cyclicpeptide: a Python package for cyclic peptide drug design DOI Creative Commons
Yang Liu, Suqi Cao, Lei Liu

et al.

Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 26(1)

Published: Nov. 22, 2024

Abstract The unique cyclic structure of peptides grants them remarkable stability and bioactivity, making powerful candidates for treating various diseases. However, the lack standardized tools peptide data has hindered their potential in today’s artificial intelligence–driven efficient drug design landscape. To bridge this gap, here we introduce a Python package named cyclicpeptide specifically design. This provides such as Structure2Sequence, Sequence2Structure, format transformation to process, convert, standardize sequence data. Additionally, it includes GraphAlignment peptide–specific alignment search PropertyAnalysis enhance understanding drug-like properties applications. comprehensive suite aims streamline integration into modern discovery pipelines, accelerating development peptide–based therapeutics.

Language: Английский

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2025 DOI Creative Commons
Yīmíng Bào, Xue Bai, Congfan Bu

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D30 - D44

Published: Nov. 11, 2024

The National Genomics Data Center (NGDC), which is a part of the China for Bioinformation (CNCB), offers comprehensive suite database resources to support global scientific community. Amidst unprecedented accumulation multi-omics data, CNCB-NGDC committed continually evolving and updating its core through big data archiving, integrative analysis value-added curation. Over past year, has expanded collaborations with international databases established new subcenters focusing on biodiversity, traditional Chinese medicine tumor genetics. Substantial efforts have been made toward encompassing broad spectrum developing innovative enhancing existing resources. Notably, developed single-cell omics (scTWAS Atlas), genome variation (VDGE), health disease (CVD Atlas, CPMKG, Immunosenescence Inventory, HemAtlas, Cyclicpepedia, IDeAS), biodiversity biosynthesis (RefMetaPlant, MASH-Ocean) research tools (CCLHunter). All services are publicly accessible at https://ngdc.cncb.ac.cn.

Language: Английский

Citations

13
Cyclic Peptide Natural Product Inspired Inhibitors of the Free-Living Amoeba Balamuthia mandrillaris DOI Creative Commons
Chenyang Lu, Samantha Nelson, Gabriela Coy

et al.

Journal of Natural Products, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 13, 2025

Balamuthia mandrillaris is a pathogenic free-living amoeba (pFLA) that can cause infection of the central nervous system (CNS), called amoebic encephalitis (BAE), as well cutaneous and systemic diseases. Patients infected with B. have high mortality rate due to lack effective treatments. A nonoptimized antimicrobial drug regimen typically recommended; however, it has poor antiparasitic activity various severe side effects. Cyclic peptides exhibit broad spectrum activities but are underexplored for their antiamoebic activity. In this study, we evaluated anti-B. effect Synthetic Natural Product Inspired Peptides (SNaPP) mined from ∼500 biosynthetic gene clusters bacterial species. The predicted natural product-43 (pNP-43; BICyP1), identified SNaPP library, its derivates displayed significant inhibition against trophozoites, five pNPs having IC50s ≤ 5 μM. Furthermore, all hit product inspired demonstrated minimal no hemolytic cytotoxic effects on human red blood cells (RBCs) immortalized carcinoma cells, respectfully. Our study first demonstrate cyclic peptides, offering promising new direction development.

Language: Английский

Citations

0
Molecular Modelling in Bioactive Peptide Discovery and Characterisation DOI Creative Commons
Clement Agoni, Raúl Fernández-Díaz, Patrick Brendan Timmons

et al.

Biomolecules, Journal Year: 2025, Volume and Issue: 15(4), P. 524 - 524

Published: April 3, 2025

Molecular modelling is a vital tool in the discovery and characterisation of bioactive peptides, providing insights into their structural properties interactions with biological targets. Many models predicting peptide function or structure rely on intrinsic properties, including influence amino acid composition, sequence, chain length, which impact stability, folding, aggregation, target interaction. Homology predicts structures based known templates. Peptide–protein can be explored using molecular docking techniques, but there are challenges related to inherent flexibility addressed by more computationally intensive approaches that consider movement over time, called dynamics (MD). Virtual screening many usually against single target, enables rapid identification potential peptides from large libraries, typically approaches. The integration artificial intelligence (AI) has transformed leveraging amounts data. AlphaFold general protein prediction deep learning greatly improved predictions conformations interactions, addition estimates model accuracy at each residue guide interpretation. Peptide being further enhanced Protein Language Models (PLMs), deep-learning-derived statistical learn computer representations useful identify fundamental patterns proteins. Recent methodological developments discussed context canonical as well those modifications cyclisations. In designing therapeutics, main outstanding challenge for these methods incorporation diverse non-canonical acids

