Molecular Docking Studies of Some Novel N’-Substituted Pyrrole Heterocyclics and Aromatic Sulphonamides as Antimycobacterial Agent

INTRODUCTION

Pyrrole analogues and aromatic sulfonamides are class of biologically important molecule. Significant amount of investigation has been focused towards pyrrole class of motifs. In specific, they are evaluated as antibacterial, antifungal, antiviral, antiprolifertive and antitubercular agents.^1-4 Moreover, pyrroles have played a major part in the expansion of theory of heterocyclic combinations, and they are also used comprehensively in organic synthesis.⁵ Pyrrole is one among the vital heterocycle in plant and animal kingdom since its participation as a subunit of chlorophyll in plant cells and hemin and vitamin B12 in animal cells. Joshi and co-workers have reported some pyrrolyl adducts and they have shown substantial antimycobacterial actions.^6,7 Literature shows the pharmacological importance of pyrroles and potentiality of peptide linkage in tuberculosis studies. Till 1950s, sulfonamides^8-13 and sulfones¹⁴ remained used as nontherapeutic medications to treat TB, the initial preparations of sulfonamides other than sulfanilamide were commonly found to obligate some efficacy. Due to high toxicity of the sulfones and sulfonamides¹⁵ isoniazid (INH) and streptomycin were found stronger antituberculousis drugs.¹⁶

Docking theory depicts structural topographies mandatory for binding of ligand with the amino acid deposits and the co-factor occur in the active part of the enzyme. Among the important class of pharmacophores responsible for antitubercular and antibacterial activity, pyrrole substituted scaffolds are measured to be the practical lead skeletal structures for the design as well as synthesis of the additional active and broad spectrum antitubercular agents. Our earlier reports defined the synthesis and docking analysis of different heterocyclic moieties.^17-19 In prolongation of reported studies, herein we outline the docking studies on pyrrole heterocyclic derivatives as antitubercular agents.

The compounds^20-22 were selected for molecular design and modelling studies (Table 1) and 4TZK have carboxamide moiety in common, which suggested that Mycobacterium tuberculosis (M. tuberculosis) enoyl reductase (InhA) complexed with 1-cyclohexyl-N-(3,5-dichlorophenyl)-5- oxopyrrolidine-3-carboxamide enzyme could be the selective target for the current study. Henceforth, the reported crystal structure of the M. tuberculosis PDB code 4TZK ((InhA complexed with 1-cyclohexyl-N-(3,5-dichlorophenyl)-5- oxopyrrolidine-3-carboxamide) was used.

Material and Methods

Molecular Modeling and Docking:

Molecular modeling was carried out by means of Sybyl-X, version 2.023, running on a Intel® Core TM i3-2130 CPU@ 3.40GHz processor using Windows 10 professional workstation. Surflex-Dock procedure of sybyl was castoff to dock intended compounds. The crystal structure of M. tuberculosis with enoyl reductase (InhA) complexed with 1-cyclohexyl-N-(3,5-dichlorophenyl)-5- oxopyrrolidine-3-carboxamide were downloaded from the Protein Data Bank (PDB entry code 4TZK, http://www.rcsb.org/pdb) and used for initial docking protocols. Co-crystalized ligand and water molecules were detached from structure, H-atoms were added and side chains were fixed throughout protein preparation. The structure was then subjected to an energy refinement method. Gasteigere-Huckel charge24 were calculated for the ligand, while Amber 7FF02 was used for the protein. The model was then subjected to energy minimization following the gradient termination of the Powell method for 3000 iterations using Tripose force field with non-bonding cutoff set at 9.0 and the dielectric constant set at 4.0. Binding of the pyrrole scaffolds was also assessed using a variety of scoring functions that have been compiled into the single consensus score (CScore). The CScore module (Total Score) available in Sybyl includes the G_Score, PMF_Score, D_Score and ChemScore scoring functions.

