Identifying RO9021 as a Potential Inhibitor of PknG fromMycobacterium tuberculosis: Combinative Computational and In Vitro Studies

Abstract

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis ( Mtb ). Despite being considered curable and preventable, the increase of antibiotic resistance is becoming a serious public health problem. Mtb is a pathogen capable of surviving in macrophages, causing long-term latent infection where the mycobacterial serine/threonine protein kinase G (PknG) plays a protective role. Therefore, PknG is an important inhibitory target to prevent Mtb from entering the latency stage. In this study, we use a pharmacophore-based virtual screening and biochemical assays to identify the compound RO9021 (CHEMBL3237561) as a PknG inhibitor. In detail, 1.5 million molecules were screened using a scalable cloud-based setup, identifying 689 candidates, which were further subjected to additional screening employing molecular docking. Molecular docking spotted 62 compounds with estimated binding affinities of −7.54 kcal/mol (s.d. = 0.77 kcal/mol). Finally, 14 compounds were selected for in vitro experiments considering previously reported biological activities and commercial availability. In vitro assays of PknG activity showed that RO9021 inhibits the kinase activity similarly to AX20017, a known inhibitor. The inhibitory effect was found to be dose dependent with a relative IC 50 value of 4.4 ± 1.1 μM. Molecular dynamics simulations predicted that the PknG-RO9021 complex is stable along the tested timescale. Altogether, our study indicates that RO9021 is a noteworthy drug candidate for further developing new anti-TB drugs that hold excellent reported pharmacokinetic parameters.

Nitrogen metabolism in mycobacteria: the key genes and targeted antimicrobials

“…To improve the affinity, selectivity and potency of AX20017, the cyclopropyl ring which does not exploit binding capacity fully may be an alternative modification site. In recent years, although some studies have found RO9021 and a few flavonoids by computer virtual screening and simulation docking, no subsequent experiments based on cells or animals have been found ( Qasaymeh et al, 2019 ; Arica-Sosa et al, 2022 ), so its effectiveness still needs to be verified and it is still far from clinical use. It is worth nothing that targeting PknG can also cause the growth inhibition of M. bovis , which has been proven through several independent reports ( Singh et al, 2015 ; Kanehiro et al, 2018 ; Kidwai et al, 2019 ).…”