Predicting drug-Protein interaction with deep learning framework for molecular graphs and sequences: Potential candidates against SAR-CoV-2

• Published in: PloS one 2024-05, Vol.19 (5), p.e0299696-e0299696
• Main Authors: Du, Weian, Zhao, Liang, Wu, Rong, Huang, Boning, Liu, Si, Liu, Yufeng, Huang, Huaiqiu, Shi, Ge
• Format: Article
• Language: English
• Subjects: Affinity; Antiviral agents; Antiviral Agents - pharmacology; Antiviral Agents - therapeutic use; Binding; Candidates; Chemical bonds; Chymotrypsin; Coronavirus 3C Proteases - antagonists & inhibitors; Coronavirus 3C Proteases - metabolism; Coronaviruses; COVID-19; COVID-19 - virology; COVID-19 Drug Treatment; Cysteine proteinase; Datasets; Decoys; Deep Learning; Epidemiology; Graph representations; Graphs; Health aspects; Humans; Mathematical models; Medical research; Medicine, Experimental; Molecular Docking Simulation; Neural networks; Proteases; Protein Binding; Proteins; R&D; Research & development; Respiratory diseases; SARS-CoV-2 - drug effects; SARS-CoV-2 - genetics; SARS-CoV-2 - metabolism; Severe acute respiratory syndrome coronavirus 2; Vaccines; Viral diseases; Zinc compounds
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0299696

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 disease, which represents a new life-threatening disaster. Regarding viral infection, many therapeutics have been investigated to alleviate the epidemiology such as vaccines and receptor decoys. However, the continuous mutating coronavirus, especially the variants of Delta and Omicron, are tended to invalidate the therapeutic biological product. Thus, it is necessary to develop molecular entities as broad-spectrum antiviral drugs. Coronavirus replication is controlled by the viral 3-chymotrypsin-like cysteine protease (3CLpro) enzyme, which is required for the virus's life cycle. In the cases of severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV), 3CLpro has been shown to be a promising therapeutic development target. Here we proposed an attention-based deep learning framework for molecular graphs and sequences, training from the BindingDB 3CLpro dataset (114,555 compounds). After construction of such model, we conducted large-scale screening the in vivo/vitro dataset (276,003 compounds) from Zinc Database and visualize the candidate compounds with attention score. geometric-based affinity prediction was employed for validation. Finally, we established a 3CLpro-specific deep learning framework, namely GraphDPI-3CL (AUROC: 0.958) achieved superior performance beyond the existing state of the art model and discovered 10 molecules with a high binding affinity of 3CLpro and superior binding mode.