The Emerging Landscape of Tubercular Targets: A Medicinal Chemistry Approach

Mi Kim Y., Park Y., Soon Son E., Lee A., Bang S., Eun Ahn J., Cui L., Kim K., Seong Yang J., Park S., Kang M., Ji Jeong M., Whang J., Seok Lee J., Choi I.

We present the development of a phenyl oxazole methyl (POM) core structure with spirocyclic derivatives as part of our efforts to discover innovative anti-tuberculosis agents. Derivatives of spirocyclic POM were synthesized and evaluated for their inhibitory effects on M.tuberculosis (M. tb) H37Rv. Notably, compound 5c displayed potent anti-tubercular activity with MIC value of 0.206 μM in culture broth medium. Furthermore MIC values of compound 5c against DS/MDR/pre-XDR clinical isolates ranged from 0.34 to 0.68 μg/mL, 0.17 to 0.68 μg/mL, and 0.17 to 0.34 μg/mL, respectively. Also, compound 5c with favorable ADME and PK properties was not cytotoxic to THP-1 human cells. Based on the spontaneous mutant generation, we have identified the target of compound 5c to be MmpL3. The computational docking study suggested its plausible binding mode against MmpL3. There is no approved drug targeting this target yet, and the outcomes of the presented research will contribute to the future discovery of novel anti-tuberculosis drugs.

Bakchi B., Maddipatla S., Gottemukkala S., Raut S., Naiyaz Ahmad M., Imran M., Saxena D., Maitra R., Kumari Agnivesh P., Pal Kalia N., Nanduri S., Dasgupta A., Chopra S., Madhavi Yaddanapudi V.

AbstractOwing to the emergence of multi‐drug resistant tuberculosis, there is a need for the exploration of new antitubercular agents. In this context, new coumarin‐based 1,2,3‐triazole hybrids were developed and evaluated for their antimicrobial activity against ESKAPE pathogens and the Mtb H37Rv strain. Among them, compounds 9 c and 12 showed MICs of 1 and 2 μg/mL, respectively, against the Mtb strain. The lead compounds exhibited a good selectivity index against Vero cells and were equally effective against ETB‐resistant and RIF‐resistant Mtb strains. Time‐kill kinetic studies revealed the bacteriostatic properties of the lead compounds, while combination studies using FDA‐approved antibiotics showed no drug interactions. Based on the structural similarity, it was envisaged that they might inhibit the DNA gyrase, which was further proved by the DNA supercoiling inhibition assay. Additionally, in silico docking studies, binding energy calculations, and ADME/T studies for the synthesized conjugates showed favourable pharmacokinetic and physicochemical characteristics. Hence, these molecules could further pave the way for discovering new potent antitubercular agents to combat AMR.

Gedeon A., Yab E., Dinut A., Sadowski E., Capton E., Dreneau A., Petit J., Gioia B., Piveteau C., Djaout K., Lecat E., Wehenkel A.M., Gubellini F., Mechaly A., Alzari P.M., et. al.

Al-Warhi T., Sabt A., Korycka-Machala M., Kassem A.F., Shaldam M.A., Ibrahim H.A., Kawka M., Dziadek B., Kuzioła M., Eldehna W.M., Dziadek J.

Because resistant variants of the disease are always emerging, tuberculosis is a global issue that affects economies.

Mohamed-Ezzat R.A., Omar M.A., Temirak A., Abdelsamie A.S., Abdel-Aziz M.M., Galal S.A., Elgemeie G.H., Diwani H.I., Flanagan K.J., Senge M.O.