Language: Английский

Citations

0
Antimicrobial peptides: from discovery to developmental applications DOI Creative Commons
Qi Zhang

Applied and Environmental Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: April 3, 2025

Antimicrobial resistance (AMR) has emerged as a significant crisis in global health. Due to their advantageous properties, antimicrobial peptides (AMPs) have garnered considerable attention potential alternative therapy address the AMR crisis. These might disrupt cell membranes or walls exhibit activity, modulate immune response promote recovery from diseases. In recent years, progress been made research of AMPs, alongside emergence new challenges. This review first systematically summarizes and critically discusses advancements understanding characteristics current landscapes well regulatory mechanisms action practical applications, particularly those reported approved within last 5 years. Additionally, principles, paths for identification, future trends AMPs are also analyzed following discussion advantages disadvantages comparison conventional antibiotics. Unlike prior literature this field, report summarized latest major discovery methods and, more importantly, emphasized applications by supporting various viewpoints using selected examples AMPs' real-life scenarios. Besides, some emerging hot topics including derived gut microbiota synergistic effects combating AMR, were profiled. All these indicate originality provide valuable references AMP discoveries applications.

Language: Английский

Citations

0
Natural and Designed Cyclic Peptides as Potential Antiviral Drugs to Combat Future Coronavirus Outbreaks DOI Creative Commons

Hilarie Uwamahoro,

Willard E. Collier,

Toufic O. Nashar

et al.

Molecules, Journal Year: 2025, Volume and Issue: 30(8), P. 1651 - 1651

Published: April 8, 2025

The COVID-19 pandemic has underscored the need for effective and affordable antiviral drugs. Anthropogenic activities have increased interactions among humans, animals, wildlife, contributing to emergence of new re-emerging viral diseases. RNA viruses pose significant challenges due their rapid mutation rates, high transmissibility, ability adapt host immune responses treatments. World Health Organization identified several diseases (COVID-19, Ebola, Marburg, Zika, others), all caused by viruses, designated as being priority concern potential causes future pandemics. Despite advances in treatments, many lack specific therapeutic options, more importantly, there is a paucity broad-spectrum Additionally, costs current treatments such Remdesivir Paxlovid highlight Cyclic peptides from natural sources or designed through molecular modeling shown promise drugs with stability, low toxicity, target specificity, resistance properties. This review emphasizes urgent develop highlights cyclic sustainable solution combat Further research into these compounds could provide weapon address gaps drug development.

Language: Английский

Citations

0
Structural information in therapeutic peptides: Emerging applications in biomedicine DOI Creative Commons
Valentín Iglesias, Oriol Bárcenas, Carlos Pintado‐Grima

et al.

FEBS Open Bio, Journal Year: 2024, Volume and Issue: 15(2), P. 254 - 268

Published: June 14, 2024

Peptides are attracting a growing interest as therapeutic agents. This trend stems from their cost-effectiveness and reduced immunogenicity, compared to antibodies or recombinant proteins, but also ability dock interfere with large protein-protein interaction surfaces, higher specificity better biocompatibility relative organic molecules. Many tools have been developed understand, predict, engineer peptide function. However, most state-of-the-art approaches treat peptides only linear entities disregard structural arrangement. Yet, details critical for properties such solubility, stability, binding affinities. Recent advances in structure prediction successfully addressed the scarcity of confidently determined structures. review will explore different biotechnological applications assemblies, emphasizing importance integrating information advance these endeavors effectively.

Language: Английский

Citations

3
Machine learning, network pharmacology, and molecular dynamics reveal potent cyclopeptide inhibitors against dengue virus proteins DOI

Mohammed A. Imam,

Thamir A. Alandijany,

Hashim R. Felemban

et al.

Molecular Diversity, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 4, 2024

Language: Английский

Citations

0
cyclicpeptide: a Python package for cyclic peptide drug design DOI Creative Commons
Yang Liu, Suqi Cao, Lei Liu

et al.

Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 26(1)

Published: Nov. 22, 2024

Abstract The unique cyclic structure of peptides grants them remarkable stability and bioactivity, making powerful candidates for treating various diseases. However, the lack standardized tools peptide data has hindered their potential in today’s artificial intelligence–driven efficient drug design landscape. To bridge this gap, here we introduce a Python package named cyclicpeptide specifically design. This provides such as Structure2Sequence, Sequence2Structure, format transformation to process, convert, standardize sequence data. Additionally, it includes GraphAlignment peptide–specific alignment search PropertyAnalysis enhance understanding drug-like properties applications. comprehensive suite aims streamline integration into modern discovery pipelines, accelerating development peptide–based therapeutics.

Language: Английский

Citations

0