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Automated In Silico Identification of Drug Candidates for Coronavirus Through a Novel Programmatic Tool and Extensive Computational (MD, DFT) Studies of Select Drug Candidates

preprint
revised on 14.08.2020 and posted on 17.08.2020 by Ben Geoffrey A S, Rafal Madaj, Akhil Sanker, Mario Sergio Valdés Tresanco, Host Antony Davidd, Gitanjali Roy, Rinnu Sarah Saji, Abdulbasit Haliru Yakubu, Beutline Malgija

The work is composed of python based programmatic tool that automates the dry lab drug discovery workflow for coronavirus. Firstly, the python program is written to automate the process of data mining PubChem database to collect data required to perform a machine learning based AutoQSAR algorithm through which drug leads for coronavirus are generated. The data acquisition from PubChem was carried out through python web scrapping techniques. The workflow of the machine learning based AutoQSAR involves feature learning and descriptor selection, QSAR modelling, validation and prediction. The drug leads generated by the program are required to satisfy the Lipinski’s drug likeness criteria as compounds that satisfy Lipinski’s criteria are likely to be an orally active drug in humans. Drug leads generated by the program are fed as programmatic inputs to an In Silico modelling package to computer model the interaction of the compounds generated as drug leads and the coronaviral drug target identified with their PDB ID : 6Y84. The results are stored in the working folder of the user. The program also generates protein-ligand interaction profiling and stores the visualized images in the working folder of the user. Select drug leads were further studied extensively using Molecular Dynamics Simulations and best binders and their reactive profiles were analysed using Molecular Dynamics and Density Functional Theory calculations. Thus our programmatic tool ushers in a new age of automatic ease in drug identification for coronavirus.



The program is hosted, maintained and supported at the GitHub repository link given below


https://github.com/bengeof/Programmatic-tool-to-automate-the-drug-discovery-workflow-for-coronavirus

History

Email Address of Submitting Author

bengeof@gmail.com

Institution

University of Madras

Country

India

ORCID For Submitting Author

0000-0001-6545-6314

Declaration of Conflict of Interest

No conflict of interest to disclose

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