1H and 13C NMR characterization of hemiamidal isoniazid-NAD(H) adducts as possible inhibitors of InhA reductase of Mycobacterium tuberculosis

Isoniazid (INH) is easily oxidized with manganese(III) pyrophosphate, a chemical model of the KatG protein involved in activation of INH inside the bacteria Mycobacterium tuberculosis. Performed in the presence of NAD(+), this oxidation generates a family of isomeric INH-NAD(H) adducts, which have been shown to be effective inhibitors of InhA, an enzyme essential in mycolic acid biosynthesis. In this work, we fully characterized by (1)H and (13)C NMR spectroscopy four main species of INH-NAD(H) adducts that coexist in solution. Two of them are open diastereoisomers consisting of the covalent attachment of the isonicotinoyl radical at position four of the nicotinamide coenzyme. The other two result from a cyclization involving the amide group from the nicotinamide and the carbonyl group from the isonicotinoyl radical to give diastereoisomeric hemiamidals. Although an INH-NAD(H) adduct with a 4S configuration has been characterized within the active site of InhA from Xray crystallography and this bound adduct interpreted as an open form (Rozwarski et al., Science 1998, 279, 98-102), it is legitimate to raise the question about the effective active form(s), open or cyclic, of INH-NAD(H) adduct(s). Is there a single active form or are several forms able to inhibit the InhA activity with different levels of inhibitory potency?     

Superoxide reactivity of KatG: insights into isoniazid resistance pathways in TB

To gain insight into the mechanism of INH activation by KatG and to understand how resistance is conferred by the single active-site point mutation of KatG(S315T), we have employed pulse radiolysis as the means to initiate a catalytic pathway capable of mimicking the in vivo oxidation of isoniazid (INH). Radiolysis of a solution containing WT KatG revealed two intermediates: compound III (oxyferrous KatG) [415 (Soret), 545, 580 nm] formed [k1 = (4.47 +/- 0.91) x 105 M-1 s-1] in the absence of INH and compound II (410 (Soret), 540, 575 nm) formed [k1 = (4.43 +/- 0.69) x 105 M-1 s-1] in the presence of INH, with a comparison of the rates suggesting that compound III (rate-limiting) precedes compound II formation. By contrast, radiolysis of KatG(S315T) only led to compound III formation, whether INH was present [k1 = (4.72 +/- 0.99) x 105 M-1 s-1] or not [k1 = (4.51 +/- 1.38) x 105 M-1 s-1]. HPLC studies to determine the rates of INH-NADH adduct formation (an inhibitor of InhA) as catalyzed by KatG were also performed employing various oxidants: air [WT: (7.18 +/- 1.25) x 10-4, S315T: (0.74 +/- 0.39) x 10-4], superoxide (SOTS-1) [WT: (9.22 +/- 1.10) x 10-4, S315T: not detected], and tert-butylhydroperoxide [WT: (20.5 +/- 1.13) x 10-4, S315T: (10.15 +/- 0.19) x 10-4]. Taken together, the results from the pulse radiolysis work as well as the InhA inhibitor studies allow us to propose a mechanism capable of correlating the inability for the oxyferrous intermediate of KatG(S315T) to oxidize ("activate") INH to the suppressed formation of the INH-NADH adduct, thereby leading to INH resistance in Mycobacterium tuberculosis.     

Cross-docking study on InhA inhibitors: a combination of Autodock Vina and PM6-DH2 simulations to retrieve bio-active conformations

