Reductase InhA Research Articles

Crystal structures, DFT calculations and Hirshfeld surface analysis of two (E)-3-(aryl)-1-(naphthalen-1-yl)prop-2-en-1-one chalcone derivatives, potential Mycobacterium tuberculosis Enoyl ACP reductase (InhA) inhibitors and optical materials: conformational differences within the prop-2-en-1-one unit

A combined structural and computational study has been conducted on two chalcone compounds, namely (E)-3-(4-bromophenyl)-1-(4,8-dimethoxynaphthalen-1-yl)prop-2-en-1-one (1), and (E)-3-(3,4-dichlorophenyl)-1-(4,8-dimethoxynaphthalen-1-yl)prop-2-en-1-one (2). These compounds are members of a series of compounds identified from a molecular modelling study as potentially active Mycobacterium tuberculosis Enoyl ACP reductase (InhA) inhibitors. In addition, the computational study indicated that the compounds have potential as optical materials.The combined study revealed that both molecules in the solid state displayed similar overall molecular conformations between a ‘‘T’’ and a ‘‘Y’’ shape, but with different arrangements in the bridging prop-2-en-1-one unit: an anti-periplanar in 1 and a syn-periplanar in 2. The experimental and calculated bond lengths and angles for anti-periplanar1 and syn-periplanar2 were generally in good agreement.Theoretical calculations at the B3LYP/DGTZVP level in the gas phase, DMSO and water media indicated that for both compounds, the syn-periplanar form was the energy local minimum while the anti-periplanar form was the energy global minimum. However, the energy differences are very small, with slight variations when using the different basis sets (0.80 and 0.84 kcal/mol using the B3LYP/DGTVP theory level in gas phase, 0.28 and 0.32 in DMSO and 0.27 and 0.31 kcal/mol in water). The differences in the solid state arrangements within the bridging prop-2-en-1-one unit in 1 and 2 arise from variations in the intermolecular interactions, with halogen bonds being considered to be an important factor in stabilizing a syn-periplanar arrangement in compound 2. PLATON and Hirshfeld surface analyses confirmed the important intermolecular interactions in 1 and 2.Calculations were also carried out on the electronic and vibrational spectra, dipole moments and charge distributions of 1 and 2. The HOMO was located in the dimethoxynaphthalenyl region of the molecule with mild donor character, while the LUMO was located in the propenyl and phenyl regions of each molecule. The energy gaps between these orbitals are 3.35 eV for 1 3.25 eV for 2. The delocalization present in compounds 1 and 2 facilitates the HOMO-LUMO charge transfer process.The total electronic molecular dipolar moments (μTotal) were calculated to be 4.1511 and 5.9316 D for 1 and 2, respectively. The values of μTotal found for 1 and 2 are both larger than reported values for similar compounds, indicating that the compounds studied here should exhibit a good non-linear optical response.

Docking-Based Virtual Screening and Molecular Dynamics Simulations of Quercetin Analogs as Enoyl-Acyl Carrier Protein Reductase (InhA) Inhibitors of Mycobacterium tuberculosis

The emergence of multidrug-resistant Mycobacterium tuberculosis (MTB) has become a major problem in treating tuberculosis (TB) and shows the need to develop new and efficient drugs for better TB control. This study aimed to use in silico techniques to discover potential inhibitors to the Enoyl-[acyl-carrier-protein] reductase (InhA), which controls mycobacterial cell wall construction. Initially, 391 quercetin analogs present in the KNApSAck_3D database were selected, filters were sequentially applied by docking-based virtual screening. After recategorizing the variables (bond energy prediction and molecular interaction, including hydrogen bond and hydrophobic bond), compounds C00013874, C00006532, and C00013887 were selected as hit ligands. These compounds showed great hydrophobic contributions, and for each hit ligand, 100 ns of molecular dynamic simulations were performed, and the binding free energy was calculated. C00013874 demonstrated the greatest capacity for the InhA enzyme inhibition with ΔGbind = −148.651 kcal/mol compare to NAD (native ligand) presented a ΔGbind = −87.570 kcal/mol. These data are preliminary studies and might be a suitable candidate for further experimental analysis.

