1
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Vitek M, Zvonar Pobirk A, Roškar R, Matjaž MG. Exploiting the potential of in situ forming liquid crystals: development and in vitro performance of long-acting depots for peptide drug thymosin alpha 1 subcutaneous administration. Drug Deliv 2025; 32:2460708. [PMID: 40066714 PMCID: PMC11899226 DOI: 10.1080/10717544.2025.2460708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 11/06/2024] [Accepted: 01/24/2025] [Indexed: 03/14/2025] Open
Abstract
The fast-growing filed of long-acting depots for subcutaneous (SC) administration holds significant potential to enhance patient adherence to treatment regimens, particularly in the context of chronic diseases. Among them, injectable in situ forming lyotropic liquid crystals (LCCs) consisting of hexagonal mesophases represent an attractive platform due to their remarkable highly ordered microstructure enabling the sustained drug release. These systems are especially relevant for peptide drugs, as their use is limited by their short plasma half-life and inherent poor stability. In this study, we thus aimed to exploit the potential of a liquid crystalline platform for the sustained release of peptide drug thymosin alpha 1 (Tα1), characterized by a short plasma half-life and with that associated twice-weekly SC administration regimen. We initially selected specified ingredients, with ethanol serving to reduce viscosity and stabilize the peptide drug Tα1, lecithin contributing to LCCs formation and stabilization, and glycerol monooleate or glycerol monolinoleate representing the hexagonal LCCs forming matrix material. The selected studied nonaqueous precursor formulations were characterized by suitable rheological properties for SC injection. A convenient and rapid in situ phase transition of precursor formulations to hexagonal LCCs, triggered by water absorption, was successfully accomplished in vitro. Notably, in situ formed LCCs demonstrated sustained release kinetics of the peptide drug Tα1 for up to 2 weeks of in vitro release testing, offering minimized dosing frequency and thus promoting patient adherence. In summary, the newly developed in situ forming liquid crystalline systems represent prospective injectable long-acting depots for SC administration of the peptide drug Tα1.
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Affiliation(s)
- Mercedes Vitek
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Alenka Zvonar Pobirk
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Robert Roškar
- Department of Biopharmaceutics and Pharmacokinetics, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Mirjam Gosenca Matjaž
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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2
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Karongo R, Li F, Fiessinger F, Sievers-Engler A, Kroth I, Resch S, Baumann L, Novak A, Gao M, Hetzel T, Holkenjans W, Hoheisel W, Pell R, Gottfried M, Lämmerhofer M. Automated derivatization with 6-aminoquinolyl-N-hydroxysccinimidyl carbamate for the enantioselective amino acid analysis of neurotensin synthesized by liquid phase peptide synthesis. J Pharm Biomed Anal 2025; 263:116916. [PMID: 40294459 DOI: 10.1016/j.jpba.2025.116916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2025] [Revised: 04/21/2025] [Accepted: 04/22/2025] [Indexed: 04/30/2025]
Abstract
This study presents an automated derivatization protocol utilizing 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) for enantioselective amino acid analysis of peptides synthesized via liquid phase peptide synthesis, as exemplified by neurotensin. The primary aim was to enhance operational efficiency to manage the derivatization of large sample sets and reduce human error in routine enantioselective amino acid analysis of peptide therapeutics. The chromatographic method based on Chiralpak QN-AX demonstrated enantio- and chemoselectivity for all proteinogenic amino acids (except D-Leu/D-Ile and Glu/pGlu), with quantitative analysis achieved by HPLC-ESI-MS/MS with MRM acquisition through external calibration using stable isotope-labeled internal standards. The goal was to test for racemization of amino acids during peptide synthesis and process optimization, respectively. The results confirmed varying susceptibility to racemization among amino acids during peptide synthesis and cleavage of protection groups, with specific amino acids exhibiting higher levels of D-enantiomer formation. The developed protocol effectively assessed the amino acid composition and stereointegrity of the liquid phase synthesized neurotensin. This research and application highlights the critical role of automation in optimizing peptide analysis workflows and sets the foundation for future improvements in peptide synthesis and chromatographic conditions to enhance specificity, particularly for challenging amino acid pairs. Ultimately, the findings contribute to advancing laboratory practices in peptide chemistry, ensuring the quality and efficacy of peptide-based therapeutics.
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Affiliation(s)
- Ryan Karongo
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany; Invite GmbH, Formulation Technology, Köln 51061, Germany; Bayer AG, Wuppertal 42096, Germany.
| | - Feiyang Li
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Franz Fiessinger
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Adrian Sievers-Engler
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | | | | | | | | | - Mimi Gao
- Bayer AG, Wuppertal 42096, Germany
| | | | | | | | | | | | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany.
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3
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Lou J, Wu X, Ji W, Yu J, Xu Y, Xiao W, Lu W, Xin K, Chen T, Tang Q, Liang G, Gao Y, Wu D. N-Terminal random curl-tandam α-helical peptide 7W: A potent antibacterial and anti-inflammatory dual-effect agent through tryptophan substitution. Eur J Med Chem 2025; 292:117686. [PMID: 40319576 DOI: 10.1016/j.ejmech.2025.117686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 04/17/2025] [Accepted: 04/24/2025] [Indexed: 05/07/2025]
Abstract
This study investigates the impact of tryptophan substitution on the properties of the Medisin family peptide MS-PT. By substituting hydrophobic amino acids in MS-PT1 with tryptophan, a series of derivative peptides were synthesized. Among them, the 7W peptide stood out with its unique N-terminal random curl and α-helix structure. In vitro, 7W effectively inhibited the secretion of pro-inflammatory cytokines like IL-6 and TNF-α in LPS-induced Membrane-Proximal Macrophages (MPMs) by blocking the MAPK/NF-κB signaling pathway. It also exhibited stronger antimicrobial activity against Gram-positive bacteria compared to the parent peptide MS-PT1, with good safety as indicated by a low hemolysis rate. In vivo, in the CLP-induced sepsis mouse model, 7W alleviated lung and liver injury, suppressed the expression of inflammatory factors in serum and tissues, and had a relatively long plasma half-life of 46.8 h. Mechanistically, 7W interacted preferentially with bacterial mimic membranes and LPS, and its anti-inflammatory effect might be mediated by binding to TLR4. These findings not only clarify the role of tryptophan substitution in modulating peptide properties but also offer a new strategy for the development of multifunctional antimicrobial peptides, suggesting that 7W has great potential as a therapeutic agent for sepsis and other inflammatory diseases.
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Affiliation(s)
- Jietao Lou
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Xinyi Wu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China; Department of Pharmacy, The First People's Hospital of Jiande, Hangzhou, 311600, China
| | - Wenwen Ji
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Jiaye Yu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yanyan Xu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Wanyang Xiao
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China; College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Weijie Lu
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Kaiyun Xin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Tianbao Chen
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Qidong Tang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China; Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325001, China
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China; School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, 310053, China
| | - Yitian Gao
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China.
| | - Di Wu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
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Rahaman KA, Mukim MSI, Hasan ML, Kim H, Pan CH, Kwon OS, Song DG, Han HS. Protein to biomaterials: Unraveling the antiviral and proangiogenic activities of Ac-Tβ 1-17 peptide, a thymosin β4 metabolite, and its implications in peptide-scaffold preparation. Bioact Mater 2025; 49:437-455. [PMID: 40177110 PMCID: PMC11964602 DOI: 10.1016/j.bioactmat.2025.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 01/20/2025] [Accepted: 02/04/2025] [Indexed: 04/05/2025] Open
Abstract
Peptide metabolites are emerging biomolecules with numerous possibilities in biomaterial-based regenerative medicine due to their inherent bioactivities. These small, naturally occurring compounds are intermediates or byproducts of larger proteins and peptides, and they can have profound effects, such as antiviral therapeutics, proangiogenic agents, and regenerative medicinal applications. This study is among the first to focus on using thymosin β4 protein-derived metabolites to pioneer novel applications for peptide metabolites in biomaterials. This study found that the novel peptide metabolite acetyl-thymosin β4 (amino acid 1-17) (Ac-Tβ1-17) exhibited significant protease inhibition activity against SARS-CoV-2, surpassing its precursor protein. Additionally, Ac-Tβ1-17 demonstrated beneficial effects, such as cell proliferation, wound healing, and scavenging of reactive oxygen species (ROS) in human umbilical vein endothelial cells (HUVEC). Integrating Ac-Tβ1-17 into a peptide-based scaffold facilitated cell growth and angiogenesis inside the scaffold and through gradual release into the surrounding environment. The Ac-Tβ1-17 peptide treatment induced significant biochemical responses in HUVEC, increasing Akt, ERK, PI3K, MEK, and Bcl-2 gene expression and proangiogenic proteins. Ac-Tβ1-17 peptide treatment showed similar results in ex vivo by enhancing mouse fetal metatarsal growth and angiogenesis. These findings highlight the potential of natural protein metabolites to generate biologically active peptides, offering a novel strategy for enhancing biomaterial compatibility. This approach holds promise for developing therapeutic biomaterials using peptide metabolites, presenting exciting prospects for future research and applications.