Tuberculosis (TB) is a global pandemic killing millions of people every year. Yet, resistant strains make curing TB quite challenging. Herein, a series of new pyrazole-linked benzothiazole hybrids was synthesized and evaluated for their anti-TB activity against three Mycobacterium tuberculosis strains (drug sensitive (DS), multidrug-resistant (MDR) and extensively drug-resistant (XDR)). The substituted 2,5-dimethylphenoxy -, 2,6-dichlorophenoxy -, 2,6-dimethoxyphenoxy -, 4-methylpiperazin-1-yl-,and pyrrolidin-1-ylpyrazole-benzothiazole conjugates (compounds 10j, 10k,10l, 11cand 12 respectively) displayed promising anti-TB activity in comparison to the reference compound isoniazid against the DS strain with (MIC: 1.74-3.68μM/mL)To further study the mode of action of these anti-TB compounds, their inhibition of the Mycobacterium tuberculosisenoyl-acyl carrier protein reductase enzyme (InhA) was tested. The 3-acetamidophenoxy-, 2,6-dichlorophenoxy -,andpyrrolidin-1-ylpyrazole-benzothiazole conjugates(Compounds 10i, 10j and 12 respectively) showed strong inhibition of InhA in comparison to the reference compound, triclosan, with IC50 values of 6.4-7.9 μM. Moreover, a molecular docking study was carried out to investigate the predicted binding interactions of the synthesized inhA inhibitors in the binding pocket of the inhA enzyme. The calculated docking energies of the developed novel pyrazole-linked benzothiazole hybrids were consistent with their tested anti-tubercular activity.

Sabt A., Abdulla M., Ebaid M.S., Pawełczyk J., Abd El Salam H.A., Son N.T., Ha N.X., Vaali Mohammed M., Traiki T., Elsawi A.E., Dziadek B., Dziadek J., Eldehna W.M.

The spread of drug-resistant tuberculosis strains has become a significant economic burden globally. To tackle this challenge, there is a need to develop new drugs that target specific mycobacterial enzymes. Among these enzymes, InhA, which is crucial for the survival of Mycobacterium tuberculosis, is a key target for drug development. Herein, 24 compounds were synthesized by merging 4-carboxyquinoline with triazole motifs. These molecules were then tested for their effectiveness against different strains of tuberculosis, including M. bovis BCG, M. tuberculosis, and M. abscessus. Additionally, their ability to inhibit the InhA enzyme was also evaluated. Several molecules showed potential as inhibitors of M. tuberculosis. Compound 5n displayed the highest efficacy with a MIC value of 12.5 μg/mL. Compounds 5g, 5i, and 5n exhibited inhibitory effects on InhA. Notably, 5n showed significant activity compared to the reference drug Isoniazid. Molecular docking analysis revealed interactions between these molecules and their target enzyme. Additionally, the molecular dynamic simulations confirmed the stability of the complexes formed by quinoline-triazole conjugate 5n with the InhA. Finally, 5n underwent in silico analysis to predict its ADME characteristics. These findings provide promising insights for developing novel small compounds that are safe and effective for the global fight against tuberculosis.

Mhetre U.V., Haval N.B., Bondle G.M., Rathod S.S., Choudhari P.B., Kumari J., Sriram D., Haval K.P.

In a quest to discover new antimalarial and antitubercular drugs, we have designed and synthesized a series of novel triazole–quinazolinone hybrids. The in vitro screening of the triazole–quinazolinone hybrid entities against the plasmodium species P. falciparum offered potent antimalarial molecules 6c, 6d, 6f, 6g, 6j & 6k owing comparable activity to the reference drugs. Furthermore, the target compounds were evaluated in vitro against Mycobacterium tuberculosis (MTB) H37Rv strain. Among the screened compounds, 6c, 6d and 6l were found to be the most active molecules with a MIC values of 19.57–40.68 μM. The cytotoxicity of the most active compounds was studied against RAW 264.7 cell line by MTT assay and no toxicity was observed. The computational study including drug likeness and ADMET profiling, DFT, and molecular docking study was done to explore the features of target molecules. The compounds 6a, 6g, and 6k exhibited highest binding affinity of −10.3 kcal/mol with docked molecular targets from M. tuberculosis. Molecular docking study indicates that all the molecules are binding to the falcipain 2 protease (PDB: 6SSZ) of the P. falciparum. Our findings indicated that these new triazole–quinazolinone hybrids may be considered hit molecules for further optimization studies.

Venugopala K.N., Chandrashekharappa S., Deb P.K., Al-Shar'i N.A., Pillay M., Tiwari P., Chopra D., Borah P., Tamhaev R., Mourey L., Lherbet C., Aldhubiab B.E., Tratrat C., Attimarad M., Nair A.B., et. al.

