In-silico analysis of Clp protease catalytic subunit-2 of Mycobacterium tuberculosis: Modeling and docking analysis

Tuberculosis (TB) is global. The World Health Organization (WHO) estimates that one third of the world's population is infected with Mtb and India accounts for one-fifth of the global TB incident cases. With the emergence of Multi Drug Resistance (MDR), Extreme Drug Resistance (XDR) and Total drug resistance (TDR), the need for identification of novel targets and inhibitors has become necessary to control TB pandemic. The proteases belong to the class of druggable enzymes and have already been validated as therapeutic targets in the treatment of HIV, hepatitis, and cancer. ClpP1P2 protease is very recently proved to be essential for growth and infection of Mycobacterium tuberculosis (Mtb) and thus makes it an attractive target for drug development. However, ClpP2 was reported earlier as one of the genes essential for growth of Mtb and the crystal structure of it is unavailable yet, We had modeled ClpP2 protease of the Mtb using crystal structure of Clp protease of E. coli (1TYF-PDB ID). The computed model's energy was minimized and validated using PROCHECK, ProSA, Verify 3D and ERRAT to obtain a stable model structure. Stable model was further investigated for the binding affinity of drugs already in use, phytoconstituents, and with compounds of zinc database using GLIDE of Virtual screening workflow of Schrödinger Suite 2012. The docked complexes were validated based on GLIDE score. Our investigation indicates that ClpP2 inhibition could be the mechanism of action of already available drugs, and interestingly, it was observed that phytoconstituents like Luteolin-7-O-glucoside, Quercetin, Aloe emodin, Naphthoquinone and Xanthone showed binding energy comparable to the second line and advanced drugs, which we believe is an important outcome as most of the second line drugs have acute toxicity. We have also performed virtual screening using ligands from zinc database and identified that amides are the most potent inhibitors of ClpP2 protease of Mycobacterium tuberculosis. Despite their potential importance in the survival and virulence of Mtb, to our knowledge, functional studies of these peptidases have not yet been reported. To our knowledge this work on structural modelling of ClpP2 of Mycobacterium is unique bringing out information on possible inhibitors of ClpP2 protease to combat Mycobacterium tuberculosis.