A covalent chemical probe for Chikungunya nsP2 cysteine protease with anti-alphaviral activity and proteome-wide selectivity
Neglected tropical diseases (NTDs) are a diverse group of infections and ailments that are commonly encountered in low- and middle-income countries that receive few resources and research attention relative to “The Big Three”: Malaria, HIV/AIDS and tuberculosis. NTDs are generally regarded as having low mortality rates, but high morbidity rates, after looking at disability-adjusted life years (DALYS) lost relative to The Big Three. So, despite having a comparable morbidity effect on the global population, NTDs don’t receive the attention that this deserves.
Viruses, bacteria, protozoa and parasites, even snake bite envenomation are examples of types of NTDs. Among these are alphaviruses, such as chikungunya virus (CHIKV), which causes chronic arthritis (the name chikungunya is derived from the term in Tanzanian dialect translated as “to walk bent over”) and displays similar epidemiology to Dengue fever, with which it also shares the same mosquito vector of transmission (Aedes Aegypti).
In this paper, researchers at the READDI (Rapidly Emerging Antiviral Drug Development Initiative) AViDD center, associated with UNC at Chapel Hill in the USA, presented their efforts at optimisation of their previously discovered CHIKV NSP2 protease inhibitor and antiviral compound: RA-0002034 (1). While 1 fulfilled many of their desires as a potent and selective CHIKV antiviral, it was found to be chemically unstable upon storage, with respect to intramolecular cyclisation to the inactive byproduct 2.
The NSP2 protease is a cysteine protease that is considered a premium target for this viral class, due to its essential role in polyprotein processing. There is no more direct a way to inhibit cysteine proteases than by forming a covalent bond with the active site cysteine. This was achieved with an unusual vinyl sulfone warhead. The remarkable thing in this work is how selective their discovered compound: 3 is for the target over host/virus proteases and other proteins. The authors postulate that while terminal vinyl sulfones are not typically seen due to high reactivity and promiscuity, internal vinyl sulfones such as 3 have uniquely different electrophilicity, explaining their presence in other compounds of clinical interest, such as: K777, VVD-133214 and rigosertib. The presented profile makes 3 a very useful chemical probe for understanding the virology of CHIKV. Interestingly, Isopropylation of the nitrogen β to the vinyl sulfone electrophilic carbon (4) rendered the compound completely inactive against CHIKV NSP2 protease and also CHIKV infection in-vitro. This provided a chemically and structurally similar control compound, complementing the high potency of 3.