Optimized Structure, in Silico interaction and Molecular Docking Analysis of Two Benzimidazole-2-Thione Derivatives (original) (raw)
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Evalution and Molecular Docking of Benzimidazole and its Derivatives as a Potent Antibacterial Agent
Biomedical and Pharmacology Journal, 2019
The study was performed to identify a potent antibacterial benzimidazole derivative using in vitro and in silico techniques. Benzimidazole and its derivatives were synthesized by reflux process. The derivatives were screened for antibiotic susceptibility test (AST) and minimum inhibitory concentration (MIC) against Gram-negative and Gram-positive clinical isolates and compared with the positive control Norfloxacin. Insilico molecular docking was performed to screen the binding potential of the derivatives with target enzymes topoisomerase II /DNA gyraseof Escherichia coli (E.coli) and Staphylococcus aureus (S.aureus) along with the control Norfloxacin.Totally fifty-four isolates were screened for antimicrobial supectibility test (AST) and minimum inhibitory concentration (MIC) and 35 clinical isolates of Gram-negative showed 86% resistance to Norfloxacin and 19 isolates of Gram-positive showed 90% resistance to Norfloxacin. However, these isolates were found to be sensitive to 1-(4-((1H-benzimidazol-1-yl) methylamino) phenyl) ethanone (3) (C2), and 2-methyl-1H-benzimidazole (C4) compounds, with MIC ranges from 6.25-12.5 µg/ml. Molecular docking analysis revealed that the compound C2 exhibited better binding affinity towards topoisomerase II / DNA gyrase of E.coli and S.aureus when compared with C4 and control Norfloxacin. The antibacterial activity of these may due to the inactivation of these enzymes which is supported by the MIC results.The obtained in vitro and in silico results suggested that C2 showed better antimicrobial activity.
Malaysian Journal of Analytical Science, 2019
The emergence of antibiotic resistance against bacterial strains has attracted great interest in the discovery and development of new antibacterial agents. Thiazole derivatives have been widely used in the biological as well as pharmacological fields and their efficiency as pharmaceutical drugs are well established. In this study, a series of thiazole derivatives were synthesized in reaction between 3-chloroacetyl acetone and ammonium thiocyanate followed by incorporating selected amines in one-pot synthesis manner. The compounds were structurally characterized by Fourier Transform Infrared (FTIR), Proton Nuclear Magnetic Resonance (1 H NMR), Ultraviolet-Visible (UV-Vis) and Gas Chromatography-Mass Spectrometry (GC-MS). Their antibacterial properties were screened using disc diffusion technique against selected Gram-positive (Bacillus cereus and Staphylococcus epidermidis) as well as Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa) with T3 exhibited the most potent antibacterial activity. Molecular docking studies were also performed against Glucosamine-6-phosphate (GlcN-6-P) synthase which is known as the essential building block of most bacteria. The docking result displayed that T3 exhibited the minimum binding energy of-7.09 kcal mol-1 as compared to T1 and T2 with-6.49 and-6.76 kcal mol-1 , respectively which is in agreement with antibacterial result. The output of this preliminary study will contribute in structural enhancement in drug discovery.
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Benzothiazole analogs are very interesting due to their potential activity against several infections. In this research, five benzothiazole derivatives were studied using density functional theory calculations. The optimized geometry, geometrical parameters and vibrational spectra were analyzed. The charge distribution diagrams, such as FMO (HOMO-LUMO), energies of HOMO-LUMO, polarizability, hyperpolarizability, MESP and density of states, were calculated. The computed energies of HOMO and LUMO showed that the transfer of charge occurred within the compound. The effect of the change of substituents on the ring on the value of the HOMO-LUMO energy gap was also observed. It was observed that, in this series, compound 4 with CF3 substituent had the lowest energy gap of HOMO-LUMO, and compound 5 with no substituent had highest HOMO-LUMO energy gap. From the energies of HOMO and LUMO, the reactivity descriptors, such as electron affinity (A), ionization potential (I), chemical softness (...
RSC Advances, 2022
Two 1,3,4-oxadiazole-2-thione-N-Mannich derivatives, specifically 5-(4-chlorophenyl)-3-[(2trifluoromethylphenylamino)methyl]-1,3,4-oxadiazole-2(3H)-thione (1) and 5-(4-chlorophenyl)-3-[(2,5difluorophenylamino)methyl]-1,3,4-oxadiazole-2(3H)-thione (2), were synthesized and then characterized by elemental analysis and NMR (1 H and 13 C) spectroscopy and the single crystal X-ray diffraction method. The formed weak intermolecular interactions in the solid-state structures of these derivatives were thoroughly investigated utilizing a variety of theoretical tools such as Hirshfeld surface analysis and quantum theory of atoms in molecules (QTAIM). Furthermore, the CLP-PIXEL and density functional theory calculations were used to study the energetics of molecular dimers. Numerous weak intermolecular interactions such as C-H/S/Cl/F/p interactions, a directional C-Cl/Cl halogen bond, p-stacking, type C-F/F-C contact and a short F/O interaction, help to stabilize the crystal structure of 1. Crystal structure 2 also stabilizes with several weak intermolecular contacts, including N-H/S, C-H/ N//Cl/F interactions, a highly directional C1-Cl1/C(p) halogen bond and C(p)/C(p) interaction. In vitro antimicrobial potency of compounds 1 and 2 was assessed against various Gram-positive and Gramnegative bacterial strains and the pathogenic yeast-like Candida albicans. Both compounds showed marked activity against all tested Gram-positive bacteria and weak activity against Escherichia coli and lacked inhibitory activity against Pseudomonas aeruginosa. In addition, compounds 1 and 2 displayed good in vitro anti-proliferative activity against hepatocellular carcinoma (HepG-2) and mammary gland breast cancer (MCF-7) cancer cell lines. Molecular docking studies revealed the binding modes of title compounds at the active sites of prospective therapeutic targets.