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Affiliation(s)
- Khandoker Asiqur Rahaman
- Center for Biomaterials, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Md Sofequl Islam Mukim
- Center for Natural Product Systems Biology, KIST Gangneung Institute of Natural Products, Gangneung, 25451, Republic of Korea
- Natural Product Applied Science, KIST School, University of Science and Technology (UST), Gangneung, 25451, Republic of Korea
| | - Md Lemon Hasan
- Center for Biomaterials, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
- Division of Bio-Medical Science & Technology, University of Science and Technology (UST), 113 Gwahangno, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Hyeok Kim
- Center for Biomaterials, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Cheol-Ho Pan
- Center for Natural Product Systems Biology, KIST Gangneung Institute of Natural Products, Gangneung, 25451, Republic of Korea
- Natural Product Applied Science, KIST School, University of Science and Technology (UST), Gangneung, 25451, Republic of Korea
| | - Oh-Seung Kwon
- Doping Control Center, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
- Division of Bio-Medical Science & Technology, University of Science and Technology (UST), 113 Gwahangno, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Dae-Geun Song
- Center for Natural Product Systems Biology, KIST Gangneung Institute of Natural Products, Gangneung, 25451, Republic of Korea
- Natural Product Applied Science, KIST School, University of Science and Technology (UST), Gangneung, 25451, Republic of Korea
| | - Hyung-Seop Han
- Center for Biomaterials, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
- Division of Bio-Medical Science & Technology, University of Science and Technology (UST), 113 Gwahangno, Yuseong-gu, Daejeon, 34113, Republic of Korea
- Research and Development Center, Elecell Corporation, Seoul, 02455, Republic of Korea
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5
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Liu D, Jiang Y, Ma B, Li L. Structure-based artificial intelligence-aided design of MYC-targeting degradation drugs for cancer therapy. Biochem Biophys Res Commun 2025; 766:151870. [PMID: 40288261 DOI: 10.1016/j.bbrc.2025.151870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2025] [Accepted: 04/21/2025] [Indexed: 04/29/2025]
Abstract
The MYC protein is an oncoprotein that plays a crucial role in various cancers. Although its significance has been well recognized in research, the development of drugs targeting MYC remains relatively slow. In this study, we developed a novel MYC peptide inhibitor based on the MYC/MAX dimer structure, integrating artificial intelligence-assisted peptide drug design. Additionally, we introduced a chaperone-mediated autophagy signal to construct a MYC-targeted degradation drug, MYC-LYSO. By incorporating nano-selenium delivery, we further formulated an enhanced MYC degradation agent, Se-MYC-LYSO. Se-MYC-LYSO demonstrated potent efficacy in inducing MYC degradation, inhibiting tumor cell proliferation, and promoting apoptosis. Moreover, our findings indicate that the efficacy of Se-MYC-LYSO is dependent on the autophagy pathway. These results provide a novel strategy for targeting MYC in cancer therapy.
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Affiliation(s)
- Donghua Liu
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yize Jiang
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Bohan Ma
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China.
| | - Lei Li
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China.
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6
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Kauffman J, Cuevas J, Feiner J, Metzger M, Shetye G, Wan B, Qader M, Nguyen D, Nugent A, Hossain A, Franzblau S, Umesiri FE. Discovery of ultra short β-peptoids with selective activity against drug-resistant Mycobacterium tuberculosis. Eur J Med Chem 2025; 290:117531. [PMID: 40147341 DOI: 10.1016/j.ejmech.2025.117531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 01/27/2025] [Accepted: 03/18/2025] [Indexed: 03/29/2025]
Abstract
There is an urgent need to develop new anti-tuberculosis (anti-TB) drugs to tackle drug-resistant strains of Mycobacterium tuberculosis (M.tb). Whereas antimicrobial peptides (AMPs) have received attention because of their antibacterial properties, oligo-N-substituted glycines (peptoids) are now seen as favorable alternatives to AMPs because they are more stable and less vulnerable to protease degradation, less expensive to produce, and better suited to potential pharmaceutical adoption and development. In this work, therefore, we designed, synthesized, and screened 22 new α- and β-peptoids against drug susceptible M. tb strain H37Rv using the Microplate Alamar Blue assay (MABA) to evaluate minimum inhibitory concentration (MIC). Eight compounds (JC5, MM2, MM5, MM9, MM10, MM11, JF11, and JF13) had MICs of less than 10 μg/ml, the most potent of which were JC5 and MM2, with MICs of 1.48 μg/ml and 2.97 μg/ml, respectively. JC5 and MM2 also retained potency against strains mono-resistant to isoniazid and rifampin, and against five of the global M. tb clade representatives. Furthermore, peptoids JC5 and MM2 showed minimum bactericidal concentration (MBC) of 3.02 μg/ml and 5.48 μg/ml respectively. Intracellular activity by luminescence showed a macrophage EC90 of less than 10 μg/ml for both JC5 and MM2. In addition, both compounds showed remarkable narrow spectrum activity. Selectivity with respect to Vero cells was modest but sufficient to consider these classes of alpha and beta-peptoids as good leads for further development of anti-TB drugs.
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Affiliation(s)
- John Kauffman
- Chemistry Department, Wheaton College, 501 College Ave, Wheaton, IL 60187, United States
| | - Jake Cuevas
- Chemistry Department, Wheaton College, 501 College Ave, Wheaton, IL 60187, United States
| | - Janaya Feiner
- Chemistry Department, Wheaton College, 501 College Ave, Wheaton, IL 60187, United States
| | - Margaret Metzger
- Chemistry Department, Wheaton College, 501 College Ave, Wheaton, IL 60187, United States
| | - Gauri Shetye
- Institute for Tuberculosis Research, Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Baojie Wan
- Institute for Tuberculosis Research, Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Mallique Qader
- Institute for Tuberculosis Research, Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Duc Nguyen
- Institute for Tuberculosis Research, Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Angela Nugent
- Institute for Tuberculosis Research, Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Akil Hossain
- Institute for Tuberculosis Research, Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Scott Franzblau
- Institute for Tuberculosis Research, Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Francis E Umesiri
- Chemistry Department, Wheaton College, 501 College Ave, Wheaton, IL 60187, United States.
