Optimizing Bedaquiline for cardiotoxicity by structure based virtual screening, DFT analysis and molecular dynamic simulation studies to identify selective MDR-TB inhibitors

Ahmad, Iqrar; Jadhav, Harsha; Shinde, Yashodeep; Jagtap, Vilas; Girase, Rukaiyya; Patel, Harun

doi:10.1007/s40203-021-00086-x

Cited by 43 publications

(25 citation statements)

References 33 publications

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“…It has been reported that azole antifungals inhibit cytochrome P450‐dependent lanosterol 14‐α demethylase enzyme resulting in a depletion of ergosterol (a chief component of the fungal cell membrane)[25–27]. As a result, we also performed a docking study on the crystal structure of sterol 14‐α demethylase (CYP51) from C. albicans co‐crystallized with tetrazole antifungal drug VT1161(PDB ID: 5TZ1)[28–30].…”

Section: Resultsmentioning

confidence: 99%

Zeolite (Y‐H)‐based green synthesis, antimicrobial activity, and molecular docking studies of imidazole bearing oxydibenzene hybrid molecules

Desai

Maheta

Jethawa

et al. 2021

Journal of Heterocyclic Chem

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In this green synthesis, zeolite (Y‐H) appears to be an intriguing choice for obtaining a high yield with a shorter reaction time. In addition, we have synthesized N‐aryl‐(4‐benzylidene‐5‐oxo‐2‐phenyl‐4,5‐dihydro‐1H‐imidazol‐1‐yl)‐3‐phenoxybenzamides (4a‐i), which will be proved to be potent antimicrobial agents. The title compounds were tested against Gram‐positive, Gram‐negative, and fungal strains using the Mueller–Hinton Broth technique. N‐(4‐benzylidene‐5‐oxo‐2‐phenyl‐4,5‐dihydro‐1H‐imidazol‐1‐yl)‐3‐phenoxybenzamide (4a) (minimum inhibitory concentration [MIC] = 25 μg/mL, S. pyogenes) and N‐(4‐[4‐fluorobenzylidene]‐5‐oxo‐2‐phenyl‐4,5‐dihydro‐1H‐imidazol‐1‐yl)‐3‐phenoxybenzamide (4f) (MIC = 100 μg/mL, C. albicans, A. niger, A. clavatus) were the most effective against Gram‐positive and Gram‐negative bacteria as well as fungal strains. To understand the mechanism of action of synthesized compounds, molecular docking experiments were performed against S. aureus tyrosyl‐tRNA synthetase and C. albicans sterol 14‐α demethylase.

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Section: Resultsmentioning

confidence: 99%

Zeolite (Y‐H)‐based green synthesis, antimicrobial activity, and molecular docking studies of imidazole bearing oxydibenzene hybrid molecules

Desai

Maheta

Jethawa

et al. 2021

Journal of Heterocyclic Chem

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“…By centralizing the cognate ligand in the crystal structure and using the default box dimension, the active side grid was assigned. Finally, the molecular docking study was carried out using Schrodinger’s glide, in which the ready minimum-energy 3D structure of the ligands and the receptor grid file were loaded into Maestro’s work area and the ligands were docked using standard precision (SP) docking methodology. , …”

Section: Methodsmentioning

confidence: 99%

Synthesis, Molecular Modeling Study, and Quantum-Chemical-Based Investigations of Isoindoline-1,3-diones as Antimycobacterial Agents

et al. 2022

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The condensation of phthalic anhydride afforded structurally modified isoindoline-1,3-dione derivatives with selected amino-containing compounds. The title compounds ( 2 – 30 ) have been characterized by thin-layer chromatography (TLC), infrared spectroscopy, 1 H and 13 C NMR spectroscopy, and mass spectroscopy. All of the compounds were assessed for their antimycobacterial activity toward the H37Rv strain by a dual read-out assay method. Among the synthesized compounds, compound 27 possessed a significant IC 50 of 18 μM, making it the most potent compound of the series. The InhA inhibitory (IC 50 ) activity of compound 27 was 8.65 μM in comparison to Triclosan (1.32 μM). Computational studies like density functional theory (DFT) study, molecular docking, and dynamic simulation studies illustrated the reactivity and stability of the synthesized compounds as InhA inhibitors. A quantum-mechanics-based DFT study was carried out to investigate the molecular and electronic properties, reactivities, and nature of bonding present in the synthesized compounds and theoretical vibrational (IR) and isotropic value ( 1 H and 13 C NMR) calculations.

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“…The charge of the system was neutralized by adding Na + and Cl À counter ions and 0.15 M NaCl Salt concentration was set corresponding to the physiological system using the Desmond 'System Builder' panel. 72,73 Then, the built solvated system was minimized and relaxed utilizing OPLS3e force eld parameters as the default protocol associated with Desmond. The isothermal isobaric ensemble (normal pressure and temperature/NPT) was set during the simulation, with a temperature of 300 K and an atmospheric pressure of 1.0315 bar using the Nose-Hoover chain thermostat method and the Martyna-Tobias-Klein barostat method, respectively.…”

Section: Computational Analysis Methodsmentioning

confidence: 99%

In vitroand computational investigations of novel synthetic carboxamide-linked pyridopyrrolopyrimidines with potent activity as SARS-CoV-2-M^Proinhibitors

et al. 2022

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Optimizing Bedaquiline for cardiotoxicity by structure based virtual screening, DFT analysis and molecular dynamic simulation studies to identify selective MDR-TB inhibitors

Cited by 43 publications

References 33 publications

Zeolite (Y‐H)‐based green synthesis, antimicrobial activity, and molecular docking studies of imidazole bearing oxydibenzene hybrid molecules

Zeolite (Y‐H)‐based green synthesis, antimicrobial activity, and molecular docking studies of imidazole bearing oxydibenzene hybrid molecules

Synthesis, Molecular Modeling Study, and Quantum-Chemical-Based Investigations of Isoindoline-1,3-diones as Antimycobacterial Agents

In vitroand computational investigations of novel synthetic carboxamide-linked pyridopyrrolopyrimidines with potent activity as SARS-CoV-2-M^Proinhibitors

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Optimizing Bedaquiline for cardiotoxicity by structure based virtual screening, DFT analysis and molecular dynamic simulation studies to identify selective MDR-TB inhibitors

Cited by 43 publications

References 33 publications

Zeolite (Y‐H)‐based green synthesis, antimicrobial activity, and molecular docking studies of imidazole bearing oxydibenzene hybrid molecules

Zeolite (Y‐H)‐based green synthesis, antimicrobial activity, and molecular docking studies of imidazole bearing oxydibenzene hybrid molecules

Synthesis, Molecular Modeling Study, and Quantum-Chemical-Based Investigations of Isoindoline-1,3-diones as Antimycobacterial Agents

In vitroand computational investigations of novel synthetic carboxamide-linked pyridopyrrolopyrimidines with potent activity as SARS-CoV-2-MProinhibitors

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Product

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In vitroand computational investigations of novel synthetic carboxamide-linked pyridopyrrolopyrimidines with potent activity as SARS-CoV-2-M^Proinhibitors