In silico generation of novel ligands for the inhibition of SARS-CoV-2 main protease (3CL pro ) using deep learning

• Published in: Frontiers in microbiology 2023, Vol.14, p.1194794
• Main Authors: Prabhakaran, Prejwal, Hebbani, Ananda Vardhan, Menon, Soumya V, Paital, Biswaranjan, Murmu, Sneha, Kumar, Sunil, Singh, Mahender Kumar, Sahoo, Dipak Kumar, Desai, Padma Priya Dharmavaram
• Format: Article
• Language: English
• ISSN: 1664-302X; 1664-302X

The recent emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the coronavirus disease (COVID-19) has become a global public health crisis, and a crucial need exists for rapid identification and development of novel therapeutic interventions. In this study, a recurrent neural network (RNN) is trained and optimized to produce novel ligands that could serve as potential inhibitors to the SARS-CoV-2 viral protease: 3 chymotrypsin-like protease (3CL ). Structure-based virtual screening was performed through molecular docking, ADMET profiling, and predictions of various molecular properties were done to evaluate the toxicity and drug-likeness of the generated novel ligands. The properties of the generated ligands were also compared with current drugs under various phases of clinical trials to assess the efficacy of the novel ligands. Twenty novel ligands were selected that exhibited good drug-likeness properties, with most ligands conforming to Lipinski's rule of 5, high binding affinity (highest binding affinity: -9.4 kcal/mol), and promising ADMET profile. Additionally, the generated ligands complexed with 3CL were found to be stable based on the results of molecular dynamics simulation studies conducted over a 100 ns period. Overall, the findings offer a promising avenue for the rapid identification and development of effective therapeutic interventions to treat COVID-19.