Shivani Sharma* and Dr. Dinesh Kaushik


Computer aided drug design (CADD) method is widely used as a new drug design approach. Virtual screening is a computational method used in drug design. In this method the large libraries of compounds are bind with specific site on the target molecules such as- proteins and well-compounds tested. CADD is categorised into two types structure based drug design and ligand based drug design. The availability of the three-dimensional structure of the therapeutic target proteins and exploration of the binding site cavity forms the basis of structure-based drug design (SBDD) The basic steps involved in SBDD consist of the preparation of target structure, identification of the ligand binding site, compound library preparation, molecular docking and scoring functions, molecular dynamic simulation. Corona an epidemic started in december 2019 from wuhan, china, where infected people suffered from pneumonia-like symptoms which later spread over more than 200 countries world-wide. The root cause of infection was found to be a novel virus that bore structural similarities with Severe Acute Respiratory Syndrome related Corona viruses, hence named as SARS-CoV-2. The CADD methods have been successfully used in the COVID-19 drug discovery process. Selvaraj solved the three-dimensional structure of SARS-CoV-2 guanine-N7 methyltransferase (nsp14) using the homology modeling method. Materials and methods are phylogenetic analysis of SARS-CoV-2 receptor binding domain (RBD). Sequences of all available SARS-CoV-2 RBD in S were retrieved from NCBI. The tertiary structure of SARS-CoV-2 was predicted using I-TASSER (Iterative Threading Assembly Refinement) which assesses functionality and structural analysis of proteins. The S of SARS-CoV-2 attaches the virus to ACE2 using defined RBD on Spike which facilitates this interaction. Virtual screening of drug from substantial libraries of compound is a popular method used in computer-aided drug design studies. Molecular docking analyses of shortlisted lead compounds were performed using Auto Dock Vina. The steady rise in the number of confirmed positive and death cases from SARS-CoV-2 infection, computer-aided drug design (CADD) emerges as a fast and reliable technique in pharmaceutical and medicinal research since it not only saves time but also helps to cut costs of designing therapeutic agents.

Keywords: Molecular docking, CADD, COVID-19, SARS-CoV-2, Ligand binding.

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