In the current study, two sets of compounds: (E)-1-(2-(4-substitutedphenyl)-2-oxoethyl)-4-((hydroxyimino)methyl)pyridinium derivatives (3a-3e); and (E)-3-(substitutedbenzoyl)-7-((hydroxyimino)methyl)-2-substitutedindolizine-1-carboxylate derivatives (5a-5j), were synthesized and biologically evaluated against two strains of Mycobacterial tuberculosis (ATCC 25177) and multi-drug resistant (MDR) strains. Further, they were also tested in vitro against the mycobacterial InhA enzyme. The in vitro results showed excellent inhibitory activities against both MTB strains and compounds 5a-5j were found to be more potent, and their MIC values ranged from 5 to 16 μg/mL and 16-64 μg/mL against the M. tuberculosis (ATCC 25177) and MDR-TB strains, respectively. Compound 5h with phenyl and 4-fluorobenzoyl groups attached to the 2- and 3-position of the indolizine core was found to be the most active against both strains with MIC values of 5 μg/mL and 16 μg/mL, respectively. On the other hand, the two sets of compounds showed weak to moderate inhibition of InhA enzyme activity that ranged from 5 to 17 % and 10-52 %, respectively, with compound 5f containing 4-fluoro benzoyl group attached to the 3-position of the indolizine core being the most active (52 % inhibition of InhA). Unfortunately, there was no clear correlation between the InhA inhibitory activity and MIC values of the tested compounds, indicating the probability that they might have different modes of action other than InhA inhibition. Therefore, a computational investigation was conducted by employing molecular docking to identify their putative drug target(s) and, consequently, understand their mechanism of action. A panel of 20 essential mycobacterial enzymes was investigated, of which β-ketoacyl acyl carrier protein synthase I (KasA) and pyridoxal-5'-phosphate (PLP)-dependent aminotransferase (BioA) enzymes were revealed as putative targets for compounds 3a-3e and 5a-5j, respectively. Moreover, in silico ADMET predictions showed adequate properties for these compounds, making them promising leads worthy of further optimization.

Pakamwong B., Thongdee P., Kamsri B., Phusi N., Taveepanich S., Chayajarus K., Kamsri P., Punkvang A., Hannongbua S., Sangswan J., Suttisintong K., Sureram S., Kittakoop P., Hongmanee P., Santanirand P., et. al.

Batran R.Z., Sabt A., Dziadek J., Kassem A.F.

New series of coumarin derivatives were synthesized as antitubercular agents targeting InhA enzyme with strong binding affinity within the active binding site.

Hoffmann P., Azéma-Despeyroux J., Goncalves F., Stamilla A., Saffon-Merceron N., Rodriguez F., Degiacomi G., Pasca M.R., Lherbet C.

Tuberculosis is a serious public health problem worldwide. The search for new antibiotics has become a priority, especially with the emergence of resistant strains. A new family of imidazoquinoline derivatives, structurally analogous to triazolophthalazines, which had previously shown good antituberculosis activity, were designed to inhibit InhA, an essential enzyme for Mycobacterium tuberculosis survival. Over twenty molecules were synthesized and the results showed modest inhibitory efficacy against the protein. Docking experiments were carried out to show how these molecules could interact with the protein’s substrate binding site. Disappointingly, unlike triazolophthlazines, these imidazoquinoline derivatives showed an absence of inhibition on mycobacterial growth.

Khan M.F., Ali A., Rehman H.M., Noor Khan S., Hammad H.M., Waseem M., Wu Y., Clark T.G., Jabbar A.

AbstractTuberculosis (TB), caused by Mycobacterium tuberculosis, ranks among the top causes of global human mortality, as reported by the World Health Organization’s 2022 TB report. The prevalence of M. tuberculosis strains that are multiple and extensive-drug resistant represents a significant barrier to TB eradication. Fortunately, having many completely sequenced M. tuberculosis genomes available has made it possible to investigate the species pangenome, conduct a pan-phylogenetic investigation, and find potential new drug targets. The 442 complete genome dataset was used to estimate the pangenome of M. tuberculosis. This study involved phylogenomic classification and in-depth analyses. Sequential filters were applied to the conserved core genome containing 2754 proteins. These filters assessed non-human homology, virulence, essentiality, physiochemical properties, and pathway analysis. Through these intensive filtering approaches, promising broad-spectrum therapeutic targets were identified. These targets were docked with FDA-approved compounds readily available on the ZINC database. Selected highly ranked ligands with inhibitory potential include dihydroergotamine and abiraterone acetate. The effectiveness of the ligands has been supported by molecular dynamics simulation of the ligand–protein complexes, instilling optimism that the identified lead compounds may serve as a robust basis for the development of safe and efficient drugs for TB treatment, subject to further lead optimization and subsequent experimental validation.

