Molecular Docking Study of New Pyrrolyl Benzohydrazide Schiff Bases as M. tuberculosis InhA Enzyme Inhibitors

Introduction

Pyrrole and its derivatives are biologically significant organic compounds owing to various pharmacological properties like antibacterial, antitubercular, antifungal, antiviral, antimicrobial, anti-inflammatory, analgesic, and anticancer activities. These compounds exist in natural molecules and can also be synthesised. Pyrrole continues to be a desirable target in the development of new synthetic processes and molecules due to its wide biological significance and presence in synthetic chemistries.¹ In particular, anti-bacterial activity exhibited by pyrrole-based scaffolds has been widely explored in recent decades focussing drug resistant mycobacteria and gram positive, negative microbes. Hydrazones, azomethines, imines related to carbonyl compounds having chemical formula (-C=NNH-) constitute an important moiety for novel drug design and development.² Hydrazones with various functional groups were combined to create molecules with distinctive physical and chemical properties. According to a literature review, hydrazones possess antibacterial, anticonvulsant, antimycobacterial, anticancer, antiinflammatory, analgesic, antifungal, cytotoxic, and anthelmintic properties.^3-11

Despite the emergence of bacterial resistance to infections, the search for antibacterials is an ongoing job. The pharmacological importance and promise of the pyrrole scaffolds with peptide links reported by Joshi and coworkers as effective antimycobacterial drugs were demonstrated in the literature.^12,13 Enzyme’s active region exhibits the structural conformations essential for ligand binding to the amino acid deposits and co-factor, according to docking theory. Our earlier reports have described the molecular modeling, synthesis, structural characterization of several pyrrole-based moieties.^14-16 We present here the docking outcomes for pyrrole-based hydrazones acting as antitubercular agents in accordance with previously published findings. For molecular design and graphical studies, compunds¹⁷ depicted in Table 1 were selected and 4TZK protein in association with the ligand was chosen. The carboxamide group of 4TZK similar to selected compounds suggested that enzyme would be a suitable target for the present study. Therefore, M. tuberculosis PDB code 4TZK, the reported crystal structure was used.

Materials and Methods

Molecular Modeling and Docking

Sybyl-X, version 2.0, which runs on an Intel® Core TM i3-2130 CPU@ 3.40 GHz processor and a Windows 10 professional workstation, was used to do molecular modelling.¹⁸ Sybyl's Surflex-Dock method was abandoned for docking the desired compounds. To download targeted protein 4TZK, PDB entry code 4TZK (http://www.rcsb.org/pdb) was utilized and used for the initial docking experiments. During the protein synthesis process, co-crystallized ligand along with water molecules were separated from the structure, added the H-atoms, and fixed the side chains. After that, the structure underwent a process of energy refinement. While Gasteigere-Huckel charge was computed for the ligand, Amber 7FF02 was used for the protein.¹⁹ The model was subjected to energy reduction utilizing the Tripose force field with a non-bonding cutoff set at 9.0 and the dielectric constant set at 4.0 for 3000 iterations after the gradient termination of the Powell technique. Binding of the pyrrole scaffolds was also assessed using a number of scoring techniques that were merged into a single consensus score (CScore). The CScore module (Total Score), which is available in Sybyl, contains the scoring functions for G_Score, PMF_Score, D_Score, and ChemScore.

Results

The 16 inhibitors were docked to the targeted enzyme’s active site as shown in Figures 1A, 1B. Figures 2A, 2B, 2C represents the docking modes of 4TZK.

Compound 5 exhibited four H-bonding interactions at the enzyme’s dynamic site and these were formed from C=O of amide group with H-atom of amino acid’s residue ALA22 (C=O -------- H-ALA22, 2.71 Å, SER94 H-atom with (C=O -------- H-SER94, 2.50 Å), NH H-atom with amino acid’s H-atom, GLY14 (NH --------H-GLY14, 1.70 Å and C=O of amide group with amino acid’s H-atom ILE21 (C=O -------- H-ILE21, 2.71 Å).

Further, compound 16 exhibited four H-bonding contacts at the enzyme’s active site (Figures 4A, 4B, 4C), C=O of amide group with amino acid’s H-atom, ALA22 (C=O -------- H-ALA22, 1.99 Å), SER94 H-atom (C=O -------- H-SER94, 2.43 Å), H-atom of NH with H- amino acid’s H-atom GLY14 (NH --------O-GLY14, 2.03A0 and C=N of imine group with amino acid’s H-atom SER20 (C=O -------- H-SER20, 2.88 Å).

Consensus scores for all of the reported compounds ranged from 5.47 to 3.32, which summarised the forces at play when ligands and enzymes come in contact. The Van der Waals exchanges range of -81.231 to -125.842 was observed between ligand and the protein. Between are the Helmholtz free energy ranged from -14.338 to -64.226 of interactions between atom pairs in protein ligands. Its energies for internal (ligand-ligand) and complex (ligand-protein) hydrogen bonds ranged from -135.765 to -269.191. Substances actively binded to the enzyme favourably against reference 4TZK according to the results depicted in Table 2

Discussion

Considering the crystal structure, 3D molecular information of 4TZK, a thorough investigation was done to analyse binding affinities of ligands and target protein using Surflex-Dock program. In protein processing ligand, solvent moieties were deleted and hydrogen atoms were added.

We noticed the examined inhibitors exposed similar kind interfaces between NAD cofactor and amino acid residue TYR15 produced by 4TZK ligand. The precise binding topographies of the pyrrole benzohydrazide schiff bases with targeted enzyme were revealed by docking results. The described chemicals appeared to interact with the enzyme’s active site concisely based on the docking score revealed by the ligand 1-cyclohexyl-N-(3, 5-dichlorophenyl)-5-oxopyrrolidine-3-carboxamide. Lipinski’s "rule of five” was determined for each of the 16 compounds. If H-bond donors are more than five, H-bond acceptors are more than 10, molecular weight is greater than 500 and cLogP greater than 5, poor absorption or retention probably may occur.²⁰ We also calculated the theoretical cLogP, numeral of hydrogen bond donors, acceptors, and molecular weight of compounds using sybyl-X.2.0. On the basis of results tabulated in Table 3, it could be stated that the 16 compounds attained important physicochemical parameter range similar to Lipinski’s constants.

Conclusion

The present study highlights the surflex molecular docking results of pyrrole benzohydrazide schiff bases against M. tuberculosis PDB: 4TZK. This study was conducted with a strategy of investigating antitubercular agents which limit TB infection by blocking InhA enzyme. Docking results of current analysis afforded binding affinity of compounds linking chemical structure and inhibition activity. Selected compounds revealed encouraging physicochemical parameters required to exhibit needed action. By using advanced computational techniques such as pharmacophore mapping along with 3D-QSAR studies, the compounds can be altered synthetically to acquire potent M. tuberculosis inhibitors.

Conflict of interest

Nil

Acknowledgements

The authors greatly acknowledge Vision Group on Science and Technology, (VGST/GRD/NO-567/2016- 17/2020-21/47, dated: 3.08.2021) for research support. Our sincere appreciation to Dr. V. G. Jamakandi, Dean, Dr. T. M. Aminabhavi, Research Director and Dr. H. V. Dambal, President, SET’s College of Pharmacy, Dharwad for providing the facilities.