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7
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Hussein AA, Okasha H, ElZallat M, Ghoname SI, Habib MR, Hammam OA, El-Dabaa E, Salem MB. Identification and exploration of anticancer activity of novel peptides isolated from the edible bivalve Callista chione in hepatic and colon cancer cell lines. Toxicol Rep 2025; 14:101915. [PMID: 39968051 PMCID: PMC11833620 DOI: 10.1016/j.toxrep.2025.101915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 10/26/2024] [Accepted: 11/03/2024] [Indexed: 02/20/2025] Open
Abstract
Background The requirement for relevant and safe drugs for cancer treatment is considered a challenge. Recently, marine isolated compounds with various therapeutic targets have attracted many researchers. Aim Isolation and identification of potential anticancer peptides from edible Callista chione soft tissues. Methodology C. chione specimens were collected and peptides were extracted, purified with FPLC, and tested on normal (hepatocytes and VERO) and cancer (HepG2, and HT-29) cells. Bioactive fractions were tested by tandem mass spectrometry. Results Five different fractions were purified according to ionic charges and two fractions (4 and 5) showed a potent anticancer activity with a total anticancer score threshold of ≥ 0.5, and hydrophilicity mean of 1.75 that related to stability and solubility. The apoptotic and autophagy-related markers were significantly up-regulated in both HepG2 and HT-29 cells treated with IC50 of bioactive peptides' fractions 4 and 5, explaining their underlying mechanism of action. Conclusion Natural source peptides derived from the soft tissue of C. chione could be exploited for the treatment of cancers and a deep in silico study will be performed for further investigation and deep function identification.
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Affiliation(s)
- Ahmed A.A. Hussein
- Departments of Medical Malacology, Theodor Bilharz Research Institute, Warrak El-Hadar, Imbaba, Giza 12411, Egypt
| | - Hend Okasha
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute, Warrak El-Hadar, Imbaba, Giza 12411, Egypt
| | - Mohamed ElZallat
- Immunology Department, Theodor Bilharz Research Institute, Warrak El-Hadar, Imbaba, Giza 12411, Egypt
| | - Samah I. Ghoname
- Departments of Medical Malacology, Theodor Bilharz Research Institute, Warrak El-Hadar, Imbaba, Giza 12411, Egypt
| | - Mohamed R. Habib
- Departments of Medical Malacology, Theodor Bilharz Research Institute, Warrak El-Hadar, Imbaba, Giza 12411, Egypt
| | - Olfat A. Hammam
- Pathology Department, Theodor Bilharz Research Institute, Warrak El-Hadar, Imbaba, Giza 12411, Egypt
| | - Ehab El-Dabaa
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute, Warrak El-Hadar, Imbaba, Giza 12411, Egypt
| | - Maha B. Salem
- Pharmacology Department, Theodor Bilharz Research Institute, Warrak El-Hadar, Imbaba, Giza 12411, Egypt
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8
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Jahandar-Lashaki S, Farajnia S, Faraji-Barhagh A, Hosseini Z, Bakhtiyari N, Rahbarnia L. Phage Display as a Medium for Target Therapy Based Drug Discovery, Review and Update. Mol Biotechnol 2025; 67:2161-2184. [PMID: 38822912 DOI: 10.1007/s12033-024-01195-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Phage libraries are now amongst the most prominent approaches for the identification of high-affinity antibodies/peptides from billions of displayed phages in a specific library through the biopanning process. Due to its ability to discover potential therapeutic candidates that bind specifically to targets, phage display has gained considerable attention in targeted therapy. Using this approach, peptides with high-affinity and specificity can be identified for potential therapeutic or diagnostic use. Furthermore, phage libraries can be used to rapidly screen and identify novel antibodies to develop immunotherapeutics. The Food and Drug Administration (FDA) has approved several phage display-derived peptides and antibodies for the treatment of different diseases. In the current review, we provided a comprehensive insight into the role of phage display-derived peptides and antibodies in the treatment of different diseases including cancers, infectious diseases and neurological disorders. We also explored the applications of phage display in targeted drug delivery, gene therapy, and CAR T-cell.
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Affiliation(s)
- Samaneh Jahandar-Lashaki
- Medical Biotechnology Department, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Safar Farajnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Aref Faraji-Barhagh
- Medical Biotechnology Department, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Hosseini
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Nasim Bakhtiyari
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Rahbarnia
- Infectious and Tropical Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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9
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Taghizadeh MS, Niazi A, Mirzapour-Kouhdasht A, Pereira EC, Garcia-Vaquero M. Enhancing cyclotide bioproduction: harnessing biological synthesis methods and various expression systems for large-scale manufacturing. Crit Rev Biotechnol 2025; 45:836-858. [PMID: 39510598 DOI: 10.1080/07388551.2024.2412780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/18/2024] [Accepted: 08/27/2024] [Indexed: 11/15/2024]
Abstract
Peptide-based medications hold immense potential in addressing a wide range of human disorders and discomforts. However, their widespread utilization encounters two major challenges: preservation and production efficiency. Cyclotides, a class of ribosomally synthesized and post-translationally modified peptides (RiPPs), exhibit unique characteristics, such as a cyclic backbone and cystine knot, enhancing their stability and contributing to a wide range of pharmacological properties exhibited by these compounds. Cyclotides are efficient in the biomedical (e.g., antitumor, antidiabetic, antimicrobial, antiviral) and agrochemical fields by exhibiting activity against pests and plant diseases. Furthermore, their structural attributes make them suitable as molecular scaffolds for grafting and drug delivery. Notably, the mutated variant of kalata B1 cyclotide ([T20K] kalata B1) has recently entered phase 1 of human clinical trials for multiple sclerosis, building upon the success observed in animal trials. To enable large-scale production of cyclotides, it is crucial to further explore their remarkable structural and bioactive properties. This necessitates extensive research focused on enhancing the efficiency of the processes required for their production. This study provides a comprehensive review of the biological synthesis methods of cyclotides, with particular emphasis on various expression systems, namely bacteria, plants, yeast, and cell-free systems. By investigating these expression systems, it becomes possible to design production systems that are adaptable, economically viable, and efficient for generating active and pure cyclotides at an industrial scale. The advantages of biological synthesis over chemical synthesis are thoroughly explored, highlighting the potential of these expression systems in meeting the demands of large-scale cyclotide production.
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Affiliation(s)
| | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Armin Mirzapour-Kouhdasht
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
- Department of Food Science, Purdue University, West Lafayette, IN, USA
| | - Eric C Pereira
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
| | - Marco Garcia-Vaquero
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
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10
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Saetang J, Yamabhai M, Rangnoi K, Prompat N, Haewphet T, Sangkhathat S, Tipmanee V, Benjakul S. Identification and characterization of oncogenic KRAS G12V inhibitory peptides by phage display, molecular docking and molecular dynamic simulation. Comput Biol Med 2025; 192:110272. [PMID: 40300294 DOI: 10.1016/j.compbiomed.2025.110272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Revised: 04/03/2025] [Accepted: 04/23/2025] [Indexed: 05/01/2025]
Abstract
The KRAS G12V mutation is a critical oncogenic driver in aggressive cancers, yet developing effective inhibitors remains challenging due to its elusive structural features. In this study, we employed phage display technology using both linear and cyclic peptide libraries to identify inhibitory peptides against KRAS G12V. Through subtractive bio-panning against wild-type KRAS, we identified two 23-mer peptides (Pep I and Pep II) that demonstrated selective binding to KRAS G12V. Molecular dynamics simulations revealed distinct binding mechanisms - Pep II showed stronger selective binding to G12V (-35.96 kcal/mol) compared to wild-type KRAS (-18.06 kcal/mol), while Pep I exhibited similar binding energies but interacted with different regions. Notably, Pep I bound to functional regions in KRAS G12V but non-functional regions in wild-type KRAS. Both peptides demonstrated significant inhibition of KRAS G12V-carrying cancer cell lines (NCI-H2444 and SW620), reducing cell viability by 70-75 % at 400 μM after 48 h while showing minimal effects (20-30 % reduction) on wild-type KRAS-carrying Caco-2 cells, which is equal to DMSO diluent control. These findings provide new insights into peptide-based targeting of KRAS G12V and demonstrate the potential of using subtractive phage display for developing selective inhibitors against oncogenic mutations.