Docking and molecular dynamic study of isoniazid derivatives as anti-tuberculosis drug candidate

In this research, we have designed four isoniazid derivatives, i.e., isonicotinohydrazide (1-isonicotinoyl semicarbazide, 1-thiosemi isonicotinoyl carbazide, N '-(1, 3-dimethyl-1 h-pyrazole-5-carbonyl) isonicotino hydrazide, and N '-(1,2,3- 4-thiadiazole-carbonyl) isonicotinohydrazide. The docking and molecular dynamic have performed to them to study its interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (InhA). Based on this research, all of the compounds were predicted to have a stable interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (InhA) receptor so that they could be used as an anti-tuberculosis drug candidate

Anti-tubercular activity and molecular docking studies of indolizine derivatives targeting mycobacterial InhA enzyme

A series of 1,2,3-trisubstituted indolizines (2a–2f, 3a–3d, and 4a–4c) were screened for in vitro whole-cell anti-tubercular activity against the susceptible H37Rv and multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) strains. Compounds 2b–2d, 3a–3d, and 4a–4c were active against the H37Rv-MTB strain with minimum inhibitory concentration (MIC) ranging from 4 to 32 µg/mL, whereas the indolizines 4a–4c, with ethyl ester group at the 4-position of the benzoyl ring also exhibited anti-MDR-MTB activity (MIC = 16–64 µg/mL). In silico docking study revealed the enoyl-acyl carrier protein reductase (InhA) and anthranilate phosphoribosyltransferase as potential molecular targets for the indolizines. The X-ray diffraction analysis of the compound 4b was also carried out. Further, a safety study (in silico and in vitro) demonstrated no toxicity for these compounds. Thus, the indolizines warrant further development and may represent a novel promising class of InhA inhibitors and multi-targeting agents to combat drug-sensitive and drug-resistant MTB strains.

Antibacterial Components of Levisticum officinale Koch against Multidrug-resistant Mycobacterium tuberculosis

Background: A bioassay-guided fractionation technique was used to evaluate the active constituents of the perennial plant L. officinale W.D.J. Koch (Apiaceae) against multidrug resistant (MDR) Mycobacterium tuberculosis. Methods: Column chromatography was used to isolation of compounds from L. officinale and spectroscopic methods including 1D and 2D NMR (Nuclear magnetic resonance) and HRMS (high resolution mass spectrometry) were used to identification of the isolated compounds. Also, to evaluate antibacterial activity, minimum inhibitory concentration (MIC) was carried out by broth micro-dilution method. Finally, molecular docking (MD) was performed using the Schrödinger package to evaluate interactions between the active compounds and InhA protein. Results: Phytochemical analysis of the ethyl acetate extract of the plant roots led to isolation of bergapten (1), isogosferol (2), oxypeucedanin (3), oxypeucedanin hydrate (4), imperatorin (5), ferulic acid (6) and falcarindiol (7). Falcarindiol and oxypeucedanin indicated a moderate activity on MDR M. tuberculosis with MIC values of = 32 and 64 μg/mL, respectively. Antibacterial activity of falcarindiol was also observed against S. aureus and methicillin-resistant S. aureus strains with the MIC values of 7.8 and 15.6 μg/mL, respectively. The results of docking analysis showed a good affinity of oxypeucedanin (3) and falcarindiol (7) to InhA enzyme with docking score values of -7.764 and -7.703 kcal/mol, respectively. Conclusion: Finally, 7 compounds were isolated from L. officinale that compounds 2-6 report for the first time from this plant. On the basis of the molecular docking (MD) study, oxypeucedanin (3) and falcarindiol (7) as active compounds against M. tuberculosis may be proposed as potential inhibitors of 2-trans-enoyl-ACP reductase (InhA), a key enzyme involved in the biosynthesis of the mycobacterial cell wall. Moreover, antibacterial activity of falcarindiol against methicillin-resistant S. aureus (MRSA) was remarkable.

Targeting Mycobacterium Tuberculosis Enoyl-Acyl Carrier Protein Reductase Using Computational Tools for Identification of Potential Inhibitor and their Biological Activity.

