Screening and Identification of Novel Small Molecule Inhibitors against <em>Mycobacterium tuberculosis</em> Dihydrodipicolinate Synthase Enzyme using <em>In Silico</em> and <em>In Vitro</em> Methods

Abstract

Emergence of multi drug resistant (MDR) and extensively drug resistant (XDR) Mycobacterium tuberculosis poses a serious threat to TB control as the available treatment options are less effective in these cases. Therefore, new strategies are required for identification of new drugs and drug targets. The M. tuberculosis dihydrodipicolinate synthase is a putative drug target with no potent inhibitor. Here in this study, we have used a comprehensive computational approach to identify small molecule inhibitors and validated them in vitro. As similar structures tend to have similar functions, therefore 3 approaches, namely, (a) known inhibitor-based approach, (b) substrate analogues, (c) product analogues were used for compound screening from various chemical libraries. The fourth approach we have taken is fragment library screening.In vitro studies revealed that &amp;beta;-hydroxypyruvic acid tartronic acid are inhibitors of Mtb-rDapA with maximum inhibition 48% and 51% at 500&amp;micro;M concentrations respectively. We have also observed that &amp;beta;-hydroxypyruvic acid is a time dependent inhibitor of Mtb-rDapA. Further, thermal shift assays showed that &amp;beta;-hydroxypyruvic acid interacts with Mtb-rDapA and the thermal stability of Mtb-rDapA shifted by 3˚C. Among the product analogues of Mtb-DapA, dipicolinic acid showed to bind to Mtb-rDapB shifting thermal stability of Mtb-rDapB by 0.5˚C in binding. Additionally, we have designed a new approach by combining substrate and product analogues to achieve better inhibitions. In vitro assays validated that this combination approach increased maximum inhibition up to 100%. We envision that these compounds would serve as potent leads for tuberculosis drug discovery.

Amino Acid Biosynthesis Inhibitors in Tuberculosis Drug Discovery

“…Meso-DAP is then converted to Lys by diaminopimelate decarboxylase (LysA), a pyridoxal 5′-phosphate (PLP)-dependent enzyme [ 106 ] ( Figure 20 ). The genes of this pathway are essential for Mtb growth, and some of them have already been investigated as targets for potential inhibitors [ 107 , 108 , 109 , 110 ]. The importance of dihydrodipicolinate reductase (DapB), encoded by dapB , has only been recently elucidated [ 104 ].…”