Computer-aided study of the relationship between structure and antituberculosis activity of a series of isoniazid derivatives

The cleavage kinetics of hydrazide derivatives of isoniazid by HPLC-UV/DAD and its impact on activity against Mycobacterium tuberculosis

Isoniazid is a first-line drug for the treatment of tuberculosis, a bacterial disease caused by Mycobacterium tuberculosis. Its terminal amino group is highly reactive, leading to significant metabolic deactivation, drug interactions and hepatotoxicity. It is speculated that the activity of isoniazid derivatives is, in part, related to the cleavage of the protecting group. Therefore, this study aimed to evaluate the cleavage characteristics of previously developed isoniazid derivatives through kinetic studies by high-performance liquid chromatography with ultraviolet-diode array detectio to establish a comparison between the rates of the process and the respective activities against M. tuberculosis. Chromatographic separations were performed on an XDB C18 column coupled to an XDB C18 precolumn. The mobile phase consisted of ultrapure water and acetonitrile in gradient mode. The flow rate was 1.0 mL/min, the injection volume was 20 μL, and the detection wavelengths were 230 nm (derivatives and isatins) and 270 nm (isoniazid). Incubation of derivatives was carried out for 5 days in 10 mmol/L phosphate buffer solution (pH 3.0, 7.4, 8.0) or in fetal bovine serum at 37 °C. The incubation reduced the concentration of the derivatives and led to the formation of isoniazid in a first-order kinetic reaction. Isoniazid formation was logarithmically correlated with the minimum inhibitory concentration of the derivatives. The results showed that higher cleavage rates are associated with greater activities against M. tuberculosis, providing important information for the development of future generations of isoniazid derivatives and for screening drug candidates for the treatment of tuberculosis.

Synergistic Effect of Biogenics Derived from Potential Probiotics Together with Zingerone Against Biofilm Formation by Pseudomonas aeruginosa PAO1

Biogenics are compounds produced by living organisms such as animals, plants, bacteria, etc. Probiotics and their biogenics are known for their antimicrobial potential. Therefore, the present study was designed to evaluate the antibiofilm potential of probiotic-derived biogenics in conjunction with zingerone against the Pseudomonas aeruginosa PAO1 biofilm. Cell-free supernatant (CFS) of potential probiotics Pediococcus acidilactici BNS5B and Lactobacillus fermentum PUM was found to inhibit the growth of Ps. aeruginosa PAO1 maximally among the nineteen isolated lactic acid bacteria. L. fermentum PUM produced precipitated protein fraction (PP), organic acids (OAs), exopolysaccharides (EPSs), biosurfactants (BSs) and various volatile antimicrobial compounds, while Ped. acidilactici BNS5B was found to produce PP, OA, EPS, BS and fewer volatile antimicrobial compounds only. More specifically, CFS and selected biogenics (OA and PP from L. fermentum PUM; OA from Ped. acidilactici BNS5B) of both potential probiotics showed synergy with zingerone against Ps. aeruginosa growth as observed by FIC index (< 0.5). Interestingly, CFS of both potential probiotics in combination with zingerone led to the formation of a more distorted biofilm compared with OA of L. fermentum PUM and zingerone, OA of Ped. acidilactici BNS5B and zingerone, PP of L. fermentum PUM and zingerone as well as their individual counterparts. Similarly, both confocal laser scanning microscopy and XTT assay showed an increased number of dead and impaired cells along with the decreased viability of biofilm cells. Thus, it can be reckoned that a combination of probiotic-derived biogenics and zingerone can have therapeutic application against Ps. aeruginosa infections which needs to be validated clinically.