Enoyl-acyl carrier protein reductase (InhA) of type II fatty acid synthase system is involved in the synthesis of mycolic acids which is a major component of the bacterial cell wall. Since they are the key enzymes playing a very significant role in the FASII pathway of the bacterium. In this study, we have developed a workflow for identification of InhA inhibitors by utilizing in silico virtual screening approaches based on various machine learning algorithms followed by pharmacophore based virtual screening. The hits screened from the models were further subjected to molecular docking. Further, based on the XP docking score best twenty compounds were subjected to molecular dynamics study. Finally, nine compounds were shortlisted on the basis of best stable ligand RMSD, c-alpha RMSD, and RMSF plot for biological evaluation studies. Experimental validation of the shortlisted compounds identified one compound JFD01724 having potent inhibitory activity and was able to inhibit the growth of mycobacterium tuberculosis. Further medicinal chemistry efforts may help to improve the inhibitory potency of the identified compound.

Amide-Linked Monocarbonyl Curcumin Analogues: Efficient Synthesis, Antitubercular Activity and Molecular Docking Study

An approach toward the synthesis of novel conjugates of 3,5-bis (arylidene)-4-piperidones (DAP) pharmacophore with amide-linkage has been developed via one-pot multicomponent reaction of aryl aldehydes, piperidinone and 2-chloro-N-phenylacetamide using [Et3NH][HSO4] as a catalyst/medium. Both substitutions on arylidene rings and piperidinone nitrogen (substituted 2-chloro-N-phenylacetamide) were varied. The synthesized conjugates were evaluated for their in vitro antitubercular activity against M. tuberculosis H37Ra (MTB) and M. bovis BCG strains. Among the series, compounds 4f, 4g, 4i and 4j showed remarkable broad spectrum antitubercular activity with low IC50 values. Furthermore, computer docking simulations, for the most active conjugates were performed with the active site of mycobacterial enoyl-acyl carrier protein reductase (InhA) support the antitubercular activity. Lower cytotoxicity, high potency and promising activity against MTB and M. Bovis BCG suggest that amide linked DAP could serve as good leads for further modifications and development.

4-Aryl-1,4-Dihydropyridines as Potential Enoyl-Acyl Carrier Protein Reductase Inhibitors: Antitubercular Activity and Molecular Docking Study.

Tuberculosis remains one of the most deadly infectious diseases worldwide due to the emergence of multi-drug resistance (MDR) and extensively drug resistance (XDR) strains of Mycobacterium tuberculosis (MTB). Currently, available drugs are getting resistant and toxic. Hence, there is an urgent need for the development of potent molecules to treat tuberculosis. Herein, the screening of a total of eight symmetrical 1,4-dihydropyridine (1,4- DHP) derivatives (4a-4h) was carried out for whole-cell anti-TB activity against the susceptible H37Rv and MDR strains of MTB. Most of the compounds exhibited moderate to excellent activity against the susceptible H37Rv. Moreover, the most promising compound 4f (against H37Rv) having paratrifluoromethyl phenyl group at 4-position and bis para-methoxy benzyl ester group at 3- and 5- positions of 1,4-dihydropyridine pharmacophore, exhibited no toxicity, but demonstrated weak activity against MTB strains resistant to isoniazid and rifampicin. In light of the inhibitory profile of the title compounds, enoyl-acyl carrier protein reductase (InhA) appeared to be the appropriate molecular target. A docking study of these derivatives against InhA receptor revealed favorable binding interactions. Further, in silico predicted ADME properties of these compounds 4a-4h were found to be in the acceptable ranges, including satisfactory Lipinski's rule of five, thereby indicating their potential as drug-like molecules. In particular, the 1,4-DHP derivative 4f can be considered an attractive lead molecule for further exploration and development of more potent anti-TB agents as InhA inhibitors.

An integrated computational investigation to unveil the structural impacts of mutation on the InhA structural gene of Mycobacterium tuberculosis

Growing concern about the difficulty in diagnosis and treatments of drug-resistant tuberculosis falls under the major global health issues. There is an urgent need for finding novel strategies to develop drugs or bioactive molecules against the global threat of Mycobacterium tuberculosis (MTB). Isoniazid (INH) is a front line drug against tuberculosis; it primarily targets the enoyl-acyl carrier protein reductase (InhA), a potent drug target in the mycolic acid pathway of MTB. To gain deeper insight into the impact of INH resistant mutation and its influence on the structural dynamics of InhA, combined conformational dynamics and residue interaction network (RIN) studies were performed. The molecular dynamics investigation provided a hint about the structural changes altering protein activity. The principal component analysis (PCA) based free energy landscape plot highlighted the highest stable part of wild-type (WT) and mutant structures. Intriguingly, the mutation at the 78th position of InhA from its native residue valine to alanine increases the structural stability with higher NADH binding affinity. The MM-PBSA based binding energy calculations confirm that electrostatic interactions played a critical role in the binding of NADH at the binding site of InhA. The calculated binding energy score, as well as potential hydrogen bonds and salt bridge networks, proved the strong binding of mutant InhA as compared to WT. Further, the mutation potentially altered the protein network topology, thereby subsequently affected the landscape of NADH binding. The present study is an attempt to understand the structural and functional impact associated with a drug-resistant mutation (V78A) thus it will be helpful in designing potent inhibitors against drug-resistant tuberculosis.