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Affiliation(s)
- Jirakrit Saetang
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla, 90110 Thailand.
| | - Montarop Yamabhai
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Kuntalee Rangnoi
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Napat Prompat
- Medical of Technology Service Center, Faculty of Medical Technology, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Thaiyawat Haewphet
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla, 90110 Thailand
| | - Surasak Sangkhathat
- Department of Surgery and Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110 Thailand; Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Varomyalin Tipmanee
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
| | - Soottawat Benjakul
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla, 90110 Thailand
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11
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Jülke EM, Beck-Sickinger AG. Peptide therapeutics: current status and future opportunity with focus on nose-to-brain delivery☆. Peptides 2025; 188:171404. [PMID: 40222598 DOI: 10.1016/j.peptides.2025.171404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Revised: 03/21/2025] [Accepted: 03/31/2025] [Indexed: 04/15/2025]
Abstract
Peptide drugs are a highly diverse group of therapeutic agents. Over the last decade, more than 40 peptides have been approved for clinical use. They target different structures, ranging from G protein-coupled receptors (GPCRs) to pathogens and are used to treat a variety of indications, including metabolic disorders, genetic diseases, acute illnesses and more. Structurally, peptide therapeutics are a heterogeneous class. This diversity allows them to bridge the gap between small molecules and biologics. However, limited metabolic stability and bioavailability must be addressed. Strategies to improve the half-life include backbone and sequence modification, cyclization and the addition of stabilizing moieties. Great strides have been made in recent years towards achieving sufficient drug uptake for oral application have been achieved within recent years. However, these methods require specialized peptide design or involve permeabilization of the gastrointestinal tract. Consequently, other routes of administration are being explored. One promising approach is the nasal application of peptides. This method can be used for systemic uptake, but also allows for direct nose-to-brain delivery of compounds. While successful nose-to-brain delivery is already used in the clinic, the underlining mechanisms are poorly understood. Strategies for rational optimization are needed to make this method more applicable to a wider range of compounds. Overall, approved peptide therapeutics cover a wide range of applications and have demonstrated a growing and novel potential in recent drug discovery.
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Affiliation(s)
- Eva-Maria Jülke
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, Leipzig 04103, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, Leipzig 04103, Germany.
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12
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Abbasi M, Heath B. Iontophoresis and electroporation-assisted microneedles: advancements and therapeutic potentials in transdermal drug delivery. Drug Deliv Transl Res 2025; 15:1962-1984. [PMID: 39433696 PMCID: PMC12037666 DOI: 10.1007/s13346-024-01722-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2024] [Indexed: 10/23/2024]
Abstract
Transdermal drug delivery (TDD) using electrically assisted microneedle (MN) systems has emerged as a promising alternative to traditional drug administration routes. This review explores recent advancements in this technology across various therapeutic applications. Integrating iontophoresis (IP) and electroporation (EP) with MN technology has shown significant potential in improving treatment outcomes for various conditions. Studies demonstrate their effectiveness in enhancing vaccine and DNA delivery, improving diabetes management, and increasing efficacy in dermatological applications. The technology has also exhibited promise in delivering nonsteroidal anti-inflammatory drugs (NSAIDs), treating multiple sclerosis, and advancing obesity and cancer therapy. These systems offer improved drug permeation, targeted delivery, and enhanced therapeutic effects. While challenges remain, including safety concerns and technological limitations, ongoing research focuses on optimizing these systems for broader clinical applications. The future of electrically assisted MN technologies in TDD appears promising, with potential advancements in personalized medicine, smart monitoring systems, and expanded therapeutic applications.
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Affiliation(s)
- Mehrnaz Abbasi
- College of Human Sciences, Department of Nutritional Sciences, Auburn University, Auburn, AL, 36849, USA.
| | - Braeden Heath
- College of Sciences and Mathematics, Department of Biomedical Sciences, Auburn University, Auburn, AL, 36849, USA
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13
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Wang DY, Wang L, Mi A, Wang J. AI-Assisted Protein-Peptide Complex Prediction in a Practical Setting. J Comput Chem 2025; 46:e70137. [PMID: 40401693 PMCID: PMC12096808 DOI: 10.1002/jcc.70137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2025] [Revised: 05/06/2025] [Accepted: 05/09/2025] [Indexed: 05/23/2025]
Abstract
Accurate prediction of protein-peptide complex structures plays a critical role in structure-based drug design, including antibody design. Most peptide-docking benchmark studies were conducted using crystal structures of protein-peptide complexes; as such, the performance of the current peptide docking tools in the practical setting is unknown. Here, the practical setting implies there are no crystal or other experimental structures for the complex, nor for the receptor and peptide. In this work, we have developed a practical docking protocol that incorporated two famous machine learning models, AlphaFold 2 for structural prediction and ANI-2x for ab initio potential prediction, to achieve a high success rate in modeling protein-peptide complex structures. The docking protocol consists of three major stages. In the first stage, the 3D structure of the receptor is predicted by AlphaFold 2 using the monomer mode, and that of the peptide is predicted by AlphaFold 2 using the multimer mode. We found that it is essential to include the receptor information to generate a high-quality 3D structure of the peptide. In the second stage, rigid protein-peptide docking is performed using ZDOCK software. In the last stage, the top 10 docking poses are relaxed and refined by ANI-2x in conjunction with our in-house geometry optimization algorithm-conjugate gradient with backtracking line search (CG-BS). CG-BS was developed by us to more efficiently perform geometry optimization, which takes the potential and force directly from ANI-2x machine learning models. The docking protocol achieved a very encouraging performance for a set of 62 very challenging protein-peptide systems which had an overall success rate of 34% if only the top 1 docking poses were considered. This success rate increased to 45% if the top 3 docking poses were considered. It is emphasized that this encouraging protein-peptide docking performance was achieved without using any crystal or experimental structures.
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Affiliation(s)
- Darren Y. Wang
- High School Student at Hampton Senior High SchoolPittsburghPennsylvaniaUSA
| | - Luxuan Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of PharmacyUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Andrew Mi
- High School Student at the School for the Talented and Gifted (TAG)DallasTexasUSA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of PharmacyUniversity of PittsburghPittsburghPennsylvaniaUSA
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14
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Lee K, Park H, Devarapalli RK, Im D, Seo J, Lee J. Expanded ribosomal synthesis of non-standard cyclic backbones in vitro. Nat Commun 2025; 16:4957. [PMID: 40436849 PMCID: PMC12120014 DOI: 10.1038/s41467-025-60126-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 05/13/2025] [Indexed: 06/01/2025] Open
Abstract
The ribosome polymerizes L-α-amino acids into polypeptides, catalyzing peptide bond formation through aminolysis. This process is facilitated by entropy trapping within its peptidyl transferase center (PTC). In this research, we harness this capability to synthesize polymers containing cyclic motifs in the backbone. We design 26 non-canonical monomers (ncMs) with two distinct substrates: dicarboxylic esters and hydrazinoesters, each containing bifunctional moieties that undergo ring-closing reactions through multiple aminolysis reactions. Using a cell-free system that enables the consecutive incorporation of these ncMs into a growing peptide, we discover that the ribosome can produce 5- and 6-membered cyclic backbones, which have never been reported. We also demonstrate that the formation of such cyclic backbones within the ribosome is tunable by altering the substituents of dicarboxylic esters. This discovery expands the range of non-standard backbones that can be synthesized by the ribosome and motivates future research towards expanding ribosome-mediated chemistries for biopolymer synthesis.
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Affiliation(s)
- Kanghun Lee
- Division of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Hyeongwoo Park
- Division of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Ravi Kumar Devarapalli
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Dahye Im
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jongcheol Seo
- Division of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Joongoo Lee
- Division of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
- Institute for Convergence Research and Education in Advanced Technology, Yonsei University, Seoul, 03722, Republic of Korea.