Ardiansah B., Farhan A., Firdaus A., Ariyani T., Arfin Fardiansyah Nasution M., Fadlan A., Herry Cahyana A., Endang Prabandari E., Carlos Menéndez J.

Khaleel E.F., Sabt A., Korycka-Machala M., Badi R.M., Son N.T., Ha N.X., Hamissa M.F., Elsawi A.E., Elkaeed E.B., Dziadek B., Eldehna W.M., Dziadek J.

Tuberculosis (TB) is a global issue that poses a significant economic burden as a result of the ongoing emergence of drug-resistant strains. The urgent requirement for the development of novel antitubercular drugs can be addressed by targeting specific enzymes. One such enzyme, Mycobacterium tuberculosis (MTB) enoyl-acyl carrier protein (enoyl-ACP) reductase (InhA), plays a crucial role in the survival of the MTB bacterium. In this research study, a series of hybrid compounds combining quinolone and isatin were synthesized and assessed for their effectiveness against MTB, as well as their ability to inhibit the activity of the InhA enzyme in this bacterium. Among the compounds tested, 7a and 5g exhibited the most potent inhibitory activity against MTB, with minimum inhibitory concentration (MIC) values of 55 and 62.5 µg/mL, respectively. These compounds were further evaluated for their inhibitory effects on InhA and demonstrated significant activity compared to the reference drug Isoniazid (INH), with IC50 values of 0.35 ± 0.01 and 1.56 ± 0.06 µM, respectively. Molecular docking studies investigated the interactions between compounds 7a and 5g and the target enzyme, revealing hydrophobic contacts with important amino acid residues in the active site. To further confirm the stability of the complexes formed by 5g and 7a with the target enzyme, molecular dynamic simulations were employed, which demonstrated that both compounds 7a and 5g undergo minor structural changes and remain nearly stable throughout the simulated process, as assessed through RMSD, RMSF, and Rg values.

Williams J.T., Giletto M., Haiderer E.R., Aleiwi B., Krieger-Burke T., Ellsworth E., Abramovitch R.B.

ABSTRACT Addressing drug resistance in Mycobacterium tuberculosis (Mtb) requires the development of new drugs with new targets. We previously identified 13 MmpL3 inhibitors from a screen of a small library of Mtb growth inhibitors. In this report, we describe the biological activities of a set of HC2099 analogs active against Mtb in vitro , intracellular Mtb, as well as M. abscessus and M. avium . Pharmacokinetic (PK) studies identified MSU-43085 as orally bioavailable with a short half-life. High dosing (100 mg/kg) saturates clearance processes, enabling efficacy studies. The results of an in vivo efficacy study found that MSU-43085 was active against Mtb in an acute murine TB infection model but lacked activity in a chronic murine TB infection model. The results of this study serve as a proof of concept for this series and support further optimizations of the HC2099 series of MmpL3 inhibitors. IMPORTANCE MmpL3 is a protein that is required for the survival of bacteria that cause tuberculosis (TB) and nontuberculous mycobacterial (NTM) infections. This report describes the discovery and characterization of a new small molecule, MSU-43085, that targets MmpL3 and is a potent inhibitor of Mycobacterium tuberculosis (Mtb) and M. abscessus survival. MSU-43085 is shown to be orally bioavailable and efficacious in an acute model of Mtb infection. However, the analog is inactive against Mtb in chronically infected mice. Pharmacokinetic and metabolite identification studies identified in vivo metabolism of MSU-43085, leading to a short half-life in treated mice. These proof-of-concept studies will guide further development of the MSU-43085 series for the treatment of TB or NTM infections.