Design and synthesis of thiourea-based derivatives as Mycobacterium tuberculosis growth and enoyl acyl carrier protein reductase (InhA) inhibitors

Tuberculosis remains the most deadly infectious disease worldwide due to the emergence of drug-resistant strains of Mycobacterium tuberculosis. Hence, there is a great need for more efficient treatment regimens. Herein, we carried out rational molecular modifications on the chemical structure of the urea-based co-crystallized ligand of enoyl acyl carrier protein reductase (InhA) (PDB code: 5OIL). Although this compound fulfills all structural requirements to interact with InhA, it does not inhibit the enzyme effectively. With the aim of improving the inhibition value, we synthesized thiourea-based derivatives by one-pot reaction of the amines with corresponding isothiocyanates. After the structural characterization using 1H NMR, 13C NMR, FTIR and HRMS, the obtained compounds were initially tested for their abilities to inhibit Mycobacterium tuberculosis growth. The results revealed that some compounds exhibited promising antitubercular activity, MIC values at 0.78 and 1.56 μg/mL, combined with low cytotoxicity. Moreover, the most active compounds were tested against latent as well as dormant forms of the bacteria utilizing nutrient starvation model and Mycobacterium tuberculosis infected macrophage assay. Enzyme inhibition assay against enoyl-acyl carrier protein reductase identified InhA as the important target of some compounds. Molecular docking studies were performed to correlate InhA inhibition data with in silico results. Finally, theoretical calculations were established to predict the physicochemical properties of the most active compounds.

Microwave-Assisted Synthesis of Some Indole and Isoniazid Derivatives as Antitubercular Agents and Molecular Docking Study

An efficient and expeditious microwave-assisted synthesis of isoniazid derivatives from various indole-3-carbaldehydes, phenols, and isoniazid via Betti’s reaction under one pot, solvent-free, and green reaction conditions is described. The same compounds were also prepared by conventional method. Relatively short reaction time and good yields make the proposed protocol highly significant. The structures of the newly synthesized compounds were confirmed by spectral and analytical data. The synthesized compounds were evaluated for their potential in vitro antitubercular activity against M. tuberculosis H37Rv strain using Alamar Blue assay. Some of the tested compounds were found to be highly active against M. tuberculosis H37Rv with minimum inhibitory concentrations of 3.12, 6.25, and 12.5 µg/mL, while the others showed a moderate activity. Docking of the potent compounds inside the active site of the target enzyme mycobacterial enoyl reductase (InhA) (FabI ENR, PDB code 4TZK) was performed in order to interpret the results.

Structural Basis for Inhibition of Enoyl-[Acyl Carrier Protein] Reductase (InhA) from Mycobacterium tuberculosis.

The enzyme trans-enoyl-[acyl carrier protein] reductase (InhA) is a central protein for the development of antitubercular drugs. This enzyme is the target for the pro-drug isoniazid, which is catalyzed by the enzyme catalase-peroxidase (KatG) to become active. Our goal here is to review the studies on InhA, starting with general aspects and focusing on the recent structural studies, with emphasis on the crystallographic structures of complexes involving InhA and inhibitors. We start with a literature review, and then we describe recent studies on InhA crystallographic structures. We use this structural information to depict protein-ligand interactions. We also analyze the structural basis for inhibition of InhA. Furthermore, we describe the application of computational methods to predict binding affinity based on the crystallographic position of the ligands. Analysis of the structures in complex with inhibitors revealed the critical residues responsible for the specificity against InhA. Most of the intermolecular interactions involve the hydrophobic residues with two exceptions, the residues Ser 94 and Tyr 158. Examination of the interactions has shown that many of the key residues for inhibitor binding were found in mutations of the InhA gene in the isoniazid-resistant Mycobacterium tuberculosis. Computational prediction of the binding affinity for InhA has indicated a moderate uphill relationship with experimental values. Analysis of the structures involving InhA inhibitors shows that small modifications on these molecules could modulate their inhibition, which may be used to design novel antitubercular drugs specific for multidrug-resistant strains.