InhA, the NADH-dependent enoyl-acyl carrier protein reductase from Mycobacterium tuberculosis (Mtb) is the proposed main target of the first-line antituberculosis drug isoniazid (INH). INH activity is dependent on activation by the catalase peroxidase KatG, a Mtb enzyme whose mutations are linked to clinical resistance to INH. Other inhibitors of InhA that do not require any preliminary activation are known. The design of such direct potent inhibitors represents a promising approach to circumvent this resistance mechanism. An ensemble-docking process with four known InhA X-ray crystal structures and employing the Autodock Vina software was performed. Five InhA inhibitors whose bioactive conformations are known were sequentially docked in the substrate cavity of each protein. The efficiency of the docking was assessed and validated by comparing the calculated conformations to the crystallographic structures. For a same inhibitor, the docking results differed from one InhA conformation to another; however, docking poses that matched correctly or were very close to the expected bioactive conformations could be identified. The expected conformations were not systematically well ranked by the Autodock Vina scoring function. A post-docking optimization was carried out on all the docked conformations with the AMMP force field implemented on the VEGAZZ software, followed by a single point calculation of the interaction energy, using the MOPAC PM6-DH2 semi-empirical quantum chemistry method. The conformations were subsequently submitted to a PM6-DH2 optimization in partially flexible cavities. The resulting interaction energies combined with the multiple receptor conformations approach allowed us to retrieve the bioactive conformation of each ligand.     

Is the isonicotinoyl radical generated during activation of isoniazid by MnIII-pyrophosphate?

The antituberculosis drug isoniazid (INH) is quickly oxidised by stoichiometric amounts of manganese(III)-pyrophosphate and the following products were identified: isonicotinic acid 1, isonicotinamide 2 and isonicotinaldehyde 3, the acid being the major product. The oxidation of INH with Mn^III-pyrophosphate was carried out in either H₂¹⁶O, or H₂¹⁸O or D₂O and under varied atmosphere composition (argon, air, O₂ or ¹⁸O₂). LC–MS analyses of isotope incorporation suggest the simultaneous presence of two competitive pathways leading to the formation of acid 1, with the isonicotinoyl radical as a common intermediate. One route is oxygen-dependent and the other is water-dependent. Analyses of isotope incorporation in amide 2 and aldehyde 3 also support this mechanism.     

An inorganic iron complex that inhibits wild-type and an isoniazid-resistant mutant 2-trans-enoyl-ACP (CoA) reductase from Mycobacterium tuberculosis

The in vitro kinetics of inactivation of both wild-type and I21V InhA enzymes by [FeII(CN)5(INH)]3- indicate that this process requires no activation by KatG, and no need for the presence of NADH. This inorganic complex may represent a new class of lead compounds to the development of anti-tubercular agents aiming at inhibition of a validated target.     

Kinetics and mechanism of the reaction between aquacobalamin and isoniazid

Kinetics of the reaction of aquacobalamin (H₂OCbl) with isoniazid (isonicotinic acid hydrazide, INH) in weakly alkaline, neutral, and weakly acidic media was studied using UV–Vis spectroscopy. It is shown that the reversible formation of a complex more stable than those of cobalamin(III) with pyridine and hydrazine occurs during the reaction. A mechanism of the reaction includes reversible stages of binding a neutral INH molecule by cobalamin(III) through an oxygen atom with its subsequent deprotonation, along with the reversible interaction of H₂OCbl and the negatively charged form of INH.     

The first chemical synthesis of the core structure of the benzoylhydrazine-NAD adduct, a competitive inhibitor of the Mycobacterium tuberculosis enoyl reductase

[reaction: see text] An isoniazid-NAD adduct has been recently proposed as the ultimate metabolite responsible for the antituberculous activity of isoniazid (INH). Its structure results from binding of the isonicotinoyl radical at C4 position of the nicotinamide ring of NAD with further possible and debated cyclization to form a cyclic hemiamidal derivative. Replacing the pyridine cycle of INH in INH-NAD adduct by a phenyl cycle (BH-NAD adduct) was shown previously to still retain the activity. On these bases, the core structure (4-benzoyl-1,4-dihydronicotinamide ribonucleoside) of the BH-NAD adduct and a series of analogues have been synthesized by using 3,4-pyridinedicarboximide as starting material. Depending on the nature of the substituent (pyridine or aryl) and on the oxidized or the reduced state of the nicotinamide nucleus, they were found either in a cyclized hemiamidal or an opened form or were shown to exist in equilibrium under cyclized or opened forms. Although none of these compounds could significantly inhibit activity of the InhA or MabA reductases (two possible targets of isoniazid), they represent attractive targets to develop potential second-generation inhibitors, including the total chemical synthesis of the bioactive BH-NAD adduct.     

