Versions
- 2020-05-06 (2)
- 2020-05-06 (1)
Keywords
GROMACS
Molecular Dynamics
SARS-CoV-2
How to Cite
Abstract
The 2019 novel coronavirus infection or COVID-19 can be designated as a global threat. Till date, there is a lack of dedicated therapeutics available against this fatal infection. In the present work, we performed structure-based drug design studies in order to identify clinically used molecules exhibiting crucial binding with 2019-coronavirus main protease enzyme. Based on ligand binding energy and interaction with essential amino acids, two molecules were selected. The stability of the complexed molecules with main protease enzyme was further studied by performing molecular dynamics simulation.References
Lai, Chih-Cheng, et al. "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): the epidemic and the challenges." International journal of antimicrobial agents (2020): 105924.
Peeri, Noah C., et al. "The SARS, MERS and novel coronavirus (COVID-19) epidemics, the newest and biggest global health threats: what lessons have we learned?." International Journal of Epidemiology (2020).
Brian, D. A., and R. S. Baric. "Coronavirus genome structure and replication." Coronavirus replication and reverse genetics. Springer, Berlin, Heidelberg, 2005. 1-30.
Arya R, Das A, Prashar V, Kumar M. Potential inhibitors against papain-like protease of novel coronavirus (SARS-CoV-2) from FDA approved drugs.
Ton AT, Gentile F, Hsing M, Ban F, Cherkasov A. Rapid Identification of Potential Inhibitors of SARSâ€CoVâ€2 Main Protease by Deep Docking of 1.3 Billion Compounds. Molecular Informatics. 2020 Feb 19
Chu CM, Cheng VC, Hung IF, Wong MM, Chan KH, Chan KS, Kao RY, Poon LL, Wong CL, Guan Y, Peiris JS. Role of lopinavir/ritonavir in the treatment of SARS: initial virological and clinical findings. Thorax. 2004 Mar 1;59(3):252-6.
Liu, X., Zhang, B., Jin, Z., Yang, H., Rao, Z The crystal structure of COVID-19 main protease in complex with an inhibitor N3,DOI: 10.2210/pdb6lu7/pdb
Bacha U, Barrila J, Velazquez-Campoy A, Leavitt SA, Freire E. Identification of novel inhibitors of the SARS coronavirus main protease 3CLpro. Biochemistry. 2004 May 4; 43(17):4906-12.
Ziebuhr J, Snijder EJ, Gorbalenya AE. Virus-encoded proteinases and proteolytic processing in the Nidovirales. Journal of General Virology. 2000 Apr 1;81(4):853-79.
Anand K, Palm GJ, Mesters JR, Siddell SG, Ziebuhr J, Hilgenfeld R. Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra αâ€helical domain. The EMBO Journal. 2002 Jul 1;21(13):3213-24.
Samdani, A. and Vetrivel, U. (2018). POAP: A GNU parallel based multithreaded pipeline of open babel and AutoDock suite for boosted high throughput virtual screening. Computational Biology and Chemistry, 74, pp.39-48. DOI:10.1016/j.compbiolchem.2018.02.012
Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein engineering, design and selection. 1995 Feb 1;8(2):127-34.
Schrödinger LL. The PyMOL Molecular Graphics System, Version 1.8. November 2015. URL https://pymol. org/2.
Cuker A, Arepally GM, Chong BH, et al. American Society of Hematology 2018 guidelines for management of venous thromboembolism: heparin-induced thrombocytopenia. Blood Adv. 2018;2(22):3360–3392.
Thabit AK, Fatani DF, Bamakhrama MS, Barnawi OA, Basudan LO, Alhejaili SF. Antibiotic penetration into bone and joints: An updated review. Int J Infect Dis. 2019;81:128–136.
Severin PN, Awad S, Shields B, Hoffman J, Bonney W, Cortez E, Ganesan R, Patel A, Barnes S, Barnes S, Al-Anani S. The pediatric cardiology pharmacopeia: 2013 update. Pediatric cardiology. 2013 Jan 1;34(1):1-29.
Occhipinti DJ, Pendland SL, Schoonover LL, Rypins EB, Danziger LH, Rodvold KA. Pharmacokinetics and pharmacodynamics of two multiple-dose piperacillin-tazobactam regimens. Antimicrobial agents and chemotherapy. 1997 Nov 1;41(11):2511-7.
Benaboud S, Urien S, Thervet E, Prié D, Legendre C, Souberbielle JC, Hirt D, Friedlander G, Treluyer JM, Courbebaisse M. Determination of optimal cholecalciferol treatment in renal transplant recipients using a population pharmacokinetic approach. European journal of clinical pharmacology. 2013 Mar 1;69(3):499-506.
Robin AL, Faulkner R, Curtis M, Patil S, McCarty G, Clifford W, Dahlin DC. Safety and Pharmacokinetics of Travoprost a Potent Prostaglandin F (FP) Receptor Agonist, in Patients With Renal and Hepatic Impairment. Investigative Ophthalmology & Visual Science. 2002 Dec 1;43(13):4106.
Leppik IE, Boucher BA, Wilder BJ, Murthy VS, Watridge C, Graves NM, Rangel RJ, Rask CA, Turlapaty P. Pharmacokinetics and safety of a phenytoin prodrug given IV or IM in patients. Neurology. 1990 Mar 1;40(3 Part 1):456.
Hsu A, Granneman GR, Cao G, Carothers L, Japour A, El-Shourbagy T, Dennis S, Berg J, Erdman K, Leonard JM, Sun E. Pharmacokinetic interaction between ritonavir and indinavir in healthy volunteers. Antimicrobial agents and chemotherapy. 1998 Nov 1;42(11):2784-91.
Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.