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Quantum chemical calculation, performance of selective antimicrobial activity using molecular docking analysis, RDG and experimental (FT-IR, FT-Raman) investigation of 4-[{2-[3-(4-chlorophenyl)-5-(4-propan-2-yl) phenyl)-4, 5-dihydro-1H-pyrazol-1-yl]-4-oxo-1, 3-thiazol-5(4H)-ylidene} methyl] benzonitrile
Synthesis, antibacterial and molecular docking studies of new benzimidazole derivatives
The new analogs of benzimidazole fused heterocyclic compounds such as triazinane and oxadiazinanes were synthesised by classical amino methylation with different aryl-N,N 0 unsymmetrical thioureas. The antibacterial activity of triazinane and oxadiazinane compounds have been assessed with zone of inhibition by well diffusion method using a panel of selected gram positive and gram negative bacterial strains and which have showed good activity. The synthesised molecules were subjected to molecular docking studies with two proteins, namely topoisomerase II (PDB ID: 1JIJ) and DNA gyrase subunit b (PDB ID: 1KZN). The molecular docking studies are supporting the antibacterial activity exhibiting high inhibition constant and binding energy.
Computational biology and chemistry, 2018
A series of 2-Cl-benzimidazole derivatives was synthesized and assessed for antibacterial activity. Antibacterial results indicated that compounds 2d, 2e, 3a, 3b, 3c, 4d and 4e showed promising activity against B. cerus, S. aureus and P. aeruginosa (MIC: 6.2 μg/mL) and excellent efficacy against E. coli (MIC: 3.1 μg/mL). Furthermore, compounds 3d and 3e displayed better activity (MIC: 3.1 μg/mL) than the reference drugs chloramphenicol and cycloheximide against gram positive and gram negative bacterial strains. The compounds 3d-e also showed better activity than the reference drug paromomycin against B. cerus and P. aeruginosa and showed similar inhibition pattern against S. aureus and E. coli. (MIC: 3.1 μg/mL). Studies on fractional inhibitory concentration (FIC) determination of compounds 1a-e, 2a-c, 4a-c and the reference antibiotic via combination approach revealed a synergistic effect as the MIC values were lowered up to / to / of the original MIC. In-vitro cytotoxicity study i...
Journal of pharmaceutical research international, 2020
In this work, molecular modeling and docking studies of antimicrobial heterocyclic compounds were carried out using Auto Dock. Docking studies were carried out for Benzodiazole derivatives to study their affinity to Cell wall anchored (CWA) protein of Staphylococcus aureus. The docking studies of the compounds showed binding energies ranging from-7 to-5 kcal/mol against clumping factor A (ClfA), a CWA protein of Staphylococcus aureus, [PDB file:1N67]. Molecular modeling and docking studies of Benzodiazole derivatives show that the main action of the compounds is inhibition of cell wall adhesion.
Egyptian Journal of Chemistry
In the present work, we have reported the theoretical and biological activities of some imidazole (MIPBD, CMIBP, MIBPBD) derivatives. Here, the synthesis of one novel substituted imidazo-amino pyridinyl derivative (MIPBD) has also been reported. The structure of this compound was identified by NMR and mass spectroscopy. Molecular modeling studies have confirmed that CMIBP (ΔE= 0.16508 eV) is more stable than others. Antibacterial investigation exhibited good to excellent activity for all these compounds against two tested bacterial strains (S. aureus and E. coli). Moreover, molecular docking studies were carried out, which was consistent with experimental studies. The results motivate us for further studies of imidazole derivatives which will be helpful for the development of novel antibacterial agents.
Anti-Infective Agents in Medicinal Chemistry, 2010
In this preliminary study eighteen p-substituted benzoic acid [(5-nitro-thiophen-2-yl)methylene]-hydrazides with antimicrobial activity were evaluated against multidrugresistant Staphylococcus aureus, correlating the three-dimensional characteristics of the ligands with their respective bioactivities. The computer programs Sybyl and CORINA were used, respectively, for the design and three-dimensional conversion of the ligands. Molecular interaction fields were calculated using GRID program. Calculations using Volsurf resulted in a statistically consistent model with 48 structural descriptors showing that hydrophobicity is a fundamental property in the analyzed biological response.