Design,synthesis and computational approach to study novel pyrrole scaffolds as active inhibitors of enoyl ACP reductase (InhA) and Mycobacterium tuberculosis antagonists

Novel 54 pyrrolyl acetohydrazide analogues were designed, synthesized and screened for antitubercular activity against InhA. Enoyl-ACP reductase/InhA one of the significant enzymes implicated in type II FAS (fatty acid synthase) biosynthetic pathway of bacterial outer cell membrane, in addition Mycobacterium tuberculosis H37Rv inhibition potency has proven to be one of the most promising drug target used for designing and testing against TB. In silico molecular modeling was achieved using Surflex-docking method to recognize important binding sites of the enoyl-ACP reductase. 3D-QSAR studies like CoMFA and CoMSIA approaches were studied to create 3D-QSAR depictions for InhA inhibitors. Based on docking results the synthesized molecules are oriented towards the core of the active site. The pyrolyl acetohydrazides exhibited one or two H-bonding connections with InhA enzyme. Molecule 8l (MIC 0.4 μg/mL, InhA- 70% at 50 μM) showed H-bonding connections with Tyr158 and NAD⁺ in a similar mode to that of ligand pyrrolidine carboxamide. The tested molecules also showed good antibacterial (Escherichia coli, Staphylococcus aureus) activity (MIC 0.4–25 μg/mL), while the study against A549 lung adenocarcinoma cell line confirms nontoxic nature of the reported molecules. The QSAR model from CoMFA and CoMSIA through the database configuration showed the most excellent data. The prognostic ability of CoMFA and CoMSIA representations was developed by a test set of 15 molecules that produced cross validated correlation coefficients (q²) of 0.642 and 0.701, respectively. This study gives insight into structural requirement needed for the development of more active InhA inhibitors through in silico approach.     

1H and 13C NMR characterization of pyridinium-type isoniazid-NAD adducts as possible inhibitors of InhA reductase of Mycobacterium tuberculosis

Oxidative activation of the antituberculous drug isoniazid (INH) in the presence of the NADH cofactor gives a pool of INH-NAD adducts proposed to be involved in the mechanism of action of this drug through inhibition of the reductase InhA. Among these adducts and besides dihydropyridine derivatives, two pyridinium-type isoniazid-NAD adducts were shown to be formed in solution and have been fully characterized by 1H/13C NMR and MS. One of them results from the oxidation of dihydropyridine-type INH-NAD adducts. The spectral data strongly support its existence under two epimeric structures. These epimers arise from a cyclization process between the carboxamide group and the ketone function with the creation of a new chiral center at C-7. The second pyridinium-type adduct was formed in acidic solution by dehydration of the cyclized dihydropyridine-type INH-NAD adducts and also exists as a cyclized structure. Both of these pyridinium-type compounds were inactive as inhibitors of InhA activity and can be considered as deactivated species.     

Evidence from Raman spectroscopy that InhA, the mycobacterial enoyl reductase, modulates the conformation of the NADH cofactor to promote catalysis

InhA, the enoyl reductase from Mycobacterium tuberculosis, catalyzes the NADH-dependent reduction of trans-2-enoyl-ACPs. In the present work, Raman spectroscopy has been used to identify catalytically relevant changes in the conformation of the nicotinamide ring that occur when NADH binds to InhA. For 4(S)-NADD, there is an 11 cm-1 decrease in the wavenumber of the C4-D stretching band (nuC-D) and a 50% decrease in the width of this band upon binding to InhA. While a similar reduction in line width is observed for the corresponding band arising from 4(R)-NADD, nuC-D for this isomer increases 34 cm-1 upon binding to InhA. These changes in nuC-D indicate that the nicotinamide ring adopts a bound conformation in which the 4(S)C-D bond is in a pseudoaxial orientation. Mutagenesis of F149, a conserved active site residue close to the cofactor, demonstrates that this enzyme-induced modulation in cofactor structure is directly linked to catalysis. In contrast to the wild-type enzyme, Raman spectra of NADD bound to F149A InhA resemble those of NADD in solution. Consequently, F149A is no longer able to optimally position the cofactor for hydride transfer, which correlates with the 30-fold decrease in kcat and 2-fold increase in D(V/KNADH) caused by this mutation. These studies thus substantiate the proposal that hydride transfer is promoted by pseudoaxial positioning of the NADH pro-4S bond, and indicate that catalysis of substrate reduction by InhA results, in part, from correct orientation of the cofactor in the ground state.     

