Screening of Antitubercular Compound Library Identifies Inhibitors of Mur Enzymes in Mycobacterium tuberculosis

Abstract

The rapid rise in the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains of Mycobacterium tuberculosis (Mtb) mandates the discovery of novel tuberculosis (TB) drugs. Mur enzymes, which are identified as essential proteins in Mtb and catalyze the cytoplasmic steps in the peptidoglycan biosynthetic pathway, are considered potential drug targets. However, none of the clinical drugs have yet been developed against these enzymes. Hence, the aim of this study was to identify novel inhibitors of Mur enzymes in Mycobacterium tuberculosis. We screened an antitubercular compound library of 684 compounds, using MurB and MurE enzymes of the Mtb Mur pathway as drug targets. For experimental validation, the top hits obtained on in silico screening were screened in vitro, using Mtb Mur enzyme-specific assays. In all, seven compounds were found to show greater than 50% inhibition, with the highest inhibition observed at 77%, and the IC50 for these compounds was found to be in the range of 28–50 μM. Compound 5175112 showed the lowest IC50 (28.69 ± 1.17 μM), and on the basis of (1) the binding affinity, (2) the stability of interaction noted on molecular dynamics simulation, and (3) an in vitro assay, MurE appeared to be its target enzyme. We believe that the overall strategy followed in this study and the results obtained are a good starting point for developing Mur enzyme-specific Mtb inhibitors.

Recent Progress in the Development of Novel Mycobacterium Cell Wall Inhibitor to Combat Drug-Resistant Tuberculosis

“…The whole Mur enzymes are crucial for cell integrity and unique to prokaryotes that make these enzymes the most promising target to develop a new drug. 51 , 52 In Gram-negative bacteria, fosfomycin inhibits the MurA enzyme, but mycobacterial MurA has no active site for fosfomycin attachment. Fosfomycin analogs that can inhibit MTB MurA are the most promising to develop a new drug.…”

Prospects for Antibacterial Discovery and Development

“…While inhibitors against these enzymes have undoubtedly been reported, ,, none have yielded medicinally viable leads. This paucity of druglike leads cannot be blamed on a lack of structural insight or assay capabilities. − In fact, a compelling case can be made for MurC–F being universal benchmarks for innovative in silico or in vitro library technologies that purport to spawn medicinal leads, with pathway assays as a possible tool for facilitating the discovery of such leads. In advance of a future bacterial pandemic, imagine how drug hunters would be empowered by a panel of selective inhibitors of these amide synthetases with excellent in vitro and in vivo potency, good safety and ADME characteristics, and compatibility with automated synthesis methods!…”

“…102 It demonstrates efficacy in Gram-negative and Grampositive bacteria such as MRSA, N. gonorrheae, and A. baumannii with no sign of resistance. 101 Similarly, while the use of rifampin ( 39) is limited to combination therapies due to the emergence of resistance against this antibiotic at appreciable frequency, TNP-2092 (40), combining the pharmacophores of RNA polymerase-targeting 39 with the DNA gyrase-targeting quinolizinone, maintains the potent activity of rifamycin against persistent pathogens and at the same time minimizes the development of rifamycin resistance. 103 Recently, a "tribrid" siderophore-cephalosporinoxazolidinone conjugate (41) was engineered; after internalization via siderophore-mediated uptake, the oxazolidinone is released by the bacteria's inherent β-lactamase activity.…”

Computational Target-Based Screening of Anti-MRSA Natural Products Reveals Potential Multitarget Mechanisms of Action through Peptidoglycan Synthesis Proteins

“…Peptidoglycan (PPC) is the primary component of the cell wall located outside the cytoplasmic membrane where they confer robustness and flexibility to the cell envelope. , The steps involved in the biosynthesis of peptidoglycan start with the production of UDP- N -acetylmuramyl-pentapeptide (UDPNAM-pentapeptide) and UDP- N -acetylglucosamine (UDP-NAG) through a series of sequential reactions catalyzed by the Mur ligases (MurA–MurF). Mur ligases are found in the cytoplasm of the bacteria cell, where they play their essential catalytic roles . The second step is the membrane-associated phase, where UDP-GlcNAc is broken down to form UDP-MurNAc by the action of MraY and MurG.…”

“…Over the years, many antibiotics that have been developed for clinical use were designed as single-target drugs. Common examples of these agents include antibacterial like rifampicin, fosfomycin, trimethoprim, sulfonamides, fusidic acid, and popular anticancer agents like carboplatin, adriamycin, and fluorouracil. , Interestingly, this ‘‘one-drug, one-target’’ paradigm has been widely accepted because of its high specificity and fewer off-target side effects, which might result in adverse effects. ,, However, recent developments in drug discovery have shown the limitations of drugs designed with this approach, especially their tendency to promote drug resistance and inability to effectively treat complex diseases and multi-drug-resistant bacterial infections. A recent study on the trend of drug research and development has revealed that multitarget tyrosine kinase inhibitor, imatinib, has a greater anticancer effect than gefitinib which is active against a single target .…”