Synthesis, In vitro and In silico Studies of Benzothiazole Azo-Ester Derivatives as Anti-TB Agents

Introduction:A new series of benzothiazole azo-ester derivatives was synthesized by using Steglish esterification reaction.Methods:All the synthesized compounds were screened for their anti-TB activities by in vitro microplate Alamar Blue assay method against M. tuberculosis (H37RV strain). All the compounds showed activities and their MIC values were over the range of 1.6 µg/mL to 50 µg/mL. The compounds 4d and 4j showed superior activity with MIC 1.6 µg/mL compared to the standard drug Streptomycin (MIC 6.25 µg/mL), Pyrazinamide (MIC 3.125 µg/mL) and Ciprofloxacin (MIC 3.125 µg/mL).Results:Molecular docking study was carried out with enoyl acyl carrier reductase (InhA) of M. tuberculosis and decaprenyl phosphoryl-D-ribose oxidase (DprE1).Conclusion:These studies showed that these compounds have more interaction with InhA protein whereas some compounds could not be docked into DprE1.

Discovery of hydrazone containing thiadiazoles as Mycobacterium tuberculosis growth and enoyl acyl carrier protein reductase (InhA) inhibitors

Tuberculosis, caused by Mycobacterium tuberculosis, is a serious infectious disease and remains a global health problem. There is an increasing need for the discovery of novel therapeutic agents for its treatment due to the emerging multi-drug resistance. Herein, we present the rational design and the synthesis of eighteen new thiadiazolylhidrazones (TDHs) which were synthesized by intramolecular oxidative N–S bond formation reaction of 2-benzylidene-N-(phenylcarbamothioyl)hydrazine-1-carboximidamide derivatives by phenyliodine(III) bis(trifluoroacetate) (PIFA) under mild conditions. The compounds were characterized by various spectral techniques including FTIR, 1H NMR, 13C NMR and HRMS. Furthermore, the proposed structure of TDH12 was resolved by single-crystal X-ray analysis. The compounds were evaluated for their in vitro antitubercular activity against M. tuberculosis H37Rv. Among them, some compounds exhibited remarkable antimycobacterial activity, MIC = 0.78–6.25 μg/mL, with low cytotoxicity. Additionally, the most active compounds were screened for their biological activities against M. tuberculosis in the nutrient starvation model. Enzyme inhibition assays and molecular docking studies revealed enoyl acyl carrier protein reductase (InhA) as the possible target enzyme of the compounds to show their antitubercular activities.

Design, synthesis, evaluation, and molecular dynamic simulation of triclosan mimic diphenyl ether derivatives as antitubercular and antibacterial agents

In the present work, we have explored triclosan mimic diphenyl ether derivatives as inhibitors of Mycobacterium tuberculosis enoyl acyl carrier protein reductase (InhA) using a structure-based drug design approach. The virtual library of diphenyl ethers was designed and compounds with acceptable absorption, distribution, metabolism, excretion, and toxicity properties were docked. The compounds with higher dock score (5a-g) than triclosan were synthesized, characterized, and evaluated for in vitro antitubercular activity against Mycobacterium tuberculosis H37Rv. Among the synthesized compounds, compounds 5f and 5c appeared to be the most promising with minimum inhibitory concentration of 18 μM and 36 μM respectively. The molecular dynamics simulation study of the most active compound 5f and triclosan was performed, which correlates with its activity in comparison with triclosan. All the compounds were further evaluated for cytotoxicity studies against Vero, and HepG2 were found to be safe. Furthermore, compound 5f was evaluated for in vitro cytotoxicity against mouse macrophage cell lines (RAW 264.7), and the study indicated its safety in eukaryotes at 50-μM concentration. In addition, compounds 5a-g were also screened for their in vitro antibacterial activity against two gram-positive and two gram-negative bacteria by resazurin-based microtiter dilution assay method. Among the synthesized compounds, 5f and 5b appeared to be promising, against various gram-positive and gram-negative microorganisms, indicating its broad-spectrum potential.

