Mycobacterium Tuberculosis Enoyl-acyl Carrier Protein Research Articles

Antitüberküloz Triptantrin analoglarının elektronik ve topolojik özelliklerinin ve enoil-ACP redüktaz ile etkileşimlerinin in silico yöntemlerle incelenmesi

Objective:
 This study aimed to investigate the structure-antitubercular activity relationships of a series of tryptanthrin analogues and the binding mechanisms of these analogues with InhA, Mycobacterium tuberculosis enoyl-acyl carrier protein (enoyl-ACP) reductase.
 Methods:
 Structure-activity relationships were investigated by using Electronic-Topological Method combined with Neural Networks (ETM-NN). Binding energies and non-covalent interactions stabilizing the ligand-InhA complex were obtained from the results of molecular docking. To assess these interactions, frontier molecular orbital analysis of the ligand-InhA complexes were also analysed. 
 Results: 
 The results of the ETM-NN application to the series of compounds in view are pharmacophoric and anti-pharmacophoric molecular fragments, which are characteristic of the class of compounds demonstrating activity against Mycobacterium tuberculosis strain H37Rv. The statistical characteristics of five pharmacophores (Phi) and five anti-pharmacophores (APhi) entering the forecasting system, are 0.90 and 0.86, correspondingly. Analysis of the electron density distribution has shown that the more effective binding with receptor was observed for active compounds.
 Conclusions: 
 A system of prognosis for the anti-tubercular activity of Mycobacterium tuberculosis H37Rv was developed on the base of the pharmacophores found, docking results, and electronic structure calculations. This prognosis system allows for designing of new potent antitubercular drugs.
 Keywords: Tryptanthrin analogues, mycobacterium tuberculosis H37Rv, InhA electronic-topological method, molecular docking, density functional theory

Design, Synthesis, Anti-tubercular and Docking Studies of Novel 2-Furanyl-3-substituted Quinazolin-4-one Derivatives

In this work, the synthesis, characterization and the anti-tubercular activity of novel 2-furanyl-3- substituted quinazolin-4-one derivatives and also predicted their affinity against Mycobacterium tuberculosis enoyl acyl carrier protein reductase were carried out. The targeted compounds were synthesized by the condensation of 2-(furan-2-yl)-4(3H)-1-benzoxazine-4-one with different primary amines. After structural elucidation using spectral data, the compounds were screened for anti-tubercular activity against Mycobacterium tuberculosis H37RV strain. The binding affinity against enoyl acyl carrier protein reductase was predicted using MOE and FITTED docking tools. The synthesized compounds showed a promising anti-tubercular activity in the range from 12.5 to 100 μg/mL. According to MOE docking, the common amino acids in the active site of InhA were found to form hydrogen bonding and hydrophobic interactions with the synthesized quinazolinones. Docking simulations also showed that an aromatic side chain capable of forming hydrogen bond interactions can increase affinity of 2-furanyl quinazolinones to enoyl acyl carrier protein reductase.

Novel 4-aminoquinolines: Synthesis, inhibition of the Mycobacterium tuberculosis enoyl-acyl carrier protein reductase, antitubercular activity, SAR, and preclinical evaluation

Herein a series of 4-aminoquinolines were synthesized in an attempt to optimize and study the structural features related to LABIO-17 biological activity, a Mycobacterium tuberculosis NADH-dependent enoyl-acyl carrier protein reductase (MtInhA) inhibitor previously identified by a virtual-ligand-screening approach. Structure-activity relationships led to novel submicromolar inhibitors of MtInhA and potent antitubercular agents. The lead compound is 87-fold more potent as enzymatic inhibitors and 32-fold more potent against M. tuberculosis H37Rv strain in comparison with LABIO-17. These molecules were also active against multidrug-resistant strains, devoid of apparent toxicity to mammalian cells and showed favorable in vitro ADME profiles. Additionally, these compounds were active in an intracellular model of tuberculosis (TB) infection, showed no genotoxicity signals, satisfactory absorption parameters and absence of in vivo acute toxicity. Finally, treatment with selected 4-aminoquinoline for two weeks produced bacteriostatic effect in a murine model of TB. Taken together, these findings indicate that this chemical class may furnish candidates for the future development of drug-sensitive and drug-resistant tuberculosis treatments.

