Abstract: The available structures of viral proteins and RNA molecules related to SARS-CoV-2 are used to screen and design a new set of drugs using the commercial databases and molecular docking protocols. The selected molecules are then studied further using molecular dynamics. Based on our earlier experiences we can target proteases, enzymes in DNA and RNA metabolism, and protein—protein interactions. In this paper we describe the planned research and development efforts for efficient screening and design of new drugs. Prior to the screening campaign, we will develop new open-source computational infrastructure, with two major outcomes. A new database containing all commercially available small-molecule ligands will be developed. A docking server with a web-based user interface will be developed and interfaced with the compound database. The docking server will use the database for sourcing of the molecules for the high-throughput virtual screening. Our approach offers major advantages that can bypass the problems that have traditionally plagued the pharmaceutical industry: our protocols are faster, cheaper, versatile, and offer minimal risks. We are developing new drugs using commercial databases, which allows us to buy the lead compounds for affordable prices that can bypass expensive and slow organic synthesis protocols.
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