Structure of the Cyclic, Cationic Antimicrobial Peptide (KKWWKF) in Octanol Solution: &lt;i&gt;in silico&lt;/i&gt; Approach

Mortazavi, Seyed Hassan; Bozorgmehr, Mohammad Reza; Heravi, Majid M.

doi:10.22146/ijc.49190

Cited by 2 publications

(1 citation statement)

References 30 publications

(33 reference statements)

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“…Therefore, there is no surprise that Indonesian researchers prefer to use chalcone as the ligand in CADD studies. Figure 8b,c,d illustrates the structures of quercetin, 78 peptide KKWWKP, 79 and chalcone, 80 respectively, as the most commonly studied ligands taken from three Indonesian journals.…”

Section: ■ Resultsmentioning

confidence: 99%

A Decade of Indonesian Atmosphere in Computer-Aided Drug Design

Hariono

Wijaya

Frederick

et al. 2021

J. Chem. Inf. Model.

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The era of drug design aided by computers has been very welcome to Indonesian researchers working on drug discovery and its related fields. The availability of software, bioinformatics, and cheminformatics data that are free and friendly to use increases the interest in carrying the software, bioinformatics, and cheminformatics out in drug discovery projects. The computational method is believed to speed up the discovery of new drugs, because the computational method can predict the molecular behavior of chemical compounds to interact with biological systems. Therefore, the real experimental study cost should be minimized, since there are a few promising molecules for a drug in silico only that would be investigated further. This article describes a decade of research concerning drug design and discovery aided by computers in Indonesia from 2011 to 2020. A number of computer-aided drug design-related articles (CADDs) from Indonesian journals were collected during the decade, and their trend was analyzed. The results show that there was an increasing trend in the use of CADD programs by Indonesian researchers during those ten years. The most common methods being used were docking and molecular dynamics with AutoDock/AutoDock Vina and AMBER/GROMACS, respectively. In addition, the most common protein targets, ligand structures, and disease targets being studied were human estrogen receptor alpha (HERa), flavonoids, and cancer.

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Section: ■ Resultsmentioning

confidence: 99%

A Decade of Indonesian Atmosphere in Computer-Aided Drug Design

Hariono

Wijaya

Frederick

et al. 2021

J. Chem. Inf. Model.

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Deciphering the Impact of Cyclization and Lysine Charges on Antimicrobial Peptides Using Molecular Dynamics Simulations and Density Functional Theory

Saghiri,

Reza Bozorgmehr,

Morsali

2024

ChemistrySelect

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This study utilized molecular dynamics simulations (MD) to explore the impact of cyclization and lysine charges on antimicrobial peptides (AMPs) across eight simulation boxes designed with water and water‐sodium dodecyl sulfate (SDS) micelles. Cyclic AMPs with positively charged lysine residues (c‐AMP+) displayed increased stability in both environments compared to linear AMPs (l‐AMP+), with removal of positive charges notably destabilizing the linear form in water‐SDS. Findings revealed enhanced mobility due to cyclization and charged lysine residues, further boosted by SDS presence. Notably, lysine residues exhibited a stronger affinity for SDS than tryptophan and phenylalanine, especially lysine number 5. Analysis extended to peptide backbone conformation and electronic features, showing cyclization's greater impact on psi and phi angles over charge presence, with linear AMPs displaying lower reactivity than cyclic counterparts. This research underscores the significance of cyclization and lysine charges in AMP behavior, suggesting the potential of c‐AMP+ for further development owing to their improved stability, mobility, and membrane interactions.

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Structure of the Cyclic, Cationic Antimicrobial Peptide (KKWWKF) in Octanol Solution: <i>in silico</i> Approach

Cited by 2 publications

References 30 publications

A Decade of Indonesian Atmosphere in Computer-Aided Drug Design

A Decade of Indonesian Atmosphere in Computer-Aided Drug Design

Deciphering the Impact of Cyclization and Lysine Charges on Antimicrobial Peptides Using Molecular Dynamics Simulations and Density Functional Theory

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