Exploring the Pharmacological Potentials of Biosurfactant Derived from Planococcus maritimus SAMP MCC 3013.

Therapeutic potential of biosurfactant (BS) has been improved in recent years. Our present study deals with production of BS from Planococcus maritimus SAMP MCC 3013 in a mineral salt medium (MSM) supplemented with glucose (1.5%w/v). Further, BS has been purified and partially characterized as glycolipid type through our previous publication. Current research article aimed to evaluate biological potential of BS against Mycobacterium tuberculosis, Plasmodium falciparum and cancerous cell lines. Planococcus derived glycolipid BS was found to be a promising inhibitor of M. tuberculosis (MTB) H37Ra at IC50 64.11 ± 1.64μg/mL and MIC at 160.8 ± 1.64μg/mL. BS also showed growth inhibition of P. falciparum at EC50 34.56 ± 0.26µM. Additionally, BS also displayed the cytotoxicity against HeLa (IC50 41.41 ± 4.21μg/mL), MCF-7 (IC50 42.79 ± 6.07μg/mL) and HCT (IC50 31.233 ± 5.08μg/mL) cell lines. Molecular docking analysis was carried for the most popular glycolipid type BS namely Rhamnolipid (RHL) aiming to interpret the possible binding interaction for anti-tubercular and anti-cancer activity. This analysis revealed the involvement of RHL binding with enoyl reductase (InhA) of M. tuberculosis. Docking studies of RHL with tubulin directed several hydrophobic and Vander Waal interactions to exhibit anti-cancer potential. The present study will be helpful for further development of marine bioactive molecules for therapeutic applications. Their anti-tubercular, anti-plasmodial and cytotoxic activities make BS molecules as a noteworthy candidate to combat several diseases. To the best of our knowledge, this is the first report on projecting the pharmacological potential of Planococcus derived BS.

Identifying the Structural Features of Diphenyl Ether Analogues for InhA Inhibition: A 2D and 3D QSAR Based Study

Background: Enoyl acyl carrier protein reductase (InhA) is a validated target for Mycobacterium. It is an enzyme which is associated with the biosynthesis of mycolic acids in type II fatty acid synthase system. Mycobacterial cell wall majorly comprises mycolic acids, which are responsible for virulence of the microorganism. Several diphenyl ether derivatives have been known to be direct inhibitors of InhA. Objective: In the present work, a Quantitative Structure Activity Relationship (QSAR) study was performed to identify the structural features of diphenyl ether analogues which contribute to InhA inhibitory activity in a favourable way. Method: Both 2D and 3D QSAR models were built and compared. Several fingerprint based 2D QSAR models were generated and their relationship with the structural features was studied. Models which corroborated the inhibitory activity of the molecules with their structural features were selected and studied in detail. Results: A 2D-QSAR model, with dendritic fingerprints having regression coefficient, for test set molecules Q2 =0.8132 and for the training set molecules, R2 =0.9607 was obtained. Additionally, an atom-based 3D-QSAR model with Q2 =0.7697 and R2 =0.9159 was also constructed. Conclusion: The data reported by various models provides guidance for the designing of structurally new diphenyl ether inhibitors with potential activity against InhA of M. tuberculosis.

Discovery of New and Potent InhA Inhibitors as Antituberculosis Agents: Structure-Based Virtual Screening Validated by Biological Assays and X-ray Crystallography.

The enoyl-acyl carrier protein reductase InhA of Mycobacterium tuberculosis is an attractive, validated target for antituberculosis drug development. Moreover, direct inhibitors of InhA remain effective against InhA variants with mutations associated with isoniazid resistance, offering the potential for activity against MDR isolates. Here, structure-based virtual screening supported by biological assays was applied to identify novel InhA inhibitors as potential antituberculosis agents. High-speed Glide SP docking was initially performed against two conformations of InhA differing in the orientation of the active site Tyr158. The resulting hits were filtered for drug-likeness based on Lipinski's rule and avoidance of PAINS-like properties and finally subjected to Glide XP docking to improve accuracy. Sixteen compounds were identified and selected for in vitro biological assays, of which two (compounds 1 and 7) showed MIC of 12.5 and 25 μg/mL against M. tuberculosis H37Rv, respectively. Inhibition assays against purified recombinant InhA determined IC50 values for these compounds of 0.38 and 0.22 μM, respectively. A crystal structure of the most potent compound, compound 7, bound to InhA revealed the inhibitor to occupy a hydrophobic pocket implicated in binding the aliphatic portions of InhA substrates but distant from the NADH cofactor, i.e., in a site distinct from those occupied by the great majority of known InhA inhibitors. This compound provides an attractive starting template for ligand optimization aimed at discovery of new and effective compounds against M. tuberculosis that act by targeting InhA.