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15
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Assefa F, Park EK. Spexin-induced MC3T3-E1 cell-derived exosomes enhance osteoblast differentiation. J Bone Miner Metab 2025:10.1007/s00774-025-01604-z. [PMID: 40434546 DOI: 10.1007/s00774-025-01604-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Accepted: 04/22/2025] [Indexed: 05/29/2025]
Abstract
INTRODUCTION The roles of exosomes in osteoblast differentiation has been widely investigated. Low exosome production from donor cells constitutes the greatest challenges in exosome-based therapies. Spexin (SPX) is a neuropeptide that is involved in various biological activities including osteogenic differentiation and bone regeneration. Therefore, the purpose of this study was to investigate the effects of SPX on exosome production in osteogenic medium (OM)-treated MC3T3-E1 cells and SPX induced MC3T3-E1 cell-derived exosomes (OM + SPX-Exos) on osteoblast differentiation. MATERIALS AND METHODS To evaluate exosome yield, MC3T3-E1 cells were treated with SPX. Exosome marker expression and particle number were validated via reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) and nanoparticle tracking analysis (NTA), respectively. MC3T3-E1 cells were then treated with various concentrations of OM + SPX-Exos and osteogenic medium treated MC3T3-E1 derived exosomes (OM-Exos). Cell proliferation, osteogenic differentiation marker expression, alkaline phosphatase (ALP) activity, and mineralization were evaluated using the CCK-8 assay, RT-qPCR, ALP staining, and alizarin red S staining, respectively. RESULTS SPX significantly increased exosome production and the expression of the exosome markers; Cd63, Rab27a and Alix in MC3T3E1 cells. Furthermore, OM + SPX-Exos significantly increased in the expression of runt-related transcription factor 2 (Runx2), alkaline phosphatase, biomineralized associated (Alpl), collagen type I alpha 1 (Col1a1), secreted phosphoprotein 1 (Spp1) and Integrin-binding sialoprotein (Ibsp) at a concentration of 5 µg/ml. ALP staining and alizarin red S staining also revealed that OM + SPX-Exos (5 µg/ml) resulted in more ALP-positive cells and markedly promoted mineralization, respectively. CONCLUSION In general, these results indicate that SPX stimulates exosome production. OM + SPX-Exos enhances MC3T3-E1 cells proliferation, osteogenic differentiation and mineralization.
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Affiliation(s)
- Freshet Assefa
- Department of Biochemistry, College of Medicine and Health Sciences, Hawassa University, P.O.Box 1560, Hawassa, Ethiopia.
| | - Eui Kyun Park
- Department of Pathology and Regenerative Medicine, School of Dentistry, IHBR, Kyungpook National University, Daegu, 41940, Republic of Korea
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16
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Koch J, Elbæk CR, Priesmann D, Damgaard RB. The Molecular Toolbox for Linkage Type-Specific Analysis of Ubiquitin Signaling. Chembiochem 2025; 26:e202500114. [PMID: 40192223 PMCID: PMC12118340 DOI: 10.1002/cbic.202500114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2025] [Revised: 04/04/2025] [Indexed: 04/22/2025]
Abstract
Modification of proteins and other biomolecules with ubiquitin regulates virtually all aspects of eukaryotic cell biology. Ubiquitin can be attached to substrates as a monomer or as an array of polyubiquitin chains with defined linkages between the ubiquitin moieties. Each ubiquitin linkage type adopts a distinct structure, enabling the individual linkage types to mediate specific functions or outcomes in the cell. The dynamics, heterogeneity, and in some cases low abundance, make analysis of linkage type-specific ubiquitin signaling a challenging and complex task. Herein, the strategies and molecular tools available for enrichment, detection, and characterization of linkage type-specific ubiquitin signaling, are reviewed. The molecular "toolbox" consists of a range of molecularly different affinity reagents, including antibodies and antibody-like molecules, affimers, engineered ubiquitin-binding domains, catalytically inactive deubiquitinases, and macrocyclic peptides, each with their unique characteristics and binding modes. The molecular engineering of these ubiquitin-binding molecules makes them useful tools and reagents that can be coupled to a range of analytical methods, such as immunoblotting, fluorescence microscopy, mass spectrometry-based proteomics, or enzymatic analyses to aid in deciphering the ever-expanding complexity of ubiquitin modifications.
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Affiliation(s)
- Julian Koch
- Department of Biotechnology and BiomedicineTechnical University of DenmarkSøltofts PladsDK‐2800Kongens LyngbyDenmark
| | - Camilla Reiter Elbæk
- Department of Biotechnology and BiomedicineTechnical University of DenmarkSøltofts PladsDK‐2800Kongens LyngbyDenmark
| | - Dominik Priesmann
- Department of Biotechnology and BiomedicineTechnical University of DenmarkSøltofts PladsDK‐2800Kongens LyngbyDenmark
| | - Rune Busk Damgaard
- Department of Biotechnology and BiomedicineTechnical University of DenmarkSøltofts PladsDK‐2800Kongens LyngbyDenmark
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17
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He Z, Zhao X, Gao WY, Bao G, Li Y, Zuo Q, Song X, Mou LY, Sun W, Wang R. Controlled reversible methionine-selective sulfimidation of peptides. SCIENCE ADVANCES 2025; 11:eadv8712. [PMID: 40397727 PMCID: PMC12094199 DOI: 10.1126/sciadv.adv8712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Accepted: 04/16/2025] [Indexed: 05/23/2025]
Abstract
Site-selective chemical peptide manipulation is an effective strategy to understand and regulate structure and function. However, methionine-selective modification remains one of the most difficult challenges in peptide chemistry, with notable limited strategies. In this study, we report a general reversible modification strategy at methionine sites that uses the ruthenium-catalyzed sulfimidation of peptides. This method provides a convenient and effective strategy for late-stage peptide functionalization. The N═S bonds of the conjugates are reduced in the presence of glutathione, resulting the traceless releasing of corresponding peptides and amides. Practical applications are then demonstrated using precise reversible modifications of bioactive peptides, the stapling and linearization of peptides, peptide-drug conjugates, and split-and-pool synthesis. This on/off strategy through methionine-selective and reversible sulfimidation provides a unique tool for peptide chemistry and peptide-based drug discovery.
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Affiliation(s)
- Zeyuan He
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, China
| | - Xiufang Zhao
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, China
| | - Wen-Yan Gao
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Guangjun Bao
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, China
| | - Yiping Li
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, China
| | - Quan Zuo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xinyi Song
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, China
| | - Ling-Yun Mou
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Wangsheng Sun
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, China
| | - Rui Wang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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18
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Gopalswamy M, Bickel D, Dienstbier N, Tu JW, Vogt M, Schott-Verdugo S, Bhatia S, Etzkorn M, Gohlke H. Identification of non-charged 7.44 analogs interacting with the NHR2 domain of RUNX1-ETO with improved antiproliferative effect in RUNX-ETO positive cells. Sci Rep 2025; 15:17720. [PMID: 40399488 PMCID: PMC12095692 DOI: 10.1038/s41598-025-02422-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Accepted: 05/13/2025] [Indexed: 05/23/2025] Open
Abstract
The RUNX1/ETO fusion protein is a chimeric transcription factor in acute myeloid leukemia (AML) created by chromosomal translocation t(8;21)(q22;q22). t(8;21) abnormality is associated with 12% of de novo AML cases and up to 40% in the AML subtype M2. Previously, we identified the small-molecule inhibitor 7.44, which interferes with NHR2 domain tetramerization of RUNX1/ETO, restores gene expression down-regulated by RUNX1/ETO, inhibits proliferation, and reduces RUNX1/ETO-related tumor growth in a mouse model. However, despite favorable properties, 7.44 is negatively charged at physiological pH and was predicted to have low to medium membrane permeability. Here, we identified M23, M27, and M10 as non-charged analogs of 7.44 using ligand-based virtual screening, in vivo hit identification, biophysical and in vivo hit validation, and integrative modeling and ADMET predictions. All three compounds interact with the NHR2 domain, have KD, app values of 39-114 µM in Microscale Thermophoresis experiments, and IC50 values of 33-77 µM as to cell viability in RUNX1/ETO-positive KASUMI cells, i.e., are ~ 5 to 10-fold more potent than 7.44. M23 is ~ 10-fold more potent than 7.44 in inhibiting cell proliferation of RUNX1/ETO-positive cells. Biological characterization of M23 in relevant RUNX1/ETO-positive -and negative cell lines indicates that M23 induces apoptosis and promotes differentiation in RUNX1/ETO-positive AML cells. M23 and M27 are negligibly protonated or in a ~ 1:1 ratio at physiological pH, while M10 has no (de-)protonatable group. The non-protonated species are predicted to be highly membrane-permeable, along with other favorable pharmacokinetic and toxicological properties. These compounds might serve as lead structures for compounds inhibiting RUNX1/ETO oncogenic function in t(8;21) AML.