Results and Discussion

To investigate the thorough intermolecular relations among the ligand and target protein, a program Surflex-Dock was used. Three-dimensional molecular information on the target protein was taken from the PDB entry 4TZK. Processing of the protein included the deletion of the ligand and the solvent moieties as well as the addition of hydrogen atoms. All 27 inhibitors were docked to the active spot on enzyme as described in figures 1A and 1B. The predicted binding energies of the molecules are enumerated in Table2. As shown in figures 3A, 3B and 3C, compound 2 showed two H-bonding interactions at the dynamic site of the enzyme, H-bonding connections were raised from the C=O group of amide with H-atom of amino acid residue TYR158 (C=O -------- H- TYR158, 1.88 Å) and H-atom of NAD+ (C=O -------- H- NAD+, 1.94 Å). Further compound 8showed two H-bonding contacts at the active site of the enzyme (figures 4A, 4B and 4C), O-atom of sulphonamide makes a H-bonding interaction with H-atom of amino acid residue TYR158 (S=O -------- H- TYR158, 1.97 Å),hydrogen atom of -NH group present at 4th position of aromatic amine makes a H-bonding interaction with oxygen atom of NAD+ (CO-NH -------- ONAD+, 1.98 Å).Figures 5A, 5B and 5C shows the connections of compound 26 with the enzyme which has similar H-bonding, complex (ligand-protein), and internal (ligand-ligand) energies as that of ligand 4TZK. Figures 2A, 2B and 2C depicts interaction of 4TZK with active site of the enzyme. Helmholtz free energies for protein-ligand interactions of atom braces for all compounds showed similar to that of ligand. Compounds scoring with respect to the reward for H-bonding, lipophilic contact, rotational entropy along with an intercept terms revealed that compound 26 shows alike interactions with the protein as that of ligand and other compounds, and showed three interactions, O-atom carbonyl group makes a two O-bonding interaction with H-atoms of amino acid residue TYR158 (C=O -------- H- TYR158, 2.08 Å) and NAD+ (C=O -------- H- NAD+, 1.89 Å). The hydrogen of amide group makes a H-bonding interaction with O-atoms of amino acid residue NAD+ (CO-NH -------- O- NAD+, 2.37 Å).

All the reported molecules showed consensus score in the range of 8.23-1.51, representing the summary of all forces of interface between ligands and enzyme. Charge and van der Waals exchanges between protein and ligands varied from -81.669 to -169.418. The Helmholtz free energies for protein ligands interactions of atom pairs range between -14.338 and -64.226. Though, its hydrogen bonding, complex (ligand-protein), and internal (ligand-ligand) energies range from -142.636 to -343.205. The resulting scores indicate that compounds favorably bind to the enzyme in contrast to the reference 4TZK ligand (Table 2). And we also saw that studied molecules have exposed same type of contacts with amino acid residue TYR158 and cofactor NAD as that of 4TZK ligand.

Docking outcomes provided the detailed structurally important binding topographies between pyrrole and sulphonamide derivatives and the enzyme. From docking score, it may be decided that the reported compounds showed decent interaction with the enzyme active site related to the ligand 1-cyclohexyl-N-(3,5- dichlorophenyl)-5-oxopyrrolidine-3-carboxamide.

The Lipinski’s ‘rule of 5’ was calculated for all the 27 compounds. The poor absorption or permeation is utmost possible when, there are more than 5 H-bond donors, the molecular weight is above 500, the cLogP is above 5 and there are more than 10 H-bond acceptors25. We also calculated the theoretical cLogP, molecular weight (MW) and numeral of hydrogen bond donors and acceptors using sybyl-X.2.0. Observing the results in Table 3 it can be said that compounds 1-27 gratified the physicochemical parameters range established by the Lipinski’s rule. 

CONCLUSION

In present study, analysis of docking study provided details on fine relationship linking structure and activity, and offer evidences for structural modifications (C=O-NH/SO-NH linkages) that can improve the potency. Stated compounds showed favorable physicochemical parameters that are required to exhibit desired action. All these molecular skeletons synthetically modified using the further advanced computational techniques such as pharmacophore mapping along with 3D-QSAR studies will yield an utmost potent M. tuberculosis inhibitor.