Design, synthesis and anti-Mycobacterium tuberculosis evaluation of new thiazolidin-4-one and thiazolo[3,2-a][1,3,5]triazine derivatives

In response to the urgent need to encounter infection diseases, and upon increasing concerns about the devastating effects of tuberculosis (TB), the promising thiazolidin-4-one scaffold was used as a starting point to design and synthesize seventeen new compounds, relying on the pharmacophoric features of different anti-Mycobacterium tuberculosis and antibacterial active compounds. Thiazolidin-4-one was elaborated to result in bi-functioning formation, and further ring fusion into a thiazolo[3,2-a][1,3,5]triazine, which was hybridized with different heterocyclic rings and sulfonamide moieties. All the newly synthesized compounds were evaluated for their activity against drug sensitive (DS), multi-drug resistant (MDR) and extensive drug resistant (XDR) Mycobacterium tuberculosis (Mtb) strains. Additionally, their anti-bacterial activity against several bronchitis causing-bacteria (ATCC) and their antifungal activity were assessed. Several compounds showed promising results regarding all of the mentioned assays without any antifungal activities. Particularly, compound 3 showed a promising activity against the three Mtb strains (DS, MDR and XDR) with MIC of 2.49, 9.91 and 39.72 µM, respectively. Furthermore, compound 7c revealed antituberculosis activity with MIC of 2.28, 18.14 and 36.31 µM against DS, MDR and XDR strains, respectively. Both of compounds 3 and 7c surpassed azithromycin on several bronchitis causing-bacteria and showed enhanced inhibitory activity against Mycobacterium tuberculosis enoyl-acyl carrier protein reductase (InhA), with IC50 of 3.90 and 2.47 µM, respectively. The enzymatic activity was augmented by the binding characteristics of 3 and 7c in the InhA active site. Further investigations confirmed their safety on normal cell lines, and promising predicted ADME characteristics.

DESIGN, SYNTHESIS AND BUILDING A QSAR MODEL FOR THE INHIBITION OF MYCOBACTERIUM TUBERCULOSIS BY PYRAZOLINE DERIVATIVES

A series of chalcone annulated pyrazoline conjugates have recently been synthesized from our laboratory and identified as possible “LEAD”s against Mycobacterium tuberculosis (MTB) through an in-silico study. The MTB enoyl acyl carrier protein reductase (InhA) plays a vital role in the MTB fatty acid synthesis pathway as essential in the mycolic acid biosynthesis. Therefore, inhibition of InhA could block the biosynthesis of mycolic acids, resulting in mycobacteria death. To further explore the potency of the compounds, a quantitative structure-activity relationship (QSAR) study is carried out. To develop a new pharmacophoric model for this inhibition, a QSAR approach of reported pyrazoline derivatives against tuberculosis has been studied. Multiple linear regression analysis was performed to derive the QSAR models, which were further evaluated internally as well as externally for the prediction of activity. The accurate MIC values (μg/ml) were collected for 23 pyrazoline analogs, and other descriptor parameters, such as log p (o/w), MR, DM, EELE, LUMO, HOMO, and TPSA were compared with these analogs. A training set of 23 analogs, all having a common pyrazoline moiety, provided a cross-validated correlation coefficient (r2) value of 0. 45112 and root mean square error (RMSE) value of 0. 0.27760. Moreover, based on this QSAR study, we have hypothetically estimated the predicted pMIC50 by using trainpred.fit file from Molecular Operating Environment 2009.10 software for the newly synthesized test set i.e., six chalcone based pyrazoline compounds. The resulting QSAR model generated from the present study may be useful in the design of a similar group of pyrazoline analogs as anti-tubercular agents.

Antitubercular and antibacterial activities of isoxazolines derived from natural products: Isoxazolines as inhibitors of Mycobacterium tuberculosis InhA

Isoxazoline derivatives of the natural products eugenol, 1’- S-acetoxychavicol acetate and sclareol are prepared through 1,3-dipolar cycloaddition reactions in an aqueous buffered system. The compounds are evaluated for their antitubercular and antibacterial activities. Compounds 2, 2a and 3f display strong antitubercular activity with minimum inhibitory concentration values of 26.68, 17.89 and 14.58 µM, respectively. Furthermore, derivative 3f exhibits antibacterial activity against Bacillus cereus (minimum inhibitory concentration value of 29.16 µM). Isoxazoline derivatives of 1’- S-acetoxychavicol acetate demonstrate improvements in cytotoxicity, and derivative 3f of sclareol demonstrates improved antitubercular and antibacterial activities. Isoxazolines derived from natural products exhibit Mycobacterium tuberculosis enoyl-acyl carrier protein reductase (InhA) inhibitory activity, and molecular modelling predicts that they form hydrogen bonding and hydrophobic interactions with NADH and with the key residues of the InhA binding site.

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

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.

Structural modification of a novel inhibitor for mycobacterium enoyl-acyl carrier protein reductase assisted by In silico structure-based drug screening.