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MESH Headings
- Humans
- Core Binding Factor Alpha 2 Subunit/metabolism
- Core Binding Factor Alpha 2 Subunit/chemistry
- Core Binding Factor Alpha 2 Subunit/genetics
- Cell Proliferation/drug effects
- RUNX1 Translocation Partner 1 Protein/metabolism
- RUNX1 Translocation Partner 1 Protein/chemistry
- RUNX1 Translocation Partner 1 Protein/antagonists & inhibitors
- RUNX1 Translocation Partner 1 Protein/genetics
- Animals
- Mice
- Cell Line, Tumor
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Oncogene Proteins, Fusion/metabolism
- Oncogene Proteins, Fusion/chemistry
- Oncogene Proteins, Fusion/antagonists & inhibitors
- Oncogene Proteins, Fusion/genetics
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/chemistry
- Protein Domains
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Affiliation(s)
- Mohanraj Gopalswamy
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - David Bickel
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussels, Brussels, Belgium
| | - Niklas Dienstbier
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jia-Wey Tu
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Melina Vogt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stephan Schott-Verdugo
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Manuel Etzkorn
- Institute for Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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19
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Dong G, Gong L, Zhang Q, Yao W, Shi Y, Gu Z, Yang X, Gao X, Zheng Y, Zhang C. Glycosylation Modification Balances the Aqueous Solubility of Lipidated Peptides and Facilitates Their Biostability. Bioconjug Chem 2025; 36:1004-1012. [PMID: 40203200 DOI: 10.1021/acs.bioconjchem.5c00057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2025]
Abstract
Protein tyrosine phosphatase N1 (PTPN1) is a key regulator of insulin and leptin signaling pathways, making it an attractive therapeutic target for type 2 diabetes. Recent studies have identified fatty acid conjugated BimBH3 analogues as promising PTPN1 inhibitors with antidiabetic potential. Peptide therapeutics have proven successful in the treatment of a wide range of medical conditions, yet challenges such as poor aqueous solubility, proteolytic degradation, and limited bioavailability still hinder their clinical application. In this study, we developed a series of novel BimBH3 peptide analogues through dual modifications involving fatty acid lipidation and glycosylation to address these limitations. These modifications significantly improved the peptides' solubility, proteolytic stability, and plasma half-life while preserving potent PTPN1 inhibitory activity, which is essential for enhancing insulin signaling in type 2 diabetes treatment. Among the analogues, compound L3 exhibited the most balanced profile, with an aqueous solubility increase over 10-fold, a half-life extension in rat plasma of 9.92-fold compared to the lead compound, and an IC50 of 0.78 μM against PTPN1. In vivo studies further demonstrated L3's efficacy in lowering blood glucose levels in mice. This study demonstrates the utility of glycosylation in overcoming the solubility and stability challenges associated with lipidated peptides. The optimized analogue L3 could serve as a proof of concept for developing novel long-acting PTPN1 inhibitors.
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Affiliation(s)
- Guozhen Dong
- State Key Laboratory Base of Eco-Chemical Engineering, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Liyan Gong
- State Key Laboratory Base of Eco-Chemical Engineering, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qianqian Zhang
- Shijiazhuang Hospital of Traditional Chinese Medicine, Shijiazhuang 050051, PR China
| | - Wenqing Yao
- State Key Laboratory Base of Eco-Chemical Engineering, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yiying Shi
- State Key Laboratory Base of Eco-Chemical Engineering, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Zongwen Gu
- State Key Laboratory Base of Eco-Chemical Engineering, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xianmin Yang
- State Key Laboratory Base of Eco-Chemical Engineering, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xiang Gao
- State Key Laboratory Base of Eco-Chemical Engineering, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yaning Zheng
- State Key Laboratory Base of Eco-Chemical Engineering, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chuanliang Zhang
- State Key Laboratory Base of Eco-Chemical Engineering, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
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20
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Alkhamach D, Khan SA, Greish K, Hassan HAFM, Haider M. Nanostructured lipid carriers in cancer therapy: Advances in passive and active targeting strategies. Int J Pharm 2025; 678:125736. [PMID: 40389069 DOI: 10.1016/j.ijpharm.2025.125736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2025] [Revised: 05/05/2025] [Accepted: 05/15/2025] [Indexed: 05/21/2025]
Abstract
Nanostructured lipid carriers (NLCs) have emerged as a promising drug delivery platform in cancer therapy, offering advantages such as enhanced drug solubility, stability, and controlled release. Recent efforts have focused on utilizing NLCs for passive and active tumor targeting to improve therapeutic outcomes. This review provides a comprehensive analysis of the role of NLCs in cancer therapy, with particular emphasis on their application in passive and active targeting strategies for precision oncology. Relevant studies were selected from recent literature, focusing on NLC formulation, targeting approaches, and therapeutic applications. NLCs enhance tumor-specific drug delivery through passive targeting via the enhanced permeability and retention (EPR) effect and active targeting via ligand-mediated mechanisms. Lymphatic-targeting NLCs enable improved drug delivery to metastatic niches, while stimuli-responsive NLCs facilitate site-specific release under tumor-associated conditions (e.g., pH, enzymatic activity, redox gradients). Advances in lipid composition, surfactant systems, and conjugation strategies significantly influence drug loading (DL), biodistribution, therapeutic efficacy, and clinical translation across various malignancies. NLCs represent a versatile and adaptable platform for precision cancer therapy. Continued optimization of formulation parameters, functionalization strategies, and clinical translation pathways is essential to fully realize their potential in targeted oncology applications.
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Affiliation(s)
- Dana Alkhamach
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, University of Sharjah 27272 Sharjah, United Arab Emirates; Research Institute of Medical & Health Sciences, University of Sharjah 27272 Sharjah, United Arab Emirates
| | - Saeed Ahmad Khan
- Research Institute of Medical & Health Sciences, University of Sharjah 27272 Sharjah, United Arab Emirates
| | - Khaled Greish
- Department of Molecular Medicine, Princess Al-Jawhara Centre for Molecular Medicine, School of Medicine and Health Sciences Arabian Gulf University, Manama 328329, Bahrain
| | - Hatem A F M Hassan
- Medway School of Pharmacy, University of Kent, Chatham Maritime, Kent ME4 4TB, UK
| | - Mohamed Haider
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, University of Sharjah 27272 Sharjah, United Arab Emirates; Research Institute of Medical & Health Sciences, University of Sharjah 27272 Sharjah, United Arab Emirates.
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21
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Urello MA, Vaughan HJ, Dockery LT, Ciciriello AJ, Rui Y, Keyser B, Ramos I, Bosco EE, Peterson N, Webster C, Subramony JA, Rice M, Marelli M, Christie RJ. Intracellular Nanodelivery of DNA with Enzyme-Degradable and pH-Responsive Peptide Dendrons. Biomacromolecules 2025. [PMID: 40380916 DOI: 10.1021/acs.biomac.5c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2025]
Abstract
Effective DNA delivery requires functional materials to package and transport genetic cargo into cells. However, many synthetic systems rely on heterogeneous mixtures, lack biodegradability, and pose toxicity concerns. Here, we introduce a peptide dendron single-molecule transfection reagent that enables targeted DNA delivery via pH-responsive, degradable nanoparticles with minimal toxicity. Peptide dendrons for intracellular delivery (PDIDs) incorporate ionizable non-natural amino acids for DNA binding and pH sensitivity. PDIDs formed stable nanoparticles that released DNA upon lysosomal acidification, facilitating cytoplasmic entry and subsequent gene expression. Rationally designed triamino acid blocks promoted protease degradation, reducing toxicity in preclinical models. Targeting ligands further enhanced the transfection efficiency by increasing cell uptake. In a lung metastasis model, targeted PDID-DNA nanoparticles selectively delivered therapeutic gene cargo to the lung, reducing tumor burden and extending survival. This platform demonstrates the potential to integrate natural and non-natural peptide features to enable safe and efficient DNA delivery in vivo.
