Pyrimidone inhibitors targeting Chikungunya Virus nsP3 macrodomain by fragment-based drug design.

Sixue Zhang,Lynn Rasmussen,Mousheng Wu,Robert Bostwick,Corinne E Augelli-Szafran,Ashish K Pathak,Daniel N Streblow,Atefeh Garzan,Mark T Haise,Nicole Haese,Yohanka Martinez-Gzegozewska,A Ganesan

doi:10.1371/journal.pone.0245013

Abstract

The macrodomain of nsP3 (nsP3MD) is highly conserved among the alphaviruses and ADP-ribosylhydrolase activity of Chikungunya Virus (CHIKV) nsP3MD is critical for CHIKV viral replication and virulence. No small molecule drugs targeting CHIKV nsP3 have been identified to date. Here we report small fragments that bind to nsP3MD which were discovered by virtually screening a fragment library and X-ray crystallography. These identified fragments share a similar scaffold, 2-pyrimidone-4-carboxylic acid, and are specifically bound to the ADP-ribose binding site of nsP3MD. Among the fragments, 2-oxo-5,6-benzopyrimidine-4-carboxylic acid showed anti-CHIKV activity with an IC50 of 23 μM. Our fragment-based drug discovery approach provides valuable information to further develop a specific and potent nsP3 inhibitor of CHIKV viral replication based on the 2-pyrimidone-4-carboxylic acid scaffold. In silico studies suggest this pyrimidone scaffold could also bind to the macrodomains of other alphaviruses and coronaviruses and thus, have potential pan-antiviral activity.

Highlights

Chikungunya Virus (CHIKV) is a re-emerging virus that is primarily transmitted by mosquitoes [1,2]
Optimization of crystal soaking for nsP3 macrodomain (nsP3MD) crystals nsP3MD crystals were found to be very robust and stable in different conditions during the crystallization, suggesting that nsP3MD crystals are suitable for fragment-based screening using crystal soaking
We were focusing on identifying fragments which can bind to the ADP-ribose binding site since studies have shown that the binding site is very critical for CHIKV viral replication [28]

Summary

Introduction

Chikungunya Virus (CHIKV) is a re-emerging virus that is primarily transmitted by mosquitoes [1,2]. CHIKV belongs to the Alphavirus genus of the Togaviridae family which includes the “old world” and “new world” alphaviruses. The “old world” alphaviruses, including CHIKV, Sindbis Virus (SINV), Semliki Forest Virus (SFV) and O’nyong nyong virus (ONNV), usually cause fever, rashes and arthritis. The “new world” alphaviruses, including Venezuelan Equine Encephalitis Virus (VEEV) and Eastern Equine Encephalitis Virus (EEEV), tend to cause encephalitis [3,4,5]. The outbreaks of CHIKV infection spread from mainly tropical regions in Africa and Asia to other countries in Europe and the Americas [6,7,8].

Methods

Results

Conclusion