Mycobacterium tuberculosis enoyl-acyl carrier protein reductase (mtInhA) is involved in the biosynthesis of mycolic acids, a major component of mycobacterial cell walls, and has been targeted in the development of anti-tuberculosis (TB) drugs. In our previous in silico structure-based drug screening study, we identified KES4, a novel class of mtInhA inhibitor. KES4 is composed of four ring structures (A-D-rings) and molecular dynamic simulation predicted that the D-ring is essential for the interaction with mtInhA. The structure-activity relationship study of the D-ring was attempted and aided by in silico docking simulations to improve the mtInhA inhibitory activity of KES4. A virtual chemical library of the D-ring-modified KES4 was then constructed and subjected to in silico docking simulation against mtInhA using the GOLD program. The candidate compound showing the highest GOLD score, referred to as KEN1, was synthesized, and its biological properties were compared with those of the lead compound KES4. We achieved the synthesis of KEN1 and evaluated its effects on InhA activity, mycobacterial growth, and cytotoxicity. The antimycobacterial activity of KEN1 was comparable to that of the lead compound (KES4), although it exhibited superior activity in mtInhA inhibition. \. We obtained a KES4 derivative with high mtInhA inhibitory activity by in silico docking simulation with a chemical library consisting of a series of D-ring-modified KES4.

Identification of Mycobacterium tuberculosis enoyl-acyl carrier protein reductase inhibitors: A combined in-silico and in-vitro analysis

Mycobacterium tuberculosis (Mtb), had developed evolutionary changes in its genome to adapt for survival and thereby generated multi-drug resistant strains. However, novel drug targets that remained unchanged for their biochemical role has impressed the research community to target such proteins. The comprehensive analysis of multiple protein targets has influenced us to make a consensus structural rule exploited by pharmacophore and other allied techniques from a large repository of protein structures. In this pursuit, we made a retrospective analysis of pharmacophores mapped from the tuberculosis structural proteome and identified unique patterns that can be employed for the novel molecules design. The current work on NADH–dependent enoyl–acyl carrier protein reductase (InhA) has yielded top scored pharmacophore models which were searched over SPECS natural product database to prioritize the molecules that can be targeted against Mtb. With efforts on rigorous validation and expertise, we have identified such pharmacophoric patterns from natural compounds that can be used as initial hits. Subsequently, these hits were subjected to in-vitro antitubercular evaluation to ensure the inhibitory activity against the mycobacterium culture growth (MtbH37Rv). Furthermore, docking simulations were carried out to provide an insight on the possible modes of interaction between the experimentally explored compounds and InhA.

DNA/BSA interaction, bio-activity, molecular docking simulation study and electrochemical properties of hydrazone Schiff base derived Cu(II)/Ni(II) metal complexes: Influence of the nuclearity and metal ions

Three new transition metal complexes of a tridentate Schiff base ligand, H2L=N-(2-hydroxybenzylideneamino) benzamide, were synthesized in the presence of pyridine, 3-methylpyridine and the corresponding metal salts, and were characterized by FT-IR, UV–Vis and Raman spectroscopies, and cyclic voltammetry (CV). The crystal structures of the three complexes, [CuII2(L)2(py)2]·2ClO4(1), CuII2(L)2(3-Mepy)2(ClO4)2 (2) and [NiII(L)(py)3]ClO4 (3), were determined through X-ray crystallography. In the Cu complexes two different kinds of contacts were be found: shorter (in typical ranges) and longer (Cu–O around 2.5Å), which assemble the complexes into dimers. The coordination geometry is (taking into account the longer contacts) square-pyramidal in 1, while complexes 2 and 3 show an octahedral geometry. Numerous biological studies have been conducted on H2L and complexes 1–3. In vitro, their antibacterial activities were examined against Gram-positive and Gram-negative bacteria. The results of these studies indicated that all compounds had antibacterial activity against Gram-positive bacteria. Furthermore, binding studies of H2L and its complexes with calf thymus DNA (CT-DNA) were studied. Results analyzing the binding of H2L and the complexes to CT-DNA revealed a hyperchromic effect and a non-intercalative mode of binding. These observations also indicate significant alterations of the bovine serum albumin (BSA) secondary structure in circular dichroism (CD) spectra, specifically in the presence of H2L and the complexes, with the reduction of the α-helices content. A molecular docking simulation study of the complexes with Mycobacterium tuberculosis enoyl-acyl carrier protein reductase, InhA, using the Hex (v8.0.0) docking software indicated their probable inhibition property.

Virtually Designed Triclosan-Based Inhibitors of Enoyl-Acyl Carrier Protein Reductase of Mycobacterium tuberculosis and of Plasmodium falciparum.

