Computational Approaches for the Prediction of Antimicrobial Potential Peptides From Ocimum Tenuiflorum.

Suryawanshi, Sunil Kumar; Chouhan, Usha

doi:10.22159/ajpcr.2018.v11i1.23008

Cited by 4 publications

(1 citation statement)

References 14 publications

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“…The default clustering RMSD 2.0 Å was used, and the complex type was chosen to be protein–small ligand. Connolly dot surface representations of the molecules as different components such as convex, concave, and flat patches were generated using the PATCH Dock algorithm [ 57 , 58 ]. Then, the PATCH Dock solutions were optimized for small-size molecules, provides a list of refined complexes, reshuffled the molecule’s relative orientation, and the side-chains interface of the top 10 candidate solutions were rescored.…”

Section: Methodsmentioning

confidence: 99%

Molecular Dynamics of Cobalt Protoporphyrin Antagonism of the Cancer Suppressor REV-ERBβ

et al. 2021

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Nuclear receptor REV-ERBβ is an overexpressed oncoprotein that has been used as a target for cancer treatment. The metal-complex nature of its ligand, iron protoporphyrin IX (Heme), enables the REV-ERBβ to be used for multiple therapeutic modalities as a photonuclease, a photosensitizer, or a fluorescence imaging agent. The replacement of iron with cobalt as the metal center of protoporphyrin IX changes the ligand from an agonist to an antagonist of REV-ERBβ. The mechanism behind that phenomenon is still unclear, despite the availability of crystal structures of REV-ERBβ in complex with Heme and cobalt protoporphyrin IX (CoPP). This study used molecular dynamic simulations to compare the effects of REV-ERBβ binding to Heme and CoPP, respectively. The initial poses of Heme and CoPP in complex with agonist and antagonist forms of REV-ERBβ were predicted using molecular docking. The binding energies of each ligand were calculated using the MM/PBSA method. The computed binding affinity of Heme to REV-ERBβ was stronger than that of CoPP, in agreement with experimental results. CoPP altered the conformation of the ligand-binding site of REV-ERBβ, disrupting the binding site for nuclear receptor corepressor, which is required for REV-ERBβ to regulate the transcription of downstream target genes. Those results suggest that a subtle change in the metal center of porphyrin can change the behavior of porphyrin in cancer cell signaling. Therefore, modification of porphyrin-based agents for cancer therapy should be conducted carefully to avoid triggering unfavorable effects.

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Section: Methodsmentioning

confidence: 99%

Molecular Dynamics of Cobalt Protoporphyrin Antagonism of the Cancer Suppressor REV-ERBβ

et al. 2021

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Computational modelling and docking insight of bacterial peptide as ideal anti-tubercular and anticancer agents

Khusro¹,

Aarti²,

Agastian³

2020

Biocatalysis and Agricultural Biotechnology

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Synthesis, Evaluation and Docking Studies of Novel Formazan Derivatives as an Enoyl-Acp Reductase Inhibitors

Thangavelu¹,

Cellappa²,

Sivakumar³

2018

Int J Pharm Pharm Sci

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Objective: To synthesize, evaluate and performing the docking studies of novel formazan derivatives as enoyl-ACP reductase inhibitors.Materials: In the present investigation, a series of formazans (Ia-d) were synthesized by stirring aryl diazonium salts solution with Schiff's base at 0-5˚C for 2 h. The intermediate azomethine (Schiff base) itself was synthesized by condensation of para aminobenzoic acid with dimethylamino benzaldehyde in presence of a glacial acetic acid as a catalyst. The antimicrobial activity was done for these synthesized compounds by cup plate method. Moreover, the antimicrobial activity was further confirmed by its molecular docking approach study by using Molecular Operating Environment (MOE) 2009.10 software.Results: In the present study all the synthesized compounds (Ia-Id) showed the enhanced zone of inhibition against S. aureus, B. subtilis, E. coli and S. typhi (5±0.12 to 12±0.45) whereas, the antifungal activity against A. niger and C. albicans were showed the zone of inhibition in the range of 9±0.51 to 12±0.43 when compared to that of the standard drug.Further the docking study reveals that, only three of the formazan compounds under observation (Ia, Ib and Ic) have higher binding affinity with the receptors enzymes enoyl-ACP reductase, which is in the narrow range of binding energy for the protein PDB: 1C14 is-24.4598 to-23.9377 kcal/mol, which shows the further confirmation of these formazan compounds as better microbial inhibitor.Conclusion: Therefore our present report shows that formazans could be the potential drug candidate that inhibits the microbial activity by interacting and inhibiting the enoyl-ACP reductase enzyme which is confirmed by its both in vitro antimicrobial study and as well as from its docking study.

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Computational Approaches for the Prediction of Antimicrobial Potential Peptides From Ocimum Tenuiflorum.

Cited by 4 publications

References 14 publications

Molecular Dynamics of Cobalt Protoporphyrin Antagonism of the Cancer Suppressor REV-ERBβ

Molecular Dynamics of Cobalt Protoporphyrin Antagonism of the Cancer Suppressor REV-ERBβ

Computational modelling and docking insight of bacterial peptide as ideal anti-tubercular and anticancer agents

Synthesis, Evaluation and Docking Studies of Novel Formazan Derivatives as an Enoyl-Acp Reductase Inhibitors

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