A dityrosine-based substrate for a protease assay: Application for the selective assessment of papain and chymopapain activity

N,N′-diBoc-dityrosine (DBDY), which was synthesized by the oxidative C–C coupling of 2 N-Boc-l-tyrosine molecules, was conjugated with two isoniazid (INH) molecules. Due to the quenching effect of INH, DBDY–(INH)₂ lacks the fluorescence of DBDY. As such, it was tested for use in the detection of proteases by measuring fluorescence recovery. In this study, serine proteases (chymotrypsin, trypsin, subtilisin, and proteinase K), metalloproteases (thermolysin and carboxypeptidase A, dispase, and collagenase), aspartic proteases (pepsin and aspergillopepsin) and cysteine proteases (papain and chymopapain) were chosen. Reported optimum assay conditions were chosen for each enzyme. Only papain and chymopapain catalyzed the hydrolysis of DBDY–(INH)₂ and led to fluorescence recovery, possibly due to their extensive binding sites and the INH-mediated inhibition of metalloproteases and aspartic proteases.     

Study of cloud point extraction and high-performance liquid chromatographic determination of isoniazid based on the formation of isonicotinylhydrazone

Isoniazid (INH) reacted with p-dimethylaminobenzaldehyde (DABD) in the presence of trichloroacetic acid to give isonicotinylhydrazone (INZ) having λ_max 365 nm. Cloud point extraction (CPE) is carried out to extract INH and IHZ in aqueous solutions using surfactant poly(ethylene glycol) 4000 (PEG4000), respectively. Langmuir model is used to study the adsorption behaviors of the two solutes on micelles of PEG4000. A linear correlation is found between variation of PEG4000 concentration required for feed concentration of the two solutes and used to predict PEG4000 concentration required for extracting INH and IHZ in CPE procedure. The results calculated show that, for a desired recovery level of 90%, only can IHZ be sufficiently extracted by PEG4000. In this experiment, the feed concentration of PEG4000 is defined by above-mentioned correlation, and the effects of other operating parameters, e.g., concentration of salt, pH and centrifugation time on extraction of PEG4000-IHZ system have also been studied in detail. The proposed CPE method coupled with HPLC-UV system is successfully used for the determination of INH in urine sample.     

The Properties of Solutions of Isoniazid in Water and Dimethylsulfoxide

The density, viscosity and conductivity of binary mixtures of the front line antitubercular drug isoniazid (INH), in aqueous solution and dimethylsulfoxide (DMSO) solution, were determined at various temperatures (25, 37 and 55?°C) up to 0.3 mol?L^?1 of INH. The apparent molar volumes were calculated from the density data. In the INH + water system the apparent molar volume of INH changed smoothly, whereas in the INH + DMSO system it passes through a maximum. Also, both systems showed pronounced maxima in their viscosity and conductivity isotherms. In addition, UV?CVis, FT-IR and ¹H NMR spectroscopy were performed on the solutions. On the basis of this data, the predominant molecular interactions occurring between INH and water and between INH and DMSO were found to be hydrogen bonds. Furthermore, the susceptibility profile of DMSO, INH and its combination was studied against M. tuberculosis H₃₇Rv and the minimum inhibitory concentration (MIC) determined. The results suggest a synergistic effect of INH at sub-MIC concentrations and DMSO.     