First unequivocal identification of the critical acyl radicals from the anti-tuberculosis drug isoniazid and its hydrazide analogs by complementary applications of ESR spin-trapping and HPLC/MS methods

The carbon-centered isonicotinic acyl radical of isoniazid (INH), a widely-used frontline anti-tuberculosis drug, has been considered to play a critical role in inhibiting Mycobacterium tuberculosis, but not fully identified. Here we show that this radical intermediate can be unequivocally characterized by complementary applications of ESR spin-trapping and HPLC/MS methods by employing N-tert-butyl-α-phenylnitrone (PBN) as the suitable spin-trapping agent, which can form the most stable radical adduct. More importantly, for the first time, analogous carbon-centered acyl radicals and their respective NAD⁺ adducts have also been detected and identified from its two isomers (nicotinic acid hydrazide and 2-pyridinecarbohydrazide) and benzhydrazide which are structurally-related to INH, but not by 2-chloroisonicotinohydrazide. This study represents the first unequivocal identification of the carbon-centered acyl radicals of INH and other hydrazide analogs by both ESR spin-trapping and HPLC/MS methods, which may have broad biomedical and toxicological significance for future research for more efficient hydrazide anti-tuberculosis drugs.

QSAR-driven design, synthesis and discovery of potent chalcone derivatives with antitubercular activity

New anti-tuberculosis (anti-TB) drugs are urgently needed to battle drug-resistant Mycobacterium tuberculosis strains and to shorten the current 6-12-month treatment regimen. In this work, we have continued the efforts to develop chalcone-based anti-TB compounds by using an in silico design and QSAR-driven approach. Initially, we developed SAR rules and binary QSAR models using literature data for targeted design of new heteroaryl chalcone compounds with anti-TB activity. Using these models, we prioritized 33 compounds for synthesis and biological evaluation. As a result, 10 heteroaryl chalcone compounds (4, 8, 9, 11, 13, 17-20, and 23) were found to exhibit nanomolar activity against replicating mycobacteria, low micromolar activity against nonreplicating bacteria, and nanomolar and micromolar against rifampin (RMP) and isoniazid (INH) monoresistant strains (rRMP and rINH) (<1 μM and <10 μM, respectively). The series also show low activity against commensal bacteria and generally show good selectivity toward M. tuberculosis, with very low cytotoxicity against Vero cells (SI = 11-545). Our results suggest that our designed heteroaryl chalcone compounds, due to their high potency and selectivity, are promising anti-TB agents.

Spectroscopic investigations, quantum chemical calculations, HOMO-LUMO and NBO/NLMO analysis of 4-pyridinecarbohydrazide

The FT-IR and FT-Raman spectra of 4-pyridinecarbohydrazide have been recorded. The complete vibrational assignment and analysis of the fundamental modes was carried out using the experimental data and quantum chemical studies. The observed vibrational data were compared with the wavenumbers derived theoretically for the optimized geometry of the compound from the DFT-B3LYP gradient calculations employing 6-311++G(d,p) basis set. The (1)H and (13)C NMR chemical shifts have been simulated. Thermodynamic properties have been calculated at different temperatures. HOMO-LUMO energy gap has been calculated. The intramolecular contacts have been interpreted using Natural Bond Orbital (NBO) and Natural Localized Molecular Orbital (NLMO) analysis.

Comparison of Multiple Linear Regressions and Neural Networks based QSAR models for the design of new antitubercular compounds

The performance of two QSAR methodologies, namely Multiple Linear Regressions (MLR) and Neural Networks (NN), towards the modeling and prediction of antitubercular activity was evaluated and compared. A data set of 173 potentially active compounds belonging to the hydrazide family and represented by 96 descriptors was analyzed. Models were built with Multiple Linear Regressions (MLR), single Feed-Forward Neural Networks (FFNNs), ensembles of FFNNs and Associative Neural Networks (AsNNs) using four different data sets and different types of descriptors. The predictive ability of the different techniques used were assessed and discussed on the basis of different validation criteria and results show in general a better performance of AsNNs in terms of learning ability and prediction of antitubercular behaviors when compared with all other methods. MLR have, however, the advantage of pinpointing the most relevant molecular characteristics responsible for the behavior of these compounds against Mycobacterium tuberculosis. The best results for the larger data set (94 compounds in training set and 18 in test set) were obtained with AsNNs using seven descriptors (R(2) of 0.874 and RMSE of 0.437 against R(2) of 0.845 and RMSE of 0.472 in MLRs, for test set). Counter-Propagation Neural Networks (CPNNs) were trained with the same data sets and descriptors. From the scrutiny of the weight levels in each CPNN and the information retrieved from MLRs, a rational design of potentially active compounds was attempted. Two new compounds were synthesized and tested against M. tuberculosis showing an activity close to that predicted by the majority of the models.

