AUTHOR=Chen Yun-Ti , Chang Yu-Hsiu , Pathak Nikhil , Tzou Shey-Cherng , Luo Yong-Chun , Hsu Yen-Chao , Li Tian-Neng , Lee Jung-Yu , Chen Yi-Cyun , Huang Yu-Wei , Yang Hsin-Ju , Hsu Nung-Yu , Tsai Hui-Ping , Chang Tein-Yao , Hsu Shu-Chen , Liu Ping-Cheng , Chin Yuan-Fan , Lin Wen-Chin , Yang Chuen-Mi , Wu Hsueh-Ling , Lee Chia-Ying , Hsu Hui-Ling , Liu Yi-Chun , Chu Jhih-Wei , Wang Lily Hui-Ching , Wang Jann-Yuan , Huang Chih-Heng , Lin Chi-Hung , Hsieh Po-Shiuan , Wu Lee Yan-Hwa , Hung Yi-Jen , Yang Jinn-Moon TITLE=Methotrexate inhibition of SARS-CoV-2 entry, infection and inflammation revealed by bioinformatics approach and a hamster model JOURNAL=Frontiers in Immunology VOLUME=13 YEAR=2022 URL=https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2022.1080897 DOI=10.3389/fimmu.2022.1080897 ISSN=1664-3224 ABSTRACT=Background

Drug repurposing is a fast and effective way to develop drugs for an emerging disease such as COVID-19. The main challenges of effective drug repurposing are the discoveries of the right therapeutic targets and the right drugs for combating the disease.

Methods

Here, we present a systematic repurposing approach, combining Homopharma and hierarchal systems biology networks (HiSBiN), to predict 327 therapeutic targets and 21,233 drug-target interactions of 1,592 FDA drugs for COVID-19. Among these multi-target drugs, eight candidates (along with pimozide and valsartan) were tested and methotrexate was identified to affect 14 therapeutic targets suppressing SARS-CoV-2 entry, viral replication, and COVID-19 pathologies. Through the use of in vitro (EC50 = 0.4 μM) and in vivo models, we show that methotrexate is able to inhibit COVID-19 via multiple mechanisms.

Results

Our in vitro studies illustrate that methotrexate can suppress SARS-CoV-2 entry and replication by targeting furin and DHFR of the host, respectively. Additionally, methotrexate inhibits all four SARS-CoV-2 variants of concern. In a Syrian hamster model for COVID-19, methotrexate reduced virus replication, inflammation in the infected lungs. By analysis of transcriptomic analysis of collected samples from hamster lung, we uncovered that neutrophil infiltration and the pathways of innate immune response, adaptive immune response and thrombosis are modulated in the treated animals.

Conclusions

We demonstrate that this systematic repurposing approach is potentially useful to identify pharmaceutical targets, multi-target drugs and regulated pathways for a complex disease. Our findings indicate that methotrexate is established as a promising drug against SARS-CoV-2 variants and can be used to treat lung damage and inflammation in COVID-19, warranting future evaluation in clinical trials.