Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians

Butt, Sania Safdar; Badshah, Yasmin; Shabbir, Maria; Rafiq, Mehak

doi:10.2196/14232

Cited by 78 publications

(55 citation statements)

References 9 publications

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“…Templates used for homology modelling were 2vch_A, 2acv_A, 2c1x_A, 2pq6_A and 5tme_A ( ; accessed on 8 September 2021). The docking of (−)-menthol and (+)-menthol in the active site of UGT93AY1 was performed with the Autodock/Vina tool [ 67 ] implemented in UCSF Chimera ( ; accessed on 8 September 2021).…”

Section: Methodsmentioning

confidence: 99%

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Glucosylation of (±)-Menthol by Uridine-Diphosphate-Sugar Dependent Glucosyltransferases from Plants

et al. 2021

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Menthol is a cyclic monoterpene alcohol of the essential oils of plants of the genus Mentha, which is in demand by various industries due to its diverse sensorial and physiological properties. However, its poor water solubility and its toxic effect limit possible applications. Glycosylation offers a solution as the binding of a sugar residue to small molecules increases their water solubility and stability, renders aroma components odorless and modifies bioactivity. In order to identify plant enzymes that catalyze this reaction, a glycosyltransferase library containing 57 uridine diphosphate sugar-dependent enzymes (UGTs) was screened with (±)-menthol. The identity of the products was confirmed by mass spectrometry and nuclear magnetic resonance spectroscopy. Five enzymes were able to form (±)-menthyl-β-d-glucopyranoside in whole-cell biotransformations: UGT93Y1, UGT93Y2, UGT85K11, UGT72B27 and UGT73B24. In vitro enzyme activity assays revealed highest catalytic activity for UGT93Y1 (7.6 nkat/mg) from Camellia sinensis towards menthol and its isomeric forms. Although UGT93Y2 shares 70% sequence identity with UGT93Y1, it was less efficient. Of the five enzymes, UGT93Y1 stood out because of its high in vivo and in vitro biotransformation rate. The identification of novel menthol glycosyltransferases from the tea plant opens new perspectives for the biotechnological production of menthyl glucoside.

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Section: Methodsmentioning

confidence: 99%

“…rcsb.org/; accessed on 8 September 2021). The docking of (−)-menthol and (+)-menthol in the active site of UGT93AY1 was performed with the Autodock/Vina tool [67] implemented in UCSF Chimera (https://www.cgl.ucsf.edu/chimera/download.html; accessed on 8 September 2021).…”

Section: Homology Modelling Of Ugt93y1 and Molecular Dockingmentioning

confidence: 99%

Glucosylation of (±)-Menthol by Uridine-Diphosphate-Sugar Dependent Glucosyltransferases from Plants

et al. 2021

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“…Selenomethionines were replaced by the methionines and charges were assigned. Further, hydrogens were added to justify the valency on the atom in the main protease of nCoV [33,34]. The structures of the three molecules, namely 2-deoxy-D-ribose (2DR-cyclic form of ribose), 2-deoxy-glucose (2DAG-acyclic form of glucose) and 2-deoxy-D-glucose (2DGcyclic form of glucose), as shown in Figure 1, were drawn using Chemdraw [32].…”

Section: Designing Of the Ligandsmentioning

confidence: 99%

In Silico Evaluation of Binding of 2-Deoxy-D-Glucose with Mpro of nCoV to Combat COVID-19

et al. 2022

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COVID-19 has threatened the existence of humanity andthis infection occurs due to SARS-CoV-2 or novel coronavirus, was first reported in Wuhan, China. Therefore, there is a need to find a promising drug to cure the people suffering from the infection. The second wave of this viral infection was shaking the world in the first half of 2021. Drugs Controllers of India has allowed the emergency use of 2-deoxy-D-glucose (2DG) in 2021 for patients suffering from this viral infection. The potentiality of 2-deoxy-D-glucose to intervene in D-glucose metabolism exists and energy deprivation is an effective parameter to inhibit cancer cell development. Once 2DG arrives in the cells, it becomes phosphorylated to 2-deoxy-D-glucose-6-phosphate (2-DG6P), a charged molecule expressively captured inside the cells. On the other hand, 2DG lacks the ability to convert into fructose-6-phosphate, resulting in a hampering of the activity of both glucose-6-phosphate isomerase and hexokinase, and finally causing cell death. Hence, the potential and effectiveness of 2DG with the main protease (Mpro) of novel coronavirus (nCoV) should be investigated using the molecular docking and molecular dynamics (MD) simulations. The ability of 2DG to inhibit the Mpro of nCoV is compared with 2-deoxyglucose (2DAG), an acyclic molecule, and 2-deoxy-D-ribose (2DR). The binding energy of the molecules with the Mpro of nCoV is calculated using molecular docking and superimposed analysis data is obtained. The binding energy of 2DG, 2DR and 2DAG was −2.40, −2.22 and −2.88 kcal/mol respectively. Although the molecular docking does not provide reliable information, therefore, the binding affinity can be confirmed by molecular dynamics simulations. Various trajectories such as Rg, RMSD, RMSF, and hydrogen bonds are obtained from the molecular dynamics (MD) simulations. 2DG was found to be a better inhibitor than the 2DAG and 2DR based on the results obtained from the MD simulations at 300 K. Furthermore, temperature-dependent MD simulations of the Mpro of nCoV with promising 2DG was performed at 295, 310 and 315 K, and the effective binding with the Mpro of nCoV occurred at 295 K. With the use of DFT calculations, optimized geometry and localization of electron density of the frontier molecular orbitals were calculated.