We report here new chemical structures of predicted nanomolar triclosan-based inhibitors (TCLs) of Mycobacterium tuberculosis enoyl-acyl carrier protein reductase (InhA) virtually proposed by computer-assisted molecular design. 3D models of InhA-TCL complexes were prepared by in situ modifications of the reference crystal structure (PDB entry 1P45) for a training set of 15 TCLs with known InhA inhibitory activities. A QSAR model was built leading to linear correlation between the calculated free energies of complexation (ΔΔGcom ) and experimental values IC50 (exp) : pIC50 =-0.0657×ΔΔGcom +3.0502, R(2) =0.96. In addition, ligand-based quantitative pharmacophore model (PH4) was built from bound conformations of the training set compounds and confirmed the correlation between molecular models and observed activities: pIC50 (exp=) 0.8929×pIC50 (pre) -0.441, R(2) =0.95. Structural information from both models helped us to propose new TCL analogues. A virtual library of TCLs with known predicted activities against enoyl-acyl carrier protein reductase of Plasmodium falciparum (PfENR) was evaluated, revealing dual target TCLs. Moreover, analysis of binding site interactions suggested enriching substitutions, which led to more potent TCLs with predicted pIC50 (pre) as low as 7 nM. The computational approach, which used both free energy estimated from molecular modeling and 3D-QSAR pharmacophore model, was helpful in virtually proposing the dual-targeted drugs and provided valuable information for the design of novel potential antituberculotic agents.

Piperazine derivatives: synthesis, inhibition of the Mycobacterium tuberculosis enoyl-acyl carrier protein reductase and SAR studies.

The Mycobacterium tuberculosis NADH-dependent enoyl-acyl carrier protein reductase (MtInhA) catalyzes hydride transfer to long-chain enoyl thioester substrates. MtInhA is a member of the mycobacterial type II dissociated fatty acid biosynthesis system, and is the bona fide target for isoniazid, the most prescribed drug for tuberculosis treatment. Here, a series of piperazine derivatives was synthesized and screened as MtInhA inhibitors, which resulted in the identification of compounds with IC50 values in the submicromolar range. A structure-activity relationship (SAR) evaluation indicated the importance of the chemical environment surrounding the carbonyl group for inhibition. In addition, the structure of one selected compound was supported by crystallographic studies, and experimental geometrical values were compared with semi-empirical quantum chemical calculations. Furthermore, the mode of inhibition and inhibitory dissociation constants were determined for the nine most active compounds. These findings suggest that these 9H-fluoren-9-yl-piperazine-containing compounds interact with MtInhA at the enoyl thioester (2-trans-dodecenoyl-CoA) substrate binding site.

Activity of IQG-607, a new orally active compound, in a murine model of Mycobacterium tuberculosis infection

We have previously demonstrated a potent in vitro inhibitory activity for two pentacyano(isoniazid)ferrate(II) compounds, namely IQG-607 and IQG-639, against the Mycobacterium tuberculosis enoyl-acyl carrier protein reductase enzyme. In this study, the activity of these compounds was evaluated using an in vivo murine model of tuberculosis. Swiss mice were infected with M. tuberculosis H37Rv strain and then IQG-607 or IQG-639 (250mg/kg) was administered for 28 days or 56 days. In addition, a dose–response study was performed with IQG-607 at 5, 10, 25, 50, 100, 200 and 250mg/kg. The activity of test compounds was compared with that of the positive control drug isoniazid (INH) (25mg/kg). After 28 days or 56 days of treatment, both IQG-607 and INH significantly reduced M. tuberculosis-induced splenomegaly as well as significantly diminishing the colony-forming units in the spleen and lungs. IQG-607 and INH ameliorated the lung macroscopic aspect, reducing lung lesions to a similar extent. However, IQG-639 did not significantly modify any evaluated parameter. Experiments using early and late controls of infection revealed a bactericidal activity for IQG-607. IQG-607 might well represent a good candidate for clinical development as a new antimycobacterial agent.

Elucidating Isoniazid Resistance Using Molecular Modeling

The continuing rise in tuberculosis incidence and the problem of drug resistance strains have prompted the research on new drug candidates and the mechanism of drug resistance. Molecular docking and molecular dynamics simulation (MD) were performed to study the binding of isoniazid onto the active site of Mycobacterium tuberculosis enoyl-acyl carrier protein reductase (InhA) in an attempt to address the mycobacterial resistance against isoniazid. Results show that isonicotinic acyl-NADH (INADH) has an extremely high binding affinity toward the wild type InhA by forming stronger interactions compared to the parent drug (isoniazid) (INH). Due to the increase of hydrophobicity and reduction in the side chain's volume of A94 of mutant type InhA, both INADH and the mutated protein become more mobile. Due to this reason, the molecular interactions of INADH with mutant type are weaker than that observed with the wild type. However, the reduced interaction caused by the fluctuation of INADH and the mutant protein only inflected minor resistance in the mutant strain as inferred from free energy calculation. MD results also showed there exists a water-mediated hydrogen bond between INADH and InhA. However, the bridged water molecule is only present in the INADH-wild type complex, reflecting the putative role of the water molecule in the binding of INADH to the wild type protein. The results support the assumption that the conversion of prodrug isoniazid into its active form INADH is mediated by KatG as a necessary step prior to target binding on InhA. Our findings also contribute to a better understanding of INH resistance in mutant type.