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The 20th Anniversary of Pharmaceuticals: Advances in Peptide Drug...
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The 20th Anniversary of Pharmaceuticals: Advances in Peptide Drug Design and Development: From Sequences to Drug Candidates

A special issue of Pharmaceuticals (ISSN 1424-8247). This special issue belongs to the section "Biopharmaceuticals".

Deadline for manuscript submissions: closed (25 April 2025) | Viewed by 7100

Special Issue Editors

Dr. Juliana C. C. Dallagnol

E-Mail Website
Guest Editor
Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Groupe de Recherche en Ingénierie des Peptides et en Pharmacothérapie (GRIPP), Université du Québec, Laval, QC H7V 5B7, Canada
Interests: medicinal chemistry; drug discovery and development; G protein-coupled receptors; drug optimization; GPCR signaling; biased signaling; allosteric modulators
Prof. Dr. David Chatenet

E-Mail Website1 Website2
Guest Editor
Institut National de la Rechercher Scientifique—Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada
Interests: peptide-based drugs; peptide chemistry; G protein-coupled receptors; pharmacology; cardiovascular pharmacology; allosteric modulators; biased agonists

Special Issue Information

Dear Colleagues, 

The upcoming Special Issue "Advances in Peptide Drug Design and Development: from Sequences to Drug Candidates" will explore the research landscape of peptide-based bioactive molecules. Peptides have emerged as versatile motifs to be explored in the drug discovery and development research field, offering unique advantages such as target specificity and low toxicity compared to small molecule counterparts. This Special Issue aims to showcase recent advances in peptide engineering, highlighting strategies such as identifying promising peptide sequences as well as translating them into viable drug candidates. 

We invite researchers in the drug development research field, medicinal chemistry, pharmacology, physiology, molecular biology, and clinicians to contribute their original research findings as well as insights and perspectives on the current trends and challenges in designing peptide-based drug candidates.

The key areas to be addressed include: 

  1. Peptide Sequencing and Screening: Identification of biologically active peptide sequences and essential pharmacophore motifs.
  2. Peptide Modifications and Engineering: Cutting-edge strategies for optimizing sequences to enhance the stability, bioavailability, pharmacokinetics, and pharmacological properties of peptides.
  3. Structural Insights: Exploring the impact of tridimensional structures on peptide activity, employing NMR spectroscopy data, and computational models.
  4. Peptide Synthesis: Advances in synthesis techniques, including solid-phase and microwave-assisted methods, orthogonal chemistry, and late-stage modifications.
  5. Bioconjugation and Drug Delivery: Development of peptide–drug conjugates and strategies for targeted delivery and controlled release.
  6. Peptide-Based Therapeutics: Case studies characterizing the pharmacological properties of peptide-based therapeutics, from in vitro to clinical settings.
  7. Toxicology and Safety Assessment: Methodologies for and challenges in evaluating safety, toxicity, and the immunogenicity of peptide-based drug candidates.
  8. Emerging Technologies: Exploration of innovative technologies, such as mRNA-encoding peptides, CRISPR-mediated therapies, and AI-driven drug design.
  9. Future Perspectives: Insights into the evolving landscape of peptide drug development, including personalized medicine, combination therapies, and addressing unmet medical needs.

Dr. Juliana C. C. Dallagnol
Prof. Dr. David Chatenet
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Pharmaceuticals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 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-based drugs
  • drug design
  • therapeutic peptides
  • peptide synthesis
  • structure–activity relationship
  • peptide drug delivery
  • bioavailability
  • formulation strategies
  • peptide therapeutics

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Published Papers (3 papers)