Synthesis, structure, and tuberculostatic activity of dimethyl benzoylcarbonohydrazonodithioates

ABSTRACT

New dimethyl benzoylcarbonohydrazonodithioates were obtained by CS2 addition to arylcarboxylic acid hydrazides and methylation of the formed adduct. The new derivatives were tested for their activity against Mycobacterium tuberculosis. Some compounds exhibited high activity toward sensitive and resistant strains.

GRAPHICAL ABSTRACT

Elucidating drug-enzyme interactions and their structural basis for improving the affinity and potency of isoniazid and its derivatives based on computer modeling approaches

The enoyl-ACP reductase enzyme (InhA) from M. tuberculosis is recognized as the primary target of isoniazid (INH), a first-line antibiotic for tuberculosis treatment. To identify the specific interactions of INH-NAD adduct and its derivative adducts in InhA binding pocket, molecular docking calculations and quantum chemical calculations were performed on a set of INH derivative adducts. Reliable binding modes of INH derivative adducts in the InhA pocket were established using the Autodock 3.05 program, which shows a good ability to reproduce the X-ray bound conformation with rmsd of less than 1.0 A. The interaction energies of the INH-NAD adduct and its derivative adducts with individual amino acids in the InhA binding pocket were computed based on quantum chemical calculations at the MP2/6-31G (d) level. The molecular docking and quantum chemical calculation results reveal that hydrogen bond interactions are the main interactions for adduct binding. To clearly delineate the linear relationship between structure and activity of these adducts, CoMFA and CoMSIA models were set up based on molecular docking alignment. The resulting CoMFA and CoMSIA models are in conformity with the best statistical qualities, in which r2cv is 0.67 and 0.74, respectively. Structural requirements of isoniazid derivatives that can be incorporated into the isoniazid framework to improve the activity have been identified through CoMFA and CoMSIA steric and electrostatic contour maps. The integrated results from structure-based, ligand-based design approaches and quantum chemical calculations provide useful structural information facilitating the design of new and more potentially effective antitubercular agents as follow: the R substituents of isoniazid derivatives should contain a large plane and both sides of the plane should contain an electropositive group. Moreover, the steric and electrostatic fields of the 4-pyridyl ring are optimal for greater potency.

Pharmacophoric model building for antitubercular activity of the individual Schiff bases of small combinatorial library

Synthesis and evaluation of anti-TB activity of individual compounds of Schiff bases combinatorial library were done against Mycobacterium tuberculosis H(37)Rv at a single concentration of 6.25mug/mL according to the protocol of TAACF. Compounds 2C and 3D produced 99% inhibitory activity on the investigated organism, while the other tested compounds showed lower activity ranging from 35 to 84%. It was found that there are no relation between the anti-TB activity of the tested compounds and their lipophilicity expressed by ClogP of these compounds. A 3D pharmacophoric model has been generated by Molecular Operating Environment (MOE) using a training set of 10 reported anti-TB compounds and testing the synthesized compounds (1A, 1B, 1D, 1E, 2C, 3A, 3C, 3D, 3E and 4A-4E). The generated pharmacophoric features include, F1: hydrogen bond donors (Don), F2: aromatic rings (Aro), F3: hydrogen bond acceptors (Acc)/metal ligator (ML), F4: Aro/hydrophobic (Hyd). In all hit set, it was found that the amidic nitrogen CONH-NC fitted the region of the Don, F1, while the amidic carbonyl group fitted the region of the Acc/ML, F3. The distances bridging F1 to F2, F3 and F4 were essential for anti-TB activity in the developed pharmacophore model, as it was confirmed from model validation procedure.