Rational design of InhA inhibitors in the class of diphenyl ether derivatives as potential anti-tubercular agents using molecular dynamics simulations

A series of diphenyl ether derivatives were developed and showed promising potency for inhibiting InhA, an essential enoyl acyl carrier protein reductase involved in mycolic acid biosynthesis, leading to the lysis of Mycobacterium tuberculosis. To understand the structural basis of diphenyl ether derivatives for designing more potent inhibitors, molecular dynamics (MD) simulations were performed. Based on the obtained results, the dynamic behaviour in terms of flexibility, binding free energy, binding energy decomposition, conformation, and the inhibitor–enzyme interaction of diphenyl ether inhibitors were elucidated. Phe149, Tyr158, Met161, Met199, Val203 and NAD+ are the key residues for binding of diphenyl ether inhibitors in the InhA binding pocket. Our results could provide the structural concept to design new diphenyl ether inhibitors with better enzyme inhibitory activity against M. tuberculosis InhA. The present work facilitates the design of new and potentially more effective anti-tuberculosis agents.     

Spectroscopic and theoretical study of the o-vanillin hydrazone of the mycobactericidal drug isoniazid

A complete and detailed study of the hydrazone obtained from condensation of antituberculous isoniazid (hydrazide of the isonicotinic acid, INH) and o-vanillin (2-hydroxy-3-methoxybenzaldehyde, o-HVa) is performed. It includes structural and spectroscopic analyses, comparing experimental and theoretical results. The compound was obtained as a chloride of the pyridinic salt (INHOVA⁺Cl^?) but it will be referred as INHOVA for the sake of simplicity. The conformational space was searched and optimized geometries were determined both in gas phase and including solvent effects. Vibrational (IR and Raman), electronic and NMR spectra were registered and assigned with the help of computational methods based on the Density Functional Theory. Isoniazid hydrazones are good candidates for therapeutic agents against tuberculosis with conserved efficiency and lower toxicity and resistance than parent INH.     

Insight into crucial inhibitor–enzyme interaction of arylamides as novel direct inhibitors of the enoyl ACP reductase (InhA) from Mycobacterium tuberculosis: computer-aided molecular design

Abstract  

The enoyl ACP reductase enzyme (InhA) involved in the type II fatty acid biosynthesis pathway of Mycobacterium tuberculosis is an attractive target enzyme for antitubercular drug development. Arylamide derivatives are a novel class of InhA inhibitors used to overcome the drug-resistance problem of isoniazid, the frontline drug for tuberculosis treatment. Their remarkable property of inhibiting the InhA enzyme directly without requiring any coenzyme, makes them especially appropriate for the design of new antibacterials. In order to find a sound binding conformation for the different arylamide analogs, molecular docking experiments were performed with subsequent QSAR investigations. The X-ray conformation of one arylamide within its cocrystallized complex with InhA was used as a starting conformation for the docking experiments. The results thus obtained are perfectly consistent (rmsd = 0.73 ?) with the results from X-ray analysis. A thorough investigation of the arylamide binding modes with InhA provided ample information about structural requirements for appropriate inhibitor–enzyme interactions. Three different QSAR models were established using two three-dimensional (CoMFA and CoMSIA) and one two-dimensional (HQSAR) techniques. With statistically ensured models, the QSAR results obtained had high correlation coefficients between molecular structure properties of 28 arylamide derivatives and their biological activity. Molecular fragment contributions to the biological activity of arylamides could be obtained from the HQSAR model. Finally, a graphic interpretation designed in different contour maps provided coincident information about the ligand–receptor interaction thus offering guidelines for syntheses of novel analogs with enhanced biological activity.     

Therapeutic Monitoring of Isoniazid, Pyrazinamide and Rifampicin in Tuberculosis Patients Using LC

