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Harnessing Peptides and Peptidomimetics in Modern Drug Discovery

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: 30 August 2026 | Viewed by 392

Special Issue Editor

Department of Cellular Biology & Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
Interests: organic chemistry; medicinal chemistry; small molecules; drug-like compounds; tethered and fused diazacyclic compounds; heterocyclic peptidomimetics; combinatorial chemistry; solid phase organic synthesis
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Special Issue Information

Dear Colleagues,

Peptide and peptidomimetic drug discovery has progressed tremendously over the last two decades to become an extraordinary field that has resulted in a substantial body of multidisciplinary research. It has engaged synthetic, computational, and biophysical chemists, biochemists, pharmacologists, and drug development scientists worldwide to create novel molecule lead compounds, clinical candidates, and breakthrough medicines. Immense efforts have been dedicated towards developing therapeutic entities that can modulate intracellular proteins. Molecules that can readily cross cell membranes are becoming a frequent need in biological research, drug discovery, and medicine. A wide variety of natural peptides and peptidomimetics have been obtained and studied, and many others are advancing through clinical trials, covering multiple therapeutic areas.

Taking advantage of the diversity within the amino acid functionalities and stereochemistry that are commercially available as standard Fmoc/Boc amino acids, as well as the benefits of solid-phase peptide synthesis, various synthetic strategies have been developed over the years to modulate the conformational flexibility and peptide character of peptidomimetic compounds. This Special Issue “Harnessing Peptides and Peptidomimetics in Modern Drug Discovery” calls for papers to elucidate the most effective strategy for the synthesis of peptides, cyclic peptides, and peptidomimetics and the use of such approaches in the identification of active therapeutics with peptide structures.

Dr. Adel Nefzi
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • peptide synthesis
  • peptidomimetics
  • cyclic peptides
  • peptide therapeutics
  • peptide drug discovery
  • modified peptides
  • bioactive peptides

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Published Papers (1 paper)

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Research

15 pages, 1595 KB  
Article
Integrating Single-Cell Profiling with Generative AI for De Novo Design of MMP9 Protein Binders in Diffuse Large B-Cell Lymphoma
by Ziyang Miao, Siyi Zhu, Liwei Qin, Dawei Ma, Mingyang Lai, Pingping Xu, Yaping Jin, Huimin Cai, Shuai Zhao and Yang Wang
Molecules 2026, 31(11), 1969; https://doi.org/10.3390/molecules31111969 (registering DOI) - 5 Jun 2026
Abstract
To clarify the cellular origin of matrix metalloproteinase-9 (MMP9) and explore targeted research, we utilized single-cell RNA sequencing analysis, which revealed that MMP9 is predominantly enriched in specific macrophages within the activated B-cell-like (ABC) subtype. Guided by this target information, we applied a [...] Read more.
To clarify the cellular origin of matrix metalloproteinase-9 (MMP9) and explore targeted research, we utilized single-cell RNA sequencing analysis, which revealed that MMP9 is predominantly enriched in specific macrophages within the activated B-cell-like (ABC) subtype. Guided by this target information, we applied a generative AI pipeline incorporating RFdiffusion, ProteinMPNN, and AlphaFold to de novo design protein binders targeting the hemopexin (PEX) domain of MMP9. ELISA experiments confirmed the in vitro binding capability of these designs; among them, MMP9-30 displayed the strongest binding, with an apparent EC50 of approximately 1.1 μM, followed by MMP9-34, while MMP9-97 showed the weakest interaction. This study successfully integrates single-cell sequencing with AI-assisted protein design, providing a preliminary exploratory framework for subsequent MMP9-targeted research and protein binder development. Full article
(This article belongs to the Special Issue Harnessing Peptides and Peptidomimetics in Modern Drug Discovery)
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