Application of quantitative structure-activity relationships to the modeling of antitubercular compounds. 1. The hydrazide family

A QSAR/QSPR methodology was used to analyze a set of 173 hydrazides, a great part of which are isoniazid (INH) derivatives. Nineteen molecular descriptors of various types (physicochemical, steric, geometrical, and electronic) have been systematically tested through a careful application of MLR. The analysis revealed that the biological activity of these compounds against M. tuberculosis does not depend on lipophilicity, as measured by log P. Properties that account for the biological response of isoniazid and related compounds, consistent with a mechanism involving the formation of radical species, were identified. The role of substituents in the stabilization of the intermediate species that gives rise to the active agent, the acyl radical, is discussed. It is postulated that the activation of INH derivatives' prodrugs (hydrazines and hydrazones) occurs near the surface of M. tuberculosis.

Characterization of the Binding of Isoniazid and Analogues to Mycobacterium tuberculosis Catalase-Peroxidase

The first-line antituberculosis drug isonicotinic hydrazide (INH) is a prodrug whose bactericidal function requires activation by Mycobacterium tuberculosis catalase-peroxidase (KatG) to produce an acyl-NAD adduct. Peroxidation of INH is considered a required catalytic process for drug action. The binding of INH and a series of hydrazide analogues to resting KatG was examined using optical and calorimetric techniques to provide thermodynamic parameters, binding stoichiometries, and kinetic constants (on and off rates). This work revealed high-affinity binding of these substrates to a small fraction of ferric enzyme in a six-coordinate heme iron form, a species most likely containing a weakly bound water molecule, which accumulates during storage of the enzyme. The binding of hydrazides is associated with a large enthalpy loss (>100 kcal/mol); dissociation constants are in the range of 0.05-1.6 microM, and optical stopped-flow measurements demonstrated kon values in the range of 0.5-27 x 10(3) M-1 s-1 with very small koff rates. Binding parameters did not depend on pH in the range 5-8. High-affinity binding of INH is disrupted in two mutant enzymes bearing replacements of key distal side residues, KatG[W107F] and KatG[Y229F]. The rates of reduction of KatG Compound I by hydrazides parallel the on rates for association with the resting enzyme. In a KatG-mediated biomimetic activation assay, only isoniazid generated in good yield the acyl-NAD adduct which is considered a key molecule in INH action, providing a better understanding of the action mechanism of INH.

Diaryloxy methano phenanthrenes: a new class of antituberculosis agents

A new series of diaryloxy methano phenanthrenes were prepared through tertiary-aminoalkylations of [(methoxy-phenyl)-phenanthren-9-yl-methyl]-phenols obtained from Friedel-Crafts alkylations on (methoxy-phenyl)-phenanthren-9-yl-methanols. These series of compounds were evaluated against Mycobacterium tuberculosis H37Rv and showed the desired activity in the range of 6.25 microg/mL in vitro. One of the compound 12j protects the mice from the challenge of M. tuberculosis in vivo, as 30% of the mice were survived at treatment of 50 mg/kg body weight.

Rational design of new antituberculosis agents: receptor-independent four-dimensional quantitative structure-activity relationship analysis of a set of isoniazid derivatives

A 4D-QSAR analysis was carried out for a set of 37 hydrazides whose minimum inhibitory concentrations against M. tuberculosis var. bovis were evaluated. These ligands are thought to act like isoniazid in mycolic acid biosynthesis. Results indicate that nonpolar groups in the acyl moiety of ligands markedly decrease biological activity. Molecular modifications of the ligand NAD moiety, including nonpolar groups and hydrogen bond donor and acceptor groups, seemingly improve ligand interactions with amino acid residues of the InhA active site.