Predicting commercially available antiviral drugs that may act on the novel coronavirus (2019-nCoV), Wuhan, China through a drug-target interaction deep learning model
Open Access
- 2 February 2020
- preprint content
- Published by Cold Spring Harbor Laboratory
Abstract
The infection of a novel coronavirus found in Wuhan of China (2019-nCoV) is rapidly spreading, and the incidence rate is increasing worldwide. Due to the lack of effective treatment options for 2019-nCoV, various strategies are being tested in China, including drug repurposing. In this study, we used our pretrained deep learning-based drug-target interaction model called Molecule Transformer-Drug Target Interaction (MT-DTI) to identify commercially available drugs that could act on viral proteins of 2019-nCoV. The result showed that atazanavir, an antiretroviral medication used to treat and prevent the human immunodeficiency virus (HIV), is the best chemical compound, showing a inhibitory potency with Kd of 94.94 nM against the 2019-nCoV 3C-like proteinase, followed by efavirenz (199.17 nM), ritonavir (204.05 nM), and dolutegravir (336.91 nM). Interestingly, lopinavir, ritonavir, and darunavir are all designed to target viral proteinases. However, in our prediction, they may also bind to the replication complex components of 2019-nCoV with an inhibitory potency with Kd < 1000 nM. In addition, we also found that several antiviral agents, such as Kaletra, could be used for the treatment of 2019-nCoV, although there is no real-world evidence supporting the prediction. Overall, we suggest that the list of antiviral drugs identified by the MT-DTI model should be considered, when establishing effective treatment strategies for 2019-nCoV.Keywords
This publication has 12 references indexed in Scilit:
- Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected PneumoniaNew England Journal of Medicine, 2020
- An end-to-end deep learning architecture for extracting protein–protein interactions affected by genetic mutationsDatabase: The Journal of Biological Databases and Curation, 2018
- Human Coronaviruses: A Review of Virus–Host InteractionsDiseases, 2016
- Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi ArabiaNew England Journal of Medicine, 2012
- Coronavirus PathogenesisAdvances in Virus Research, 2011
- Coronavirus Genomics and Bioinformatics AnalysisViruses, 2010
- Coronavirus avian infectious bronchitis virusVeterinary Research, 2007
- BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinitiesNucleic Acids Research, 2006
- Global mapping of pharmacological spaceNature Biotechnology, 2006
- Newly discovered coronavirus as the primary cause of severe acute respiratory syndromeThe Lancet, 2003