In silico molecular docking of SARS-CoV-2 surface proteins with microbial non-ribosomal peptides: identification of potential drugs

Agrawal S, Acharya D, Adholeya A, Barrow CJ, Deshmukh SK (2017) Nonribosomal peptides from marine microbes and their antimicrobial and anticancer potential. Front Pharmacol 8:828

Alazmi M, Motwalli O (2020) Molecular basis for drug repurposing to study the interface of the S protein in SARS-CoV-2 and human ACE2 through docking, characterization, and molecular dynamics for natural drug candidates. J Mol Model 26:338

Alrasheid AA, Babiker MY, Awad TA (2021) Evaluation of certain medicinal plants compounds as new potential inhibitors of novel corona virus (COVID-19) using molecular docking analysis. Silico Pharmacol 9:10

Báez-Santos YM, John SE, Mesecar AD (2015) The SARS-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds. Antiviral Res 115:21–38

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235–242

Chen B, Tian EK, He B, Tian L, Han R, Wang S, Xiang Q, Zhang S, El Arnaout T, Cheng W (2020) Overview of lethal human coronaviruses. Signal Transduct Target Ther 5:89

Fang WY, Dahiya R, Qin HL, Mourya R, Maharaj S (2016) Natural proline-rich cyclopolypeptides from marine organisms: chemistry, synthetic methodologies and biological status. Mar Drugs 14:194

Hiremath S, Kumar HDV, Nandan M, Mantesh M, Shankarappa KS, Venkataravanappa V, Basha CRJ, Reddy CNL (2021) In silico docking analysis revealed the potential of phytochemicals present in Phyllanthus amarus and Andrographis paniculata, used in Ayurveda medicine in inhibiting SARS-CoV-2. 3 Biotech 11:44

Hosseini M, Chen W, Xiao D, Wang C (2021) Computational molecular docking and virtual screening revealed promising SARS-CoV-2 drugs. Precis Clin Med 4(1):1–16

Khalifa SA, Elias N, Farag MA, Chen L, Saeed A, Hegazy ME, Moustafa MS, El-Wahed A, Al-Mousawi SM, Musharraf SG, Chang FR (2019) Marine natural products: a source of novel anticancer drugs. Mar Drugs 17:491

Kim J, Zhang J, Cha Y, Kolitz S, Funt J, Chong RE, Barrett S, Kusko R, Zeskind B, Kaufman H (2020) Advanced bioinformatics rapidly identifies existing therapeutics for patients with coronavirus disease-2019 (COVID-19). J Transl Med 18:257

Lindner HA, Fotouhi-Ardakani N, Lytvyn V, Lachance P, Sulea T, Ménard R (2005) The papain-like protease from the severe acute respiratory syndrome coronavirus is a deubiquitinating enzyme. J Virol 79:15199–15208

Narkhede RR, Cheke RS, Ambhore JP, Shinde SD (2020) The molecular docking study of potential drug candidates showing anti-COVID-19 activity by exploring of therapeutic targets of SARS-CoV-2. EJMO 4:185–195

Nimgampalle M, Devanathan V, Saxena A (2020) Screening of Chloroquine, Hydroxychloroquine and its derivatives for their binding affinity to multiple SARS-CoV-2 protein drug targets. J Biomol Struct Dyn 1–13. https://doi.org/10.1080/07391102.2020.1782265

O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open babel: an open chemical toolbox. J Cheminform 3:33

Osipiuk J, Azizi SA, Dvorkin S, Endres M, Jedrzejczak R, Jones KA, Kang S, Kathayat RS, Kim Y, Lisnyak VG, Maki SL, Nicolaescu V, Taylor CA, Tesar C, Zhang Y-A, Zhou Z, Randall G, Michalska K, Snyder SA, Dickinson BC, Joachimiak A (2021) Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Nat Commun 12:743

Osipiuk J, Jedrzejczak R, Tesar C, Endres M, Stols L, Babnigg G, Kim Y, Michalska K, Joachimiak A (2020) The crystal structure of papain-like protease of SARS CoV-2. RSCB PDB. https://doi.org/10.2210/pdb6W9C/pdb

Owis AI, El-Hawary MS, El Amir D, Aly OM, Abdelmohsen UR, Kamel MS (2020) Molecular docking reveals the potential of Salvadora persica flavonoids to inhibit COVID-19 virus main protease. RSC Adv 10:19570–19575

Peele KA, Chandrasai P, Srihansa T, Krupanidhi S, Sai AV, Babu DJ, Indira M, Reddy AR, Venkateswarulu TC (2020) Molecular docking and dynamic simulations for antiviral compounds against SARS-CoV-2: a computational study. Inform Med Unlocked 19:100345

Sayed AM, Alhadrami HA, El-Gendy AO, Shamikh YI, Belbahri L, Hassan HM, Abdelmohsen UR, Rateb ME (2020) Microbial natural products as potential inhibitors of SARS-CoV-2 main protease (Mpro). Microorganisms 8:970

Shah B, Modi P, Sagar SR (2020) In silico studies on therapeutic agents for COVID-19: Drug repurposing approach. Life Sci 252:117652

Skariyachan S, Gopal D, Chakrabarti S, Kempanna P, Uttarkar A, Muddebihalkar AG, Niranjan V (2020) Structural and molecular basis of the interaction mechanism of selected drugs towards multiple targets of SARS-CoV-2 by molecular docking and dynamic simulation studies-deciphering the scope of repurposed drugs. Comput Biol Med 126:104054

Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461

Vinothkumar S, Parameswaran PS (2013) Recent advances in marine drug research. Biotechnol Adv 31:1826–1845

Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS (2020) Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 367(6483):1260–1263

Zhou Y, Hou Y, Shen J, Huang Y, Martin W, Cheng F (2020) Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discov 6:14