A novel compound active against SARS-CoV-2 targeting uridylate-specific endoribonuclease (NendoU/NSP15): in silico and in vitro investigations

Sumit Kumar; Yash Gupta; Samantha E Zak; Charu Upadhyay; Neha Sharma; Andrew S Herbert; Ravi Durvasula; Vladimir Potemkin; John M Dye; Poonam; Prakasha Kempaiah; Brijesh Rathi

doi:10.1039/d1md00202c

A novel compound active against SARS-CoV-2 targeting uridylate-specific endoribonuclease (NendoU/NSP15): in silico and in vitro investigations

RSC Med Chem. 2021 Aug 18;12(10):1757-1764. doi: 10.1039/d1md00202c. eCollection 2021 Oct 20.

Authors

Sumit Kumar¹, Yash Gupta², Samantha E Zak^{3

4}, Charu Upadhyay¹, Neha Sharma⁵, Andrew S Herbert³, Ravi Durvasula², Vladimir Potemkin⁶, John M Dye^{3

4}, Poonam¹, Prakasha Kempaiah², Brijesh Rathi^{5

6}

Affiliations

¹ Department of Chemistry, Miranda House, University of Delhi Delhi India poonam.chemistry@mirandahouse.ac.in.
² Division of Infectious Diseases Mayo Clinic, Jacksonville Florida USA Kempaiah.Prakasha@mayo.edu.
³ United States Army Medical Research Institute of Infectious Diseases Fort Detrick MD USA.
⁴ The Geneva Foundation 917 Pacific Avenue Tacoma WA USA.
⁵ Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi India brijeshrathi@hrc.du.ac.in.
⁶ South Ural State University, Laboratory of Computational Modelling of Drugs 454080 Russia.

Abstract

NendoU (NSP15) is an Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond. Our in-house library was subjected to high throughput virtual screening (HTVS) to identify compounds with potential to inhibit NendoU enzyme, high-rank compounds (those that bound to multiple target structures) were further subjected to 100 nanoseconds MD simulations. Among these, one was found to be bound highly stable within the active site of the NendoU protein structure. Here, we are reporting a derivative of piperazine based '(2S,3S)-3-amino-1-(4-(4-(tert-butyl)benzyl)piperazin-1-yl)-4-phenylbutan-2-ol' (IV) from our in-house libraries having potential efficacy against SARS-CoV-2 in in vitro assays. This compound demonstrated inhibition of viral replication at the same level as Ivermectin, a known SARS-CoV-2 inhibitor, which is not used due to its toxicity at a higher than the currently approved dosage. Compound IV was not toxic to the cell lines up to a 50 μM concentration and exhibited IC_50s of 4.97 μM and 8.46 μM in viral entry and spread assay, respectively. Therefore, this novel class of NendoU inhibitor could provide new insights for the development of treatment options for COVID-19.