated derivatives as anti-Alzheimer's agents targeting presenilin-1 and presenilin-2 inhibition: A computational approach.
Martiz RM, Patil SM, Ramu R, M K J, P A, Ranganatha LV, Khanum SA, Silina E, Stupin V, Achar RR. Martiz RM, et al. PLoS One. 2022 Apr 8;17(4):e0265022. doi: 10.1371/journal.pone.0265022. eCollection 2022. PLoS One. 2022. PMID: 35395008 Free PMC article.
Bioactive profiling and evaluation of anti-proliferative and anti-cancerous properties of Shivagutika, an Indian polyherbal formulation synchronizing in vitro and in silico approaches.
V H P, Kuruburu MG, M K J, N AS, Taha Babakr A, Sreenivasan R, Ramu R, Madhunapantula SV. V H P, et al. Front Chem. 2023 May 17;11:1195209. doi: 10.3389/fchem.2023.1195209. eCollection 2023. Front Chem. 2023. PMID: 37265589 Free PMC article.

See all "Cited by" articles

References

1. Patil SM, et al. Biomed. Pharmacol. J. . 2020
2. {'text': '', 'ref_index': 2, 'ids': [{'type': 'DOI', 'value': '10.13005/bpj/2033', 'is_inner': False, 'url': 'https://doi.org/10.13005/bpj/2033'}]}
1. Kumari VC, et al. Int. J. Pharm. Pharm. Sci. . 2020;12:1.
2. {'text': '', 'ref_index': 2, 'ids': [{'type': 'DOI', 'value': '10.22159/ijpps.2020v12i8.38206', 'is_inner': False, 'url': 'https://doi.org/10.22159/ijpps.2020v12i8.38206'}]}
1. Patil SM, et al. J. Biomol. Struct. Dyn. . 2021 - PubMed
1. Painter GR, et al. Curr. Opin. Virol. . 2021;50:17. - PMC - PubMed
1. Holman W, et al. Trials. . 2021;22:561. - PMC - PubMed

LinkOut - more resources

Full Text Sources
- Europe PubMed Central
- PubMed Central
Research Materials
- NCI CPTC Antibody Characterization Program
Miscellaneous
- NCI CPTAC Assay Portal

[1] Patil SM, et al. Biomed. Pharmacol. J. . 2020

{'text': '', 'ref_index': 2, 'ids': [{'type': 'DOI', 'value': '10.13005/bpj/2033', 'is_inner': False, 'url': 'https://doi.org/10.13005/bpj/2033'}]}

[2] Patil SM, et al. Biomed. Pharmacol. J. . 2020

[3] {'text': '', 'ref_index': 2, 'ids': [{'type': 'DOI', 'value': '10.13005/bpj/2033', 'is_inner': False, 'url': 'https://doi.org/10.13005/bpj/2033'}]}

[4] Kumari VC, et al. Int. J. Pharm. Pharm. Sci. . 2020;12:1.

{'text': '', 'ref_index': 2, 'ids': [{'type': 'DOI', 'value': '10.22159/ijpps.2020v12i8.38206', 'is_inner': False, 'url': 'https://doi.org/10.22159/ijpps.2020v12i8.38206'}]}

[5] Kumari VC, et al. Int. J. Pharm. Pharm. Sci. . 2020;12:1.

[6] {'text': '', 'ref_index': 2, 'ids': [{'type': 'DOI', 'value': '10.22159/ijpps.2020v12i8.38206', 'is_inner': False, 'url': 'https://doi.org/10.22159/ijpps.2020v12i8.38206'}]}

[7] Patil SM, et al. J. Biomol. Struct. Dyn. . 2021 - PubMed

[8] Patil SM, et al. J. Biomol. Struct. Dyn. . 2021 - PubMed

[9] Painter GR, et al. Curr. Opin. Virol. . 2021;50:17. - PMC - PubMed

[10] Painter GR, et al. Curr. Opin. Virol. . 2021;50:17. - PMC - PubMed

[11] Holman W, et al. Trials. . 2021;22:561. - PMC - PubMed

[12] Holman W, et al. Trials. . 2021;22:561. - PMC - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Comparative molecular docking and simulation analysis of molnupiravir and remdesivir with SARS-CoV-2 RNA dependent RNA polymerase (RdRp)

Affiliations

Comparative molecular docking and simulation analysis of molnupiravir and remdesivir with SARS-CoV-2 RNA dependent RNA polymerase (RdRp)

Authors

Affiliations

Abstract

Conflict of interest statement

Similar articles

Cited by

References

LinkOut - more resources

Full Text Sources

Research Materials

Miscellaneous

Abstract

Conflict of interest statement

Similar articles

Cited by

References

Related information

LinkOut - more resources

Full Text Sources

Research Materials

Miscellaneous