The objective of this study was to measure plasma concentration of isoniazide (INH), pyrazinamide (PZA) and rifampisin (RIF) in tuberculosis patients by using HPLC. 100 μL of plasma was deproteinized by adding trichloroacetic acid and acetonitrile to yield INH, PZA and RIF respectively. They were analysed by HPLC using a reversed phase C₁₈ pre-column linked to a 4 μm C₁₈ analytical column with a gradient solvent programme, which delivered 3% to 40% (v/v) acetonitrile in phosphate buffer in 20 min at rate of 0.8 mL min^?1. Signals were monitored by diode-array detector. Acetanilide was used as internal standard. The method is reproducible and accurate with lower limits of quantification of 0.6 mg L^?1 for INH, 1.5 mg L^?1 for PZA and 0.7 mg L^?1 for RIF. The plasma of 25 patients receiving daily standard therapy were assayed for INH, PZA and RIF 3 h after administration. Plasma concentration were found between 0.98 and 6.27 mg L^?1 for INH, 11.05 and 47.26 mg L^?1 for PZA, 5.09 and 33.20 mg L^?1 for RIF respectively. Many of the plasma levels were found to be sub therapeutic. This practical method may be used for monitoring drug plasma levels of patients who fail to respond to treatment.     

Development and Validation of a Novel Gradient LC Method for Simultaneous Determination of Isoniazid and Acetylisoniazid in Human Plasma

The goal of this study was to develop and validate a new gradient high-performance liquid chromatography method for the simultaneous determination of isoniazid (INH) and acetylisoniazid (Ac-INH) in human plasma samples. A C18 reversed-phase column was employed for separation followed by UV detection at 266 nm. The calibration involved the use of five concentration levels ranging from 1 to 20 μg mL^?1 for both analytes. The developed method was validated using ICH guidelines. The calibration curve was found to be linear with correlation coefficient values (r ²) above 0.9991 and the highest RSD% values for intra-day assays were found to be 6.34 and 2.57% for INH and Ac-INH, respectively. The highest RSD% values for inter-day assays were 9.31 and 10.17% for INH and Ac-INH, respectively. LOD was calculated to be 0.1 and 0.15 μg mL^?1 for INH and Ac-INH, respectively. LOQ was calculated to be 0.33 and 0.5 μg mL^?1 for INH and Ac-INH, respectively.     

Molecular Adducts of Isoniazid: Crystal Structure,Electronic Properties,and Hirshfeld Surface Analysis

Three molecular adducts of the antituberculosis drug isoniazid (INH) are synthesized with γ-resorcylic acid (γRA), phloroglucinol (PG), and gallic acid (GA). The new solid phases are preliminarily characterized by the thermal analysis (DSC/TGA) and powder X-ray diffraction. The formation of new solid phases is confirmed by single crystal X-ray diffraction, infrared (FT-IR) and Raman spectroscopy. All three new solid crystalline forms are stabilized by various hydrogen bonding interactions such as N⁺···H–O^–, N···H–O, O···H–O, and π–π stacking. The FT-IR analysis puts forward that the solid form of INH1 is a salt whereas the INH2 and INH3 molecular complexes are cocrystals. We have also investigated the density of states (DOS), band structure, and atomic orbit projected density of state (PDOS) of title compounds by adopting the density functional theory (DFT) technique in the local density approximation (LDA). The electronic structure calculations show that energy states are delocalized in the k-space due the hydrogen and covalent bonds in the crystals. The frontier molecular orbital (FMO) analysis reveals that charge transfer takes place within the compounds. The Hirshfeld analysis shows that H–H and N?H–O hydrogen bonding interactions are dominant in all three molecular adducts of INH.     

Substrate inhibition in an enzymatic ordered bireactant system: non-linear modelling of the kinetics of hypoxanthine-guanine-phosphoribosyltransferase

Hypoxanthine-guanine-phosphoribosyltransferase (HGPRT; EC 2.4.2.8) was determined as an enzyme following an ordered bireaction in the presence of substrate inhibition due to hypoxanthine. This kind of inhibition has not been postulated for HGPRT so far. The mechanism and the kinetic constants of the reaction of HGPRT from Saccharomyces cerevisiae were investigated by initial velocity studies involving a non-linear regression analysis. In addition, two kinds of experimental designs were compared: the variation of hypoxanthine concentrations over wide ranges at different of fixed levels of 5-phosphoribosyl-1-pyrophosphate, and the use of five appropriate sets of experimental conditions each characterized by different hypoxanthine and 5-phosphoribosyl-1-pyrophosphate concentrations. Both experimental designs were consistent with an ordered bi bi mechanism including a dead-end-complex between the enzyme and hypoxanthine.