ReviewFrontiers in molecular biosciences2020
Bioinformatics and Biosimulations as Toolbox for Peptides and Peptidomimetics Design: Where Are We?
Review in Frontiers in molecular biosciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- DyME: An MD-based engine exploiting HTP mutagenesis for protein engineering and recognition mimicry.PLoS computational biology · 2026Article
- Establishment of an I-ELISA method based on multi-epitope fusion protein for diagnosis of human brucellosis.PLoS neglected tropical diseases · 2025Article
- A claudin5-binding peptide enhances the permeability of the blood-brain barrier in vitro.Science advances · 2025Article
- Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study.Journal of chemical information and modeling · 2024Article
- A New Advanced Approach: Design and Screening of Affinity Peptide Ligands Using Computer Simulation Techniques.Current topics in medicinal chemistry · 2024Review
- Molecular View on theJournal of chemical information and modeling · 2023Article
- CRISPR/Cas9 Genome Editing for Tissue-Specific In Vivo Targeting: Nanomaterials and Translational Perspective.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Review
- Non-Canonical Amino Acids as Building Blocks for Peptidomimetics: Structure, Function, and Applications.Biomolecules · 2023Review
- Large scale peptide screening against main protease of SARS CoV-2.Journal of computational chemistry · 2023Article
- White Paper: Mimetics of Class 2 Tumor Suppressor Proteins as Novel Drug Candidates for Personalized Cancer Therapy.Cancers · 2022Article
- The development of ADAM10 endocytosis inhibitors for the treatment of Alzheimer's disease.Molecular therapy : the journal of the American Society of Gene Therapy · 2022Article
- Conceptual DFT-Based Computational Peptidology, Pharmacokinetics Study and ADMET Report of the Veraguamides A-G Family of Marine Natural Drugs.Marine drugs · 2022Article
- What a Difference an Amino Acid Makes: An All-Atom Simulation Study of Nonameric Peptides in Inhibitory HLA-E/NKG2A/CD94 Immune Complexes.Frontiers in pharmacology · 2022Article
- Natural and Synthetic Halogenated Amino Acids-Structural and Bioactive Features in Antimicrobial Peptides and Peptidomimetics.Molecules (Basel, Switzerland) · 2021Review
- Control of the eIF4E activity: structural insights and pharmacological implications.Cellular and molecular life sciences : CMLS · 2021Review
- Paper-based ELISA diagnosis technology for human brucellosis based on a multiepitope fusion protein.PLoS neglected tropical diseases · 2021Article
- The Role of Peptides in the Design of Electrochemical Biosensors for Clinical Diagnostics.Biosensors · 2021Review
- Halting the Spread of Herpes Simplex Virus-1: The Discovery of an Effective Dual αvβ6/αvβ8 Integrin Ligand.Journal of medicinal chemistry · 2021Article
- 1,2,3-Triazoles as Biomimetics in Peptide Science.Molecules (Basel, Switzerland) · 2021Review
- Implementing and Assessing an Alchemical Method for Calculating Protein-Protein Binding Free Energy.Journal of chemical theory and computation · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Peptides and peptidomimetics are strongly re-emerging as amenable candidates in the development of therapeutic strategies against a plethora of pathologies. In particular, these molecules are extremely suitable to treat diseases in which a major role is played by protein-protein interactions (PPIs). Unlike small organic compounds, peptides display both a high degree of specificity avoiding secondary off-targets effects and a relatively low degree of toxicity. Further advantages are provided by the possibility to easily conjugate peptides to functionalized nanoparticles, so improving their delivery and cellular uptake. In many cases, such molecules need to assume a specific three-dimensional conformation that resembles the bioactive one of the endogenous ligand. To this end, chemical modifications are introduced in the polypeptide chain to constrain it in a well-defined conformation, and to improve the drug-like properties. In this context, a successful strategy for peptide/peptidomimetics design and optimization is to combine different computational approaches ranging from structural bioinformatics to atomistic simulations. Here, we review the computational tools for peptide design, highlighting their main features and differences, and discuss selected protocols, among the large number of methods available, used to assess and improve the stability of the functional folding of the peptides. Finally, we introduce the simulation techniques employed to predict the binding affinity of the designed peptides for their targets.
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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.