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21 pages, 3146 KiB  
Article
TnP as a Multifaceted Therapeutic Peptide with System-Wide Regulatory Capacity
by Geonildo Rodrigo Disner, Emma Wincent, Carla Lima and Monica Lopes-Ferreira
Pharmaceuticals 2025, 18(8), 1146; https://doi.org/10.3390/ph18081146 (registering DOI) - 1 Aug 2025
Abstract
Background: The candidate therapeutic peptide TnP demonstrates broad, system-level regulatory capacity, revealed through integrated network analysis from transcriptomic data in zebrafish. Our study primarily identifies TnP as a multifaceted modulator of drug metabolism, wound healing, proteolytic activity, and pigmentation pathways. Results: Transcriptomic profiling [...] Read more.
Background: The candidate therapeutic peptide TnP demonstrates broad, system-level regulatory capacity, revealed through integrated network analysis from transcriptomic data in zebrafish. Our study primarily identifies TnP as a multifaceted modulator of drug metabolism, wound healing, proteolytic activity, and pigmentation pathways. Results: Transcriptomic profiling of TnP-treated larvae following tail fin amputation revealed 558 differentially expressed genes (DEGs), categorized into four functional networks: (1) drug-metabolizing enzymes (cyp3a65, cyp1a) and transporters (SLC/ABC families), where TnP alters xenobiotic processing through Phase I/II modulation; (2) cellular trafficking and immune regulation, with upregulated myosin genes (myhb/mylz3) enhancing wound repair and tlr5-cdc42 signaling fine-tuning inflammation; (3) proteolytic cascades (c6ast4, prss1) coupled to autophagy (ulk1a, atg2a) and metabolic rewiring (g6pca.1-tg axis); and (4) melanogenesis-circadian networks (pmela/dct-fbxl3l) linked to ubiquitin-mediated protein turnover. Key findings highlight TnP’s unique coordination of rapid (protease activation) and sustained (metabolic adaptation) responses, enabled by short network path lengths (1.6–2.1 edges). Hub genes, such as nr1i2 (pxr), ppara, and bcl6aa/b, mediate crosstalk between these systems, while potential risks—including muscle hypercontractility (myhb overexpression) or cardiovascular effects (ace2-ppp3ccb)—underscore the need for targeted delivery. The zebrafish model validated TnP-conserved mechanisms with human relevance, particularly in drug metabolism and tissue repair. TnP’s ability to synchronize extracellular matrix remodeling, immune resolution, and metabolic homeostasis supports its development for the treatment of fibrosis, metabolic disorders, and inflammatory conditions. Conclusions: Future work should focus on optimizing tissue-specific delivery and assessing genetic variability to advance clinical translation. This system-level analysis positions TnP as a model example for next-generation multi-pathway therapeutics. Full article
(This article belongs to the Special Issue The 20th Anniversary of Pharmaceuticals: Advances in Peptide Drug Design and Development: From Sequences to Drug Candidates)
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18 pages, 3075 KiB  
Article
Snake Venom Peptide Fractions from Bothrops jararaca and Daboia siamensis Exhibit Differential Neuroprotective Effects in Oxidative Stress-Induced Zebrafish Models
by Felipe Assumpção da Cunha e Silva, Brenda Rufino da Silva, Leticia Ribeiro de Barros, Emidio Beraldo-Neto, Adolfo Luis Almeida Maleski and Carlos Alberto-Silva
Pharmaceuticals 2025, 18(5), 678; https://doi.org/10.3390/ph18050678 - 2 May 2025
Cited by 1 | Viewed by 2773
Abstract
Introduction: Snake venoms are rich sources of bioactive peptides with therapeutic potential, particularly against neurodegenerative diseases linked to oxidative stress. While the peptide fraction (<10 kDa) from Bothrops jararaca venom has shown in vitro neuroprotection, analogous fractions from related species remain unexplored in vivo. [...] Read more.
