ArticleACS omega2019
Antimicrobial Peptide Designing and Optimization Employing Large-Scale Flexibility Analysis of Protein-Peptide Fragments.
Article in ACS omega, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 62 citations in OpenAlex.
- Selectivity Modulation of Small Cationic Membrane-Active Cyclic Peptides with Broad-Spectrum Activity against Bacteria and Fungi.Journal of medicinal chemistry · 2026Article
- Phosphorylated tau exhibits antimicrobial activity capable of neutralizing herpes simplex virus 1 infectivity in human neurons.Nature neuroscience · 2026Article
- From computational screening toFrontiers in microbiology · 2026Article
- Pharmacokinetics Screening, Molecular Docking, and Dynamics Simulations Revealed Novel Antimicrobial Peptide NKLF2 Mutants as Potent Inhibitors of Mycobacterium tuberculosis.Probiotics and antimicrobial proteins · 2026Article
- Novel antimicrobial peptide HFIAP-1 mutant as a β-lactamase inhibitor against extended-spectrum β-lactamases of Escherichia coli: a comprehensive in-silico approach.Archives of microbiology · 2025Article
- Structure-based design of an antibacterial peptide from the Myotoxin II sequence, evaluating its effectiveness against Gram-negative bacteria and its safety.Scientific reports · 2025Article
- Carbapenem Resistance inMicroorganisms · 2025Review
- Potential of Indole-3-Carbinol compounds from broccoli (Open veterinary journal · 2025Article
- Article
- AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides.Database : the journal of biological databases and curation · 2024Article
- Design of inhibitor peptide sequences based on the interfacial knowledge of the protein G-IgG crystallographic complex and their binding studies with IgG.European biophysics journal : EBJ · 2024Article
- Novel Antimicrobial Peptide SAAP Mutant as a Better Adjuvant to Sulbactam-Based Treatments Against Clinical Strains of XDR Acinetobacter baumannii.Probiotics and antimicrobial proteins · 2024Article
- Antioxidant and Anti-inflammatory Activity of Sea Cucumber (Bioinformatics and biology insights · 2023Article
- Predicting the effects of rare genetic variants on oncogenic signaling pathways: A computational analysis of HRAS protein function.Frontiers in chemistry · 2023Article
- A Computational Study of Carbazole Alkaloids from Murraya koenigii as Potential SARS-CoV-2 Main Protease Inhibitors.Applied biochemistry and biotechnology · 2023Article
- Noscapine-Amino Acid Conjugates Suppress the Progression of Cancer Cells.ACS pharmacology & translational science · 2022Article
- Designing Anti-Microbial Peptides Against Major β-Lactamase Enzymes in Clinically Important Gram-Negative Bacterial Pathogens: An In-Silico Study.Probiotics and antimicrobial proteins · 2022Article
- Antitussive noscapine and antiviral drug conjugates as arsenal against COVID-19: a comprehensive chemoinformatics analysis.Journal of biomolecular structure & dynamics · 2022Article
- Investigation of Plant Antimicrobial Peptides against Selected Pathogenic Bacterial Species Using a Peptide-Protein Docking Approach.BioMed research international · 2022Article
- In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations.Interdisciplinary sciences, computational life sciences · 2021Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The mankind relies on the use of antibiotics for a healthy life. The epidemic-like emergence of drug-resistant bacterial strains is increasingly becoming one of the leading causes of morbidity and mortality, which gives rise to design a potential antimicrobial peptide (AMP). Here, we have designed the potential AMP using the extensive dynamics simulation since protein-peptide interactions are linked to large conformational changes. Therefore, we have employed the advanced computational avenue CABS molecular docking method that enabled the flexible peptide-protein molecular docking with a large-scale rearrangement of the protein. Lead AMP was investigated against the wild-type (WT) and mutant-PBP5 (MT-PBP5) proteins (antiresistance property). AMP20 showed strong interactions with wtPBP5 and mtPBP5 and involvement of a large number of elements in interactions determined through an atomic model study. Full flexibility analysis showed the stable interaction of AMP20 with both the wild-type and mutant form of PBP5 with root-mean-square deviation (RMSD) values of ∼4.51 and 4.85 Å, respectively. Moreover, peptide dynamics showed involvement of all residues of AMP20 through contact map analysis, and extensive simulation confirmed the stable interaction of AMP20, with lower values of RMSD, radius of gyration, and root-mean-square fluctuation. This study paves the way for a potential approach to design the AMP with amino acid walking and large-scale conformational rearrangements of amino acids.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.