ArticleFrontiers in chemistry2020
Rapid
Article in Frontiers in chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 30 citations in OpenAlex.
- cPEPmatch Webserver: A comprehensive tool and database to aid rational design of cyclic peptides for drug discovery.Computational and structural biotechnology journal · 2024Article
- Rational design of glycosaminoglycan binding cyclic peptides using cPEPmatch.Computational and structural biotechnology journal · 2024Article
- Tackling Undruggable Targets with Designer Peptidomimetics and Synthetic Biologics.Chemical reviews · 2024Review
- Recent advances in Alzheimer's disease: Mechanisms, clinical trials and new drug development strategies.Signal transduction and targeted therapy · 2024Review
- Influence of heterochirality on the structure, dynamics, biological properties of cyclic(PFPF) tetrapeptides obtained by solvent-free ball mill mechanosynthesis.Scientific reports · 2024Article
- Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools.International journal of molecular sciences · 2024Review
- Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization.Journal of chemical information and modeling · 2023Article
- Targeting Peptides: The New Generation of Targeted Drug Delivery Systems.Pharmaceutics · 2023Review
- What Makes a Good Protein-Protein Interaction Stabilizer: Analysis and Application of the Dual-Binding Mechanism.ACS central science · 2023Article
- Des3PI: a fragment-based approach to design cyclic peptides targeting protein-protein interactions.Journal of computer-aided molecular design · 2022Article
- Targeting the "undruggable" RAS with biologics.Advances in cancer research · 2022Review
- Cyclisation strategies for stabilising peptides with irregular conformations.RSC medicinal chemistry · 2021Review
- Heterocyclic Substitutions Greatly Improve Affinity and Stability of Folic Acid towards FRα. an In Silico Insight.Molecules (Basel, Switzerland) · 2021Article
- Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering.Frontiers in molecular biosciences · 2021Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rational design of specific inhibitors of protein-protein interactions is desirable for drug design to control cellular signal transduction but also for studying protein-protein interaction networks. We have developed a rapid computational approach to rationally design cyclic peptides that potentially bind at desired regions of the interface of protein-protein complexes. The methodology is based on comparing the protein backbone structure of short peptide segments (epitopes) at the protein-protein interface with a collection of cyclic peptide backbone structures. A cyclic peptide that matches the backbone structure of the segment is used as a template for a binder by adapting the amino acid side chains to the side chains found in the target complex. For a small library of cyclic peptides with known high resolution structures we found for the majority (~82%) of 154 protein-protein complexes at least one very well fitting match for a cyclic peptide template to a protein-protein interface segment. The majority of the constructed protein-cyclic peptide complexes was very stable during Molecular Dynamics simulations and showed an interaction energy score that was typically more favorable compared to interaction scores of typical peptide-protein complexes. Our cPEPmatch approach could be a promising approach for rapid suggestion of cyclic peptide binders that could be tested experimentally and further improved by chemical modification.
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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.