Introduction: Snake venoms are rich sources of bioactive peptides with therapeutic potential, particularly against neurodegenerative diseases linked to oxidative stress. While the peptide fraction (<10 kDa) from Bothrops jararaca venom has shown in vitro neuroprotection, analogous fractions from related species remain unexplored in vivo. Methods: This study comparatively evaluated the neuroprotective effects of two peptide fractions (pf) from Daboia siamensis (pf-Ds) and B. jararaca (pf-Bj) against H2O2-induced oxidative stress using in vitro (PC12 cells) and in vivo (zebrafish, Danio rerio) models. Results: In vitro, pf-Ds (1 µg mL−1) did not protect PC12 cells against H2O2-induced cytotoxicity, unlike previously reported effects of pf-Bj. In vivo, neither pf-Ds nor pf-Bj (1–20 µg mL−1) induced significant developmental toxicity in zebrafish larvae up to 120 h post-fertilization (hpf). The neuroprotective effects of both pf were evaluated using two experimental models: (I) Larvae at 96 hpf were exposed to either pf-Ds or pf-Bj (10 µg mL−1) for 4 h, followed by co-exposure to H2O2 (0.2 mmol L−1) for an additional 10 h to induce oxidative stress (4–20 h model); (II) Embryos at 4 hpf were treated with pf-Ds or pf-Bj (10 µg mL−1) continuously until 96 hpf, after which they were exposed to H2O2 (0.2 mmol L−1) for another 24 h (96–120 h model). In a short-term treatment model, neither fraction reversed H2O2-induced deficits in metabolism or locomotor activity. However, in a prolonged treatment model, pf-Bj significantly reversed the H2O2-induced locomotor impairment, whereas pf-Ds did not confer protection. Conclusions: These findings demonstrate, for the first time, the in vivo neuroprotective potential of pf-Bj against oxidative stress-induced behavioral deficits in zebrafish, contingent on the treatment regimen. The differential effects between pf-Ds and pf-Bj highlight species-specific venom composition and underscore the value of zebrafish for evaluating venom-derived peptides. Full article
(This article belongs to the Special Issue The 20th Anniversary of Pharmaceuticals: Advances in Peptide Drug Design and Development: From Sequences to Drug Candidates)
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13 pages, 3336 KiB  
Article
Biological Activities of Deer Antler-Derived Peptides on Human Chondrocyte and Bone Metabolism
by Tsung-Jung Ho, Wan-Ting Tsai, Jia-Ru Wu and Hao-Ping Chen
Pharmaceuticals 2024, 17(4), 434; https://doi.org/10.3390/ph17040434 - 28 Mar 2024
Cited by 6 | Viewed by 3477
Abstract
Orally administered “tortoiseshell and deer antler gelatin” is a common traditional medicine for patients with osteoporosis or osteoarthritis. From the pepsin-digested gelatin, we previously isolated and identified the osteoblast-stimulating pentapeptide, TSKYR. Its trypsin digestion products include the dipeptide YR, enhancing calcium ion uptake, [...] Read more.
Orally administered “tortoiseshell and deer antler gelatin” is a common traditional medicine for patients with osteoporosis or osteoarthritis. From the pepsin-digested gelatin, we previously isolated and identified the osteoblast-stimulating pentapeptide, TSKYR. Its trypsin digestion products include the dipeptide YR, enhancing calcium ion uptake, and tripeptide TSK, resulting in remarkable 30- and 50-fold increases in mineralized nodule area and density in human osteoblast cells. These peptides were chemically synthesized in this study. The composition of deer antler preparations comprises not only proteins and peptides but also a significant quantity of metal ion salts. By analyzing osteoblast growth in the presence of peptide YR and various metal ions, we observed a synergistic effect of calcium and strontium on the effects of YR. Those peptides could also stimulate the growth of C2C12 skeletal muscle cells and human chondrocytes, increasing collagen and glycosaminoglycan content in a three-dimensional environment. The maintenance of bone homeostasis relies on a balance between osteoclasts and osteoblasts. Deer antler peptides were observed to inhibit osteoclast differentiation, as evidenced by ROS generation, tartrate-resistant acid phosphatase (TRACP) activity assays, and gene expression in RAW264.7 cells. In summary, our findings provide a deep understanding of the efficacy of this folk medicine. Full article
(This article belongs to the Special Issue The 20th Anniversary of Pharmaceuticals: Advances in Peptide Drug Design and Development: From Sequences to Drug Candidates)
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