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Affiliation(s)
- M A Urello
- Biologics Engineering, Oncology Research, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - H J Vaughan
- Biologics Engineering, Oncology Research, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - L T Dockery
- Biologics Engineering, Oncology Research, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - A J Ciciriello
- Biologics Engineering, Oncology Research, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Y Rui
- Biologics Engineering, Oncology Research, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - B Keyser
- Biologics Engineering, Oncology Research, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - I Ramos
- Oncology Research, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - E E Bosco
- Oncology Research, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - N Peterson
- Oncology Research, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - C Webster
- Discovery Sciences, Biopharmaceuticals Research, AstraZeneca, Cambridge CB2 0AA, U.K
| | - J Anand Subramony
- Biologics Engineering, Oncology Research, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - M Rice
- Biologics Engineering, Oncology Research, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - M Marelli
- Biologics Engineering, Oncology Research, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - R James Christie
- Biologics Engineering, Oncology Research, AstraZeneca, Gaithersburg, Maryland 20878, United States
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22
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Zaidi N, Jaffee EM, Yarchoan M. Recent advances in therapeutic cancer vaccines. Nat Rev Cancer 2025:10.1038/s41568-025-00820-z. [PMID: 40379970 DOI: 10.1038/s41568-025-00820-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/04/2025] [Indexed: 05/19/2025]
Abstract
The success of cancer prevention vaccines targeting cancer-causing viruses has drastically reduced cancer mortality worldwide. However, the development of therapeutic cancer vaccines, which aim to elicit an immune response directly against cancer cells, has faced notable clinical setbacks. In this Review, we explore lessons learned from past cancer vaccine trials and how the field has progressed into an era of renewed promise. Previous vaccines primarily targeted tumour-associated antigens and were mainly tested as monotherapies in late-stage cancers. In contrast, contemporary vaccines focus on targeting tumour-specific antigens (neoantigens) and are showing initial evidence of clinical efficacy, particularly in early-stage cancers and precancers when combined with immune checkpoint inhibitors. Advances in tumour profiling and novel vaccine platforms have enhanced vaccine specificity and potency. We discuss recent clinical trials of therapeutic cancer vaccines and outline future directions for the field.
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Affiliation(s)
- Neeha Zaidi
- Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Elizabeth M Jaffee
- Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
| | - Mark Yarchoan
- Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
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23
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Lawrenz J, Wettstein L, Rodríguez Alfonso A, Nchioua R, von Maltitz P, Albers DPJ, Zech F, Vandeput J, Naesens L, Fois G, Neubauer V, Preising N, Schmierer E, Almeida-Hernandez Y, Petersen M, Ständker L, Wiese S, Braubach P, Frick M, Barth E, Sauter D, Kirchhoff F, Sanchez-Garcia E, Stevaert A, Münch J. Trypstatin as a Novel TMPRSS2 Inhibitor with Broad-Spectrum Efficacy against Corona and Influenza Viruses. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025:e2506430. [PMID: 40365759 DOI: 10.1002/advs.202506430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2025] [Indexed: 05/15/2025]
Abstract
Respiratory viruses, such as SARS-CoV-2 and influenza, exploit host proteases like TMPRSS2 for entry, making TMPRSS2 a prime antiviral target. Here, the identification and characterization of Trypstatin, a 61-amino acid Kunitz-type protease inhibitor derived from human hemofiltrate are reported. Trypstatin inhibits TMPRSS2 and related proteases with high potency, exhibiting half-maximal inhibitory concentration values in the nanomolar range, comparable to the small molecule inhibitor camostat mesylate. In vitro assays demonstrate that Trypstatin effectively blocks spike-driven entry of SARS-CoV-2, SARS-CoV-1, MERS-CoV, and hCoV-NL63, as well as hemagglutinin-mediated entry of influenza A and B viruses. In primary human airway epithelial cultures, Trypstatin significantly reduces SARS-CoV-2 replication and retained activity in the presence of airway mucus. In vivo, intranasal administration of Trypstatin to SARS-CoV-2-infected Syrian hamsters reduces viral titers and alleviates clinical symptoms. These findings highlight Trypstatin's potential as a broad-spectrum antiviral agent against TMPRSS2-dependent respiratory viruses.
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Affiliation(s)
- Jan Lawrenz
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Lukas Wettstein
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Armando Rodríguez Alfonso
- Core Facility Functional Peptidomics, Ulm University Medical Center, 89081, Ulm, Germany
- Core Unit Mass Spectrometry and Proteomics, Ulm University Medical Center, 89081, Ulm, Germany
| | - Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Pascal von Maltitz
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | | | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Julie Vandeput
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, 3000, Leuven, Belgium
| | - Lieve Naesens
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, 3000, Leuven, Belgium
| | - Giorgio Fois
- Institute of General Physiology, Ulm University, 89081, Ulm, Germany
| | - Veronika Neubauer
- Institute of General Physiology, Ulm University, 89081, Ulm, Germany
| | - Nico Preising
- Core Facility Functional Peptidomics, Ulm University Medical Center, 89081, Ulm, Germany
| | - Emilia Schmierer
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Yasser Almeida-Hernandez
- Chair of Computational Bioengineering, Faculty of Biochemical and Chemical Engineering, Technical University of Dortmund, 44227, Dortmund, Germany
| | - Moritz Petersen
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center, 89081, Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University Medical Center, 89081, Ulm, Germany
| | - Peter Braubach
- Institute of Pathology, Hannover Medical School, 30625, Hannover, Germany
| | - Manfred Frick
- Institute of General Physiology, Ulm University, 89081, Ulm, Germany
| | - Eberhard Barth
- Anesthesiology and Intensive Medicine Clinic, Ulm University Medical Center, 89081, Ulm, Germany
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Elsa Sanchez-Garcia
- Chair of Computational Bioengineering, Faculty of Biochemical and Chemical Engineering, Technical University of Dortmund, 44227, Dortmund, Germany
| | - Annelies Stevaert
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, 3000, Leuven, Belgium
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
- Core Facility Functional Peptidomics, Ulm University Medical Center, 89081, Ulm, Germany
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24
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Song EJ, Kim WS, Han Y, Lee C, Moon EJ, Kim HJ, Kang NS. Discovery of a transforming growth factor-β1 inhibitory peptide, Charis 1000 to enhance the therapeutic efficacy of paclitaxel in triple-negative breast cancer. Int J Biol Macromol 2025; 314:144216. [PMID: 40379179 DOI: 10.1016/j.ijbiomac.2025.144216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Revised: 05/11/2025] [Accepted: 05/12/2025] [Indexed: 05/19/2025]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive and invasive subtype of breast cancer for which chemotherapy, such as paclitaxel (PTX), remains a primary treatment option. However, resistance to chemotherapy poses a significant challenge, necessitating the development of novel therapeutic strategies. This study aimed to address PTX resistance in TNBC by developing a peptide drug, Charis 1000 (C1K), designed to target transforming growth factor beta (TGF-β) signaling. C1K was synthesized using standard solid-phase peptide synthesis and optimized for enhanced stability. Molecular docking predicted the binding interactions between C1K and TGF-β1, and surface plasmon resonance (SPR) confirmed a moderate binding affinity. The therapeutic potential of C1K was evaluated in TNBC cell lines (4T1, MDA-MB-231, and PTX-resistant MDA-MB-231) and in vivo using a syngeneic 4T1 mouse model. Functional assays demonstrated that C1K inhibited TGF-β-mediated signaling, reduced autophagy, a key mechanism underlying PTX resistance, and significantly enhanced PTX-induced apoptosis. In vivo studies further revealed synergistic effects of C1K and PTX, resulting in enhanced apoptosis in both sensitive and PTX-resistant TNBC cells. These findings suggest that C1K effectively targets TGF-β to inhibit autophagy and potentiate the apoptotic effects of PTX, as a promising combinatorial therapeutic agent for improving treatment outcomes in TNBC patients.
