Identifying RO9021 as a Potential Inhibitor of PknG from<i>Mycobacterium tuberculosis</i>: Combinative Computational and In Vitro Studies

Abstract

Tuberculosis (TB) is an infectious disease caused by <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>). Despite being considered curable and preventable, the increase of antibiotic resistance is becoming a serious public health problem. <i>Mtb</i> 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 <i>Mtb</i> 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 <i>in vitro</i> experiments considering previously reported biological activities and commercial availability. <i>In vitro</i> 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 IC₅₀ 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.