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“…Thereafter the minimized structures were converted to a ready-to-dock PDBQT format [35,36].To study the binding a nity and interaction pro les of HL and ZnL 2 , protein targets representing the key virulence factors in S. aureus, S. pyogenes, K. pneumonia, and E. coli were identi ed as reported by previous studies [37,38]. The crystal structures of the proteins (Table 1) were retrieved from the protein data bank (http://www.RCSB.org) [39], and prepared for docking using the dock prep toolbar on UCSF Chimera (https://www.cgl.ucsf.edu/chimera/) [40]. The resultant prepared proteins were saved in PDB format, imported into PyRx software, and converted to a ready-to-dock macromolecule PDBQT le format [35].…”

Section: Molecular Docking Studies 2721 Preparation Of the Synthesize...mentioning

confidence: 99%

Zinc (II) complex of (Z)-4-((4-nitrophenyl) amino) pent-3-en-2-one, a potential antimicrobial agent: Synthesis, characterization, electrochemical, antimicrobial, DFT and docking studies

Wahab¹,

Waziri²,

Oselusi³

et al. 2022

Preprint

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Herein, the syntheses, characterizations, antimicrobial activities, density functional theory (DFT) predictions, and molecular docking (MD) studies are reported on (Z)-4-((4-nitrophenyl) amino) pent-3-en-2-one (HL) and its Zn (II) complex. The deployed characterization techniques include elemental analysis, solubility and conductivity measurements, TGA, electrochemical studies, FTIR, UV-Vis, 1H and 13C{H}NMR, HRMS, and PXRD. Antimicrobial activity was studied using some Gram-positive and Gram-negative bacteria. DFT predictions were achieved using B3LYP, WB97XD and M06-2X functionals with 6-31+G(d,p) and LANL2DZ basis sets for nonmetallic and metallic atoms, respectively. The therapeutic potentials of the compounds were evaluated based on protein binding energy, ADME/T and drug-likeness properties. The experimental results revealed the formation of a complex in which two molecules of the ligand are coordinated to the zinc ion in a tetrahedral arrangement that involve the carbonyl and amino portions of the ligand. Both the ligand and the complex displayed a cyclic voltammetric behavior that is indicative of an irreversible one-electron transfer and redox diffusion-controlled process. The results of the antimicrobial study showed that the complex possesses higher antimicrobial potency than the free ligand. The B3LYP emerged as the best performing functional because it yielded the best IR spectra and geometrical parameters relative to the experimental data. The DFT predictions revealed that the complex is more reactive than the ligand, and its formation is thermodynamically feasible and exothermic. However, both the ligand and the complex showed comparable polarity. The MD results revealed the relative binding affinities of the compounds as well as their binding modes, which are in good correlation with the in-vitro data. Finally, drug-likeness studies showed that the studied compounds are promising therapeutic candidates.

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Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians

Cited by 78 publications

References 9 publications

Glucosylation of (±)-Menthol by Uridine-Diphosphate-Sugar Dependent Glucosyltransferases from Plants

Glucosylation of (±)-Menthol by Uridine-Diphosphate-Sugar Dependent Glucosyltransferases from Plants

In Silico Evaluation of Binding of 2-Deoxy-D-Glucose with Mpro of nCoV to Combat COVID-19

Zinc (II) complex of (Z)-4-((4-nitrophenyl) amino) pent-3-en-2-one, a potential antimicrobial agent: Synthesis, characterization, electrochemical, antimicrobial, DFT and docking studies

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