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Affiliation(s)
- Eun Ju Song
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; Department of New Drug Research Institute, Ensol Biosciences Inc., Techno 10-ro 51, Yuseong-gu, Daejeon 34036, Republic of Korea
| | - Won-Sam Kim
- Department of New Drug Research Institute, Ensol Biosciences Inc., Techno 10-ro 51, Yuseong-gu, Daejeon 34036, Republic of Korea
| | - Yunhee Han
- Department of New Drug Research Institute, Ensol Biosciences Inc., Techno 10-ro 51, Yuseong-gu, Daejeon 34036, Republic of Korea
| | - Cheolmin Lee
- Department of New Drug Research Institute, Ensol Biosciences Inc., Techno 10-ro 51, Yuseong-gu, Daejeon 34036, Republic of Korea; Graduate School of Chemistry, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeonbuk State, 54896 Republic of Korea
| | - Eun-Joung Moon
- Department of New Drug Research Institute, Ensol Biosciences Inc., Techno 10-ro 51, Yuseong-gu, Daejeon 34036, Republic of Korea
| | - Hae-Jin Kim
- Department of New Drug Research Institute, Ensol Biosciences Inc., Techno 10-ro 51, Yuseong-gu, Daejeon 34036, Republic of Korea.
| | - Nam Sook Kang
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea.
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25
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Szefczyk M, Szulc N, Bystranowska D, Szczepańska A, Lizandra Pérez J, Dudek A, Pawlak A, Ożyhar A, Berlicki Ł. Construction and cytotoxicity evaluation of peptide nanocarriers based on coiled-coil structures with a cyclic β-amino acid at the knob-into-hole interaction site. J Mater Chem B 2025. [PMID: 40364573 DOI: 10.1039/d5tb00752f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2025]
Abstract
Peptides are highly attractive as nanocarriers for drug delivery and other biomedical applications due to their unique combination of biocompatibility, efficacy, safety, and versatility-qualities that are difficult to achieve with other nanocarrier types. Particularly promising in this context are peptide foldamers containing non-canonical residues, which can yield nanostructures with diverse physicochemical properties. Additionally, the introduction of non-proteinogenic amino acids into the sequence enhances conformational stability and resistance to proteolysis, critical features for bioapplications. In this article, we report the development of novel foldameric bundles based on a coiled-coil structure incorporating trans-(1S,2S)-2-aminocyclopentanecarboxylic acid (trans-ACPC) at the key interacting site. We also provide both theoretical and experimental analyses of how this cyclic β-residue affects the thermodynamic and proteolytic stability, oligomerization state, and encapsulation properties of the resulting foldamers compared to standard coiled-coils. Additionally, we assessed the cytotoxicity of these foldamers using the MTT assay on 3T3 cells. The results demonstrate that neither the foldamers nor trans-ACPC exhibit toxic effects on the 3T3 cell line, highlighting their potential as safe and effective nanocarriers.
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Affiliation(s)
- Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Natalia Szulc
- Department of Physics and Biophysics, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375, Wrocław, Poland
| | - Dominika Bystranowska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Anna Szczepańska
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Juan Lizandra Pérez
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Anita Dudek
- Department of Physics and Biophysics, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375, Wrocław, Poland
| | - Aleksandra Pawlak
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Norwida 31, 50-375, Wrocław, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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26
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Mao Q, Shang T, Xu W, Zhai S, Zhang C, Guo J, Su A, Li C, Duan H. NCPepFold: Accurate Prediction of Noncanonical Cyclic Peptide Structures via Cyclization Optimization with Multigranular Representation. J Chem Theory Comput 2025; 21:4979-4991. [PMID: 40255206 DOI: 10.1021/acs.jctc.5c00139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2025]
Abstract
Artificial intelligence-based peptide structure prediction methods have revolutionized biomolecular science. However, restricting predictions to peptides composed solely of 20 natural amino acids significantly limits their practical application; as such, peptides often demonstrate poor stability under physiological conditions. Here, we present NCPepFold, a computational approach that can utilize a specific cyclic position matrix to directly predict the structure of cyclic peptides with noncanonical amino acids. By integrating multigranularity information at the residual and atomic level, along with fine-tuning techniques, NCPepFold significantly improves prediction accuracy, with the average peptide root-mean-square deviation (RMSD) for cyclic peptides being 1.640 Å. In summary, this is a novel deep learning model designed specifically for cyclic peptides with noncanonical amino acids, offering great potential for peptide drug design and advancing biomedical research.
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Affiliation(s)
- Qingyi Mao
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Tianfeng Shang
- AI Department, Shenzhen Highslab Therapeutics Inc., Shenzhen 518000, China
| | - Wen Xu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Silong Zhai
- Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
| | - Chengyun Zhang
- AI Department, Shenzhen Highslab Therapeutics Inc., Shenzhen 518000, China
| | - Jingjing Guo
- Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
| | - An Su
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chengxi Li
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hongliang Duan
- Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
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27
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Birro BA, Pesce C, Tognetti F, Fragassi A, Casagrande L, Garofalo M, Salmaso S, Caliceti P. Unlocking the potential of microfluidic assisted formulation of exenatide-loaded solid lipid nanoparticles. Int J Pharm 2025; 678:125686. [PMID: 40354907 DOI: 10.1016/j.ijpharm.2025.125686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2025] [Revised: 05/02/2025] [Accepted: 05/03/2025] [Indexed: 05/14/2025]
Abstract
Exenatide, a first-in-class GLP-1 receptor agonist, is used to control glycaemic levels in type 2 diabetes. There are two approved injectable formulations: one solution for immediate action and one dispersion for prolonged action. Oral exenatide has low bioavailability due to poor gastrointestinal stability and absorption. To address these obstacles, we designed Solid Lipid Nanoparticles (SLN) including DOTAP in the formulation to yield high exenatide encapsulation by hydrophobic ion pairing and DSPE-PEG2kDa to convey colloidal stability and mucus diffusivity. The microfluidic production of SLN yielded 9.7 % exenatide encapsulation and 94.2 % loading efficiency. SLN exhibited solid cored-spherical morphology with sizes of about 120 nm and zeta potential of + 53 mV. The SLN surface charge was modulated by DSPE-PEG2kDa coating; 10 and 30 w/w% DSPE-PEG2kDa /lipid ratios yielded slightly positive and neutral zeta potentials, respectively. All SLN formulations provided exenatide protection from proteolytic enzymes. The non-PEGylated SLN resulted in a twofold increase of exenatide delivery across Caco-2 cell monolayers compared to the peptide solution. The 10 w/w% SLN PEGylation reduced the exenatide delivery compared to non-PEGylated SLN through Caco-2 cell monolayers. However, the exenatide delivery with 10 w/w% PEGylated SLN across mucus-producing Caco-2/HT29-MTX coculture layer was 2-fold higher compared to the unformulated peptide, and 1.5 higher than non-PEGylated SLN. The 30 w/w% SLN PEGylation did not improve the peptide transport neither through Caco-2 cell monolayers nor through Caco-2/HT29-MTX coculture layer.
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Affiliation(s)
- Büşra Arpaç Birro
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Cristiano Pesce
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Francesco Tognetti
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Agnese Fragassi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Lisa Casagrande
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Mariangela Garofalo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Stefano Salmaso
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy.
| | - Paolo Caliceti
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
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28
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Swan CT, Edmonds AG, Argent SP, Mitchell NJ. A Modular and Scalable Route to Protected Cyclopropane Amino Acid Building Blocks. Org Lett 2025; 27:4800-4805. [PMID: 40272394 PMCID: PMC12070460 DOI: 10.1021/acs.orglett.5c01341