Synthesis, bioevaluation and molecular docking study of new piperazine and amide linked dimeric 1,2,3-triazoles

In search of more potent new antitubercular agents, a library of novel piperazine tethered dimeric 1,2,3-triazoles were designed by assembling 1,2,3-triazoles and piperazine in a single molecular architectural framework. The titled compounds (3a–m) were synthesized by 1,3-dipolar cycloaddition of 1,4-di(prop-2-yn-1-yl)piperazine (1) and various azides (2a–m) using click chemistry approach with good yields. All the synthesized compounds (3a–m) have been screened for their in vitro antitubercular, antifungal and antioxidant activities against their respective strains. Among them, 3b, 3d, and 3i have revealed promising antitubercular activity against Mycobacterium tuberculosis (Mtb) H37Rv with MIC 12.5 µg/mL. Molecular docking results provided well-clustered solutions to the mode of binding for these molecules into the active site of Mtb enoyl reductase (InhA). In addition to this, most of synthesized compounds were found to have potential antifungal as well as antioxidant activity.

Structure-Based Design and in Silico Screening of Virtual Combinatorial Library of Benzamides Inhibiting 2-trans Enoyl-Acyl Carrier Protein Reductase of Mycobacterium tuberculosis with Favorable Predicted Pharmacokinetic Profiles.

Background: During the previous decade a new class of benzamide-based inhibitors of 2-trans enoyl-acyl carrier protein reductase (InhA) of Mycobacterium tuberculosis (Mt) with unusual binding mode have emerged. Here we report in silico design and evaluation of novel benzamide InhA-Mt inhibitors with favorable predicted pharmacokinetic profiles. Methods: By using in situ modifications of the crystal structure of N-benzyl-4-((heteroaryl)methyl) benzamide (BHMB)-InhA complex (PDB entry 4QXM), 3D models of InhA-BHMBx complexes were prepared for a training set of 19 BHMBs with experimentally determined inhibitory potencies (half-maximal inhibitory concentrations IC50exp). In the search for active conformation of the BHMB1-19, linear QSAR model was prepared, which correlated computed gas phase enthalpies of formation (∆∆HMM) of InhA-BHMBx complexes with the IC50exp. Further, taking into account the solvent effect and entropy changes upon ligand, binding resulted in a superior QSAR model correlating computed complexation Gibbs free energies (∆∆Gcom). The successive pharmacophore model (PH4) generated from the active conformations of BHMBs served as a virtual screening tool of novel analogs included in a virtual combinatorial library (VCL) of compounds containing benzamide scaffolds. The VCL filtered by Lipinski’s rule-of-five was screened by the PH4 model to identify new BHMB analogs. Results: Gas phase QSAR model: −log10(IC50exp) = pIC50exp = −0.2465 × ∆∆HMM + 7.95503, R2 = 0.94; superior aqueous phase QSAR model: pIC50exp = −0.2370 × ∆∆Gcom + 7.8783, R2 = 0.97 and PH4 pharmacophore model: = 1.0013 × p − 0.0085, R2 = 0.95. The VCL of more than 114 thousand BHMBs was filtered down to 73,565 analogs Lipinski’s rule. The five-point PH4 screening retained 90 new and potent BHMBs with predicted inhibitory potencies IC50pre up to 65 times lower than that of BHMB1 (IC50exp = 20 nM). Predicted pharmacokinetic profile of the new analogs showed enhanced cell membrane permeability and high human oral absorption compared to current anti-tuberculotics. Conclusions: Combined use of QSAR models that considered binding of the BHMBs to InhA, pharmacophore model, and ADME properties helped to recognize bound active conformation of the benzamide inhibitors, permitted in silico screening of VCL of compounds sharing benzamide scaffold and identification of new analogs with predicted high inhibitory potencies and favorable pharmacokinetic profiles.