In Silico Analysis of Various Antiviral Compounds Against Spike Protein of COVID 19 using Docking Methods

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In Silico Analysis of Various Antiviral Compounds Against Spike Protein of COVID 19 using Docking Methods

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C. Shanmathi. , P. Ponmurugan2, N.Karthik 3*, M.Anita3, A.Ezhilarasu3, A.Rohini4

1Department of Chemical Engineering, National Institute of Technology, Trichy -620015,Tamil Nadu, India

2Department of Botany, Bharathiar University, Coimbatore- 641 046, Tamil Nadu, India

3*Corresponding author: Assistant Professor, Department of Biotechnology,Selvamm Arts and Science College, Namakkal- 637 003, Tamil Nadu, India

4Department of Biochemistry,Annai Violet Arts and science College,Chennai-600053,Tamil Nadu,India

Abstract:- The current examination assessed the adequacy of hostile to viral compounds against the objective protein, Spike protein of COVID19 utilizing in silico approach. Structure based docking studies was performed using PyRx 8.0 tool to retrieve potential candidates with high affinities binding against antiviral compound models with several targeted proteins repositories. The chosen target protein was 6LU7. Molecular docking was carried out using various anti-viral compounds with the target protein of microorganisms.Free vitality of restricting was recorded for the compound with its objective. Nine different compounds were docked with the target protein, within which was found to own higher binding affinity. Therefore, the current study plays a guiding role in developing new inhibitors with better binding affinities with the virulent protein of pathogens, followed by invention of novel drug to treat bacterial infections.

Keywords: Spike protein, COVID 19, PyRx8.0


Pneumonia of unknown cause was detected in Wuhan of Hubei province in China and reported first on 31st December 2019 [3]. On 30thJanuary, 2020 the outbreak was declared as Public Health Emergency of International Concern. On 11thFebruary ,2020 the new corona virus disease was named as COVID 19 by World Health Organization (WHO). The WHO declared it as world pandemic on March 11, 2020. In exception to Antarctic the virus contact the majority parts of the globe [9]

COVID 19 is a communicable disease caused by newly discovered corona virus. These are RNA group virus which will infect mammals and birds [6]. This cause the intense tract infection. there’s no medication or vaccine yet discovered to forestall the human corona infectious. The National Institute of Health (NIH) stated that this virus is believed to own genetic similarity to bat corona virus [8]. The virus either directly via close contact and respiratory droplets of sneeze and cough or indirectly via contact through contaminated surfaces. this can be associated with SARS (Severe Acute Respiratory Syndrome) and MERS (Mideast Respiratory Syndrome). The Symptoms of corona virus include Fever, dry Cough and difficulty in breathing [9]. It takes a minimum of of 5-6 days to indicate symptoms when the person is affected from virus. The foremost promising test for the identification of virus is RT – PCR technique.

The COVID 19 belongs to the subfamily Orthocoronavirinae,within the family Coronaviridae, order Nidovirales, and realm Riboviria. COVID 19 is an enveloped, positive sense single stranded RNA genome encoding quite 20 proteins. This has higher binding affinity with human ACE2. this is often wrapped duringa icosahedral protein shell.The genome size of Covid ranges from around 26 to 32 kilobases, one among the greatest among RNA viruses. they need characteristic club-shaped spikes that project from their surface, which in electron micrographs create a picture paying homage to the solar corona, from which their name derives [12].

Novel approach of drug design and docking studies may be utilised for the invention of some therapeutic drug candidates against COVID 19. These in silico techniques can minimize the time and efforts within the pipeline of drug discovery. These techniques include study of the protein structure answerable for the disease or disorder, then identifying a ligand molecule which may have potent activities [1]. Molecular docking techniques are study of interaction of the ligand with the molecule at situation. The site is that three-dimensional site of molecule which directly effects the activity of the protein. Although the activity is often either positive or negative but still it helps medicinal chemist to proceed on rational path [7].

The interaction ligands are measured as binding affinity at receptor binding sites. The less the binding affinity to the receptor at the prescribed site is that the more practical. For measuring certain values, the CHARMM force fields are used. Although the values differ marginally from system to system, and from software to software. this is often due to the variations within the systemsgenetic algorithm [7].We performed the docking of some antiviral compounds with COVID 19 Spike protein main protease in complex with an inhibitor N3.

1.1 S Protein:2.1 Preparation of Receptor:2.2 Preparation of Ligand:2.3 ADME studies:2.4 PyRx3.1 TARGET AND LIGAND PREPARATION:Table 3.1: List of ligand molecules3.2 VIRTUAL SCREENING:3.3 ADME studies:

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