Admet, molecular docking studies and binding energy calculations of pyrimidine-2-thiol derivatives as cox inhibitors

2020 ◽  
Vol 13 (9) ◽  
pp. 4200
Author(s):  
Deepthi D. Kodical ◽  
Jainey P. James ◽  
K Deepthi ◽  
Pankaj Kumar ◽  
Chinchumol Cyriac ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Docking Studies ◽  
Energy Calculations ◽  
Molecular Docking Studies ◽  
Cox Inhibitors ◽  
Binding Energy Calculations

scholarly journals Molecular Docking and Dynamics Simulation Studies Predict Munc18b as a Target of Mycolactone: A Plausible Mechanism for Granule Exocytosis Impairment in Buruli Ulcer Pathogenesis

Toxins ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 181 ◽  
Author(s):  
Samuel Kwofie ◽  
Bismark Dankwa ◽  
Kweku Enninful ◽  
Courage Adobor ◽  
Emmanuel Broni ◽  
...  
Keyword(s):  
Wound Healing ◽  
Molecular Docking ◽  
Mast Cells ◽  
Binding Energy ◽  
Buruli Ulcer ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Granule Exocytosis ◽  
Molecular Docking Studies ◽  
Healing Processes

Ulcers due to infections with Mycobacterium ulcerans are characterized by complete lack of wound healing processes, painless, an underlying bed of host dead cells and undermined edges due to necrosis. Mycolactone, a macrolide produced by the mycobacterium, is believed to be the toxin responsible. Of interest and relevance is the knowledge that Buruli ulcer (BU) patients remember experiencing trauma previously at the site of the ulcers, suggesting an impairment of wound healing processes, the plausible effect due to the toxin. Wound healing processes involve activation of the blood platelets to release the contents of the dense granules mainly serotonin, calcium ions, and ADP/ATP by exocytosis into the bloodstream. The serotonin release results in attracting more platelets and mast cells to the wound site, with the mast cells also undergoing degranulation, releasing compounds into the bloodstream by exocytosis. Recent work has identified interference in the co-translational translocation of many secreted proteins via the endoplasmic reticulum and cell death involving Wiskott-Aldrich syndrome protein (WASP), Sec61, and angiotensin II receptors (AT2R). We hypothesized that mycolactone by being lipophilic, passively crosses cell membranes and binds to key proteins that are involved in exocytosis by platelets and mast cells, thus inhibiting the initiation of wound healing processes. Based on this, molecular docking studies were performed with mycolactone against key soluble n-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins and regulators, namely Vesicle-associated membrane protein (VAMP8), Synaptosomal-associated protein (SNAP23, syntaxin 11, Munc13-4 (its isoform Munc13-1 was used), and Munc18b; and also against known mycolactone targets (Sec61, AT2R, and WASP). Munc18b was shown to be a plausible mycolactone target after the molecular docking studies with binding affinity of −8.5 kcal/mol. Structural studies and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding energy calculations of the mycolactone and Munc18b complex was done with 100 ns molecular dynamics simulations using GROMACS. Mycolactone binds strongly to Munc18b with an average binding energy of −247.571 ± 37.471 kJ/mol, and its presence elicits changes in the structural conformation of the protein. Analysis of the binding interactions also shows that mycolactone interacts with Arg405, which is an important residue of Munc18b, whose mutation could result in impaired granule exocytosis. These findings consolidate the possibility that Munc18b could be a target of mycolactone. The implication of the interaction can be experimentally evaluated to further understand its role in granule exocytosis impairment in Buruli ulcer.

scholarly journals MOLECULAR DOCKING STUDIES ON SCREENING AND ASSESSMENT OF SELECTED BIOFLAVONOIDS AS POTENTIAL INHIBITORS OF COVID-19 MAIN PROTEASE

2020 ◽  
pp. 174-178
Author(s):  
SHAILENDRA SANJAY SURYAWANSHI ◽  
POOJA BHAVAKANA JAYANNACHE ◽  
RAJKUMAR SANJAY PATIL ◽  
PALLED MS ◽  
ALEGAON SG
Keyword(s):  
Molecular Docking ◽  
Treatment Options ◽  
Docking Studies ◽  
Binding Energies ◽  
Molecular Docking Studies ◽  
Discovery Studio ◽  
Main Protease ◽  
Potential Inhibitors ◽  
Binding Energy Calculations ◽  
Native Ligand

Objectives: The objective of the study was to screen and assess the selected bioactive bioflavonoids in medicinal plants as potential coronaviruses (CoV) main protease (Mpro) inhibitors using molecular docking studies. Methods: We have investigated several bioflavonoids which include apigenin, galangin, glycitein, luteolin, morin, naringin, resveratrol, and rutin. Nelfinavir and lopinavir were used as standard antiviral drugs for comparison. Mpro was docked with selected compounds using PyRx 0.8 and docking was analyzed by PyRx 0.8 and Biovia Discovery Studio 2019. Results: The binding energies obtained from the docking of 6LU7 with native ligand, nelfinavir, lopinavir, apigenin, galangin, glycitein, luteolin, morin, naringin, resveratrol, and rutin were found to be −7.4, −8.3, −8.0, −7.8, −7.3, −7, −7.4, −7.6, −7.8, −6.9, and −9 kcal/mol, respectively. Conclusion: From the binding energy calculations, we can conclude that nelfinavir and lopinavir may represent potential treatment options and apigenin, galangin, glycitein, luteolin, morin, naringin, resveratrol, and rutin found to possess the best inhibitors of CoV disease-19 main protease.

Molecular Docking Studies on the Interaction of 2-Arylpropionate Esters with Candida rugosa Lipase

2014 ◽  
Vol 496-500 ◽  
pp. 520-523
Author(s):  
Xue Ying Liu ◽  
Hong Yan Zeng ◽  
Deng Hong Peng ◽  
Bi Foua Claude Alain Gohi ◽  
Qing Jun Huang ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Molecular Mechanism ◽  
Asymmetric Catalysis ◽  
Candida Rugosa ◽  
Docking Studies ◽  
Enantioselective Hydrolysis ◽  
Molecular Docking Studies ◽  
Catalysis Mechanism

The interaction between ethyl 2-arylpropiolates and Candida rugosa lipase was studied by enantioselective hydrolysis and molecular docking. The ethyl 2-arylpropiolates with the lowest binding energy was selected to investigate the molecular mechanism of enzyme mediated asymmetric catalysis mechanism.

scholarly journals Molecular Docking Studies of N-Acetyl Cysteine, Zinc Acetyl Cysteine and Niclosamide on SARS Cov 2 Protease and Its Comparison with Hydroxychloroquine

2020 ◽  
Author(s):  
Roopa Guthappa
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Active Sites ◽  
Antiviral Drug ◽  
Docking Studies ◽  
Binding Affinities ◽  
Binding Interaction ◽  
Molecular Docking Studies ◽  
Main Protease ◽  
Acetyl Cysteine

<p><b>To</b></p> <p><b>Respected Sir/Madam</b> </p> <p>Chemarxiv</p> <p> </p> <p><b>Respected Sir/Madam</b> </p> <p> </p> <p><b>Sub</b>: submission of preprint of article to Chemarxiv for online publication.</p> <p> </p> <p>I am herewith submitting the preprint of an article entitled “Molecular docking studies of N-acetyl cysteine, zinc acetyl cysteine and niclosamide on SARS Cov 2 protease and its comparison with hydroxychloroquine” for possible publication in “Chemarxiv”.</p> <p> </p> <p>In this article, we have evaluated the binding abilities of N-acetyl cysteine, zinc acetyl cysteine and niclosamide (antiviral drug) with SARS-COV-2 protease. All the four compounds investigated are effective and selectively bind to active sites of main protease. N-acetyl cysteine being a derivative of cysteine interacts with Cys-145, His-163, Gly-143 of COV-2 protease, zinc acetyl cysteine binds to Gly-143, Ser-144, Cys-145, Glu-166 of COV-2 protease and niclosamide bind to Glu-166, Cys-145, His 41 of main protease. The data has been compared with hydroxychloroquine which effectively binds to Cys-145, Glu-166, Arg-188. The binding affinities of N-acetyl cysteine, zinc-acetyl cysteine and niclosamide are -4.24, -4.29 and -7.5 kcal mol<sup>-1</sup> while for hydroxychloroquine it is -6.66 kcal mol<sup>-1</sup>. Niclosamide with its lowest binding energy interacts with His-41 and Cys-145 which may be the first molecule to show such binding interaction. The results indicate that N-acetyl cysteine, zinc-acetyl cysteine and niclosamide can also be explored for the treatment for SARS COV-2 as an alternative for hydroxychloroquine.</p> <p>I hope that the manuscript will full fill the journal’s requirements and will get accepted for publication. </p> <p>Thanking you</p> <p> </p> <p>With regards</p> <p>Roopa Guthappa</p> <p><a href="mailto:[email protected]">[email protected]</a></p>

scholarly journals Molecular Docking Studies of N-Acetyl Cysteine, Zinc Acetyl Cysteine and Niclosamide on SARS Cov 2 Protease and Its Comparison with Hydroxychloroquine

2020 ◽  
Author(s):  
Roopa Guthappa
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Active Sites ◽  
Antiviral Drug ◽  
Docking Studies ◽  
Binding Affinities ◽  
Binding Interaction ◽  
Molecular Docking Studies ◽  
Main Protease ◽  
Acetyl Cysteine

<p><b>To</b></p> <p><b>Respected Sir/Madam</b> </p> <p>Chemarxiv</p> <p> </p> <p><b>Respected Sir/Madam</b> </p> <p> </p> <p><b>Sub</b>: submission of preprint of article to Chemarxiv for online publication.</p> <p> </p> <p>I am herewith submitting the preprint of an article entitled “Molecular docking studies of N-acetyl cysteine, zinc acetyl cysteine and niclosamide on SARS Cov 2 protease and its comparison with hydroxychloroquine” for possible publication in “Chemarxiv”.</p> <p> </p> <p>In this article, we have evaluated the binding abilities of N-acetyl cysteine, zinc acetyl cysteine and niclosamide (antiviral drug) with SARS-COV-2 protease. All the four compounds investigated are effective and selectively bind to active sites of main protease. N-acetyl cysteine being a derivative of cysteine interacts with Cys-145, His-163, Gly-143 of COV-2 protease, zinc acetyl cysteine binds to Gly-143, Ser-144, Cys-145, Glu-166 of COV-2 protease and niclosamide bind to Glu-166, Cys-145, His 41 of main protease. The data has been compared with hydroxychloroquine which effectively binds to Cys-145, Glu-166, Arg-188. The binding affinities of N-acetyl cysteine, zinc-acetyl cysteine and niclosamide are -4.24, -4.29 and -7.5 kcal mol<sup>-1</sup> while for hydroxychloroquine it is -6.66 kcal mol<sup>-1</sup>. Niclosamide with its lowest binding energy interacts with His-41 and Cys-145 which may be the first molecule to show such binding interaction. The results indicate that N-acetyl cysteine, zinc-acetyl cysteine and niclosamide can also be explored for the treatment for SARS COV-2 as an alternative for hydroxychloroquine.</p> <p>I hope that the manuscript will full fill the journal’s requirements and will get accepted for publication. </p> <p>Thanking you</p> <p> </p> <p>With regards</p> <p>Roopa Guthappa</p> <p><a href="mailto:[email protected]">[email protected]</a></p>

Design, Synthesis, Antimicrobial Evaluation and Molecular Docking Studies of Some Novel Monoterpenoids Substituted Quinoxaline Thiosemicarbazide Derivatives

2021 ◽  
Vol 14 (2) ◽  
pp. 5424-5435
Author(s):  
Bipin Bihari ◽  
Girendra Kumar Gautam ◽  
Akash Ved
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Active Sites ◽  
Docking Studies ◽  
Dilution Method ◽  
Molecular Docking Studies ◽  
Fungal Strains ◽  
Antimicrobial Evaluation ◽  
Thiosemicarbazide Derivatives ◽  
Antibacterial And Antifungal

Owing to the increasingly serious problems caused by multidrug resistance in acquired infection pathogens, it has become an urgent need to develop new classes of antibiotics for overcoming the resistance. The present study aims to increase the antimicrobial activity of quinoxaline thiosemicarbazide derivatives by introducing a hydrophobic alkyl chain, an electron-releasing group in the ring, and substitution by some acyclic, cyclic and bicyclic monoterpenes and their antimicrobial evaluation against various strains with molecular docking studies. The lead molecule (1E, 4E)-1-(7-chloro-3-isopropyl- quinoxalin-2(1H)-ylidene) thiosemicarbazide was synthesized and condensed with various monoterpenes to synthesize different derivatives. The structures of compounds were confirmed through IR., NMR & mass spectroscopy. The synthesized derivatives were evaluated in vitro for antibacterial  and  antifungal activities against various strains using the agar dilution method. Molecular docking studies of the derivatives (Va– Vg) were performed to find out essential binding sites against target protein (PDB: 3 FAP, receptor: FKBP 12) using Autodock 4.2. The compounds Va, Vd, Vf & Vg exhibited potent antibacterial and antifungal activity. Among all these compounds Vd was found to exhibit more potent activity against gram +Ve, gram –Ve bacterial and fungal strains at MIC 0.19 μg/ml, 0.39μg/ml, and 1.56 μg/ml respectively. The docking studies of all the compounds exhibit potent binding energy, but the compound Vd exhibit interactive binding energy (-9.98 kcal/mol) to the active pockets of the receptor FKBP12. The compound Vd interacting with various active sites of amino acids of receptors like PHE128, TRP190, TYR26, VAL55, ILE56, PHE99, and TRP59. In terms of structure- activity relationship study it is revealed that the activity profile against bacterial and fungal strains was altered by the formation of monoterpenoid substituted (1E, 4E)-1-(7- chloro-3-isopropylquinoxalin-2(1H)-ylidene) thiosemicar- bazide derivatives. The study reveals that bicyclic monoterpenes substituted compounds exhibit greater activity than cyclic and acyclic. The molecular docking studies also showed that all the compounds exhibit good docking energy to bind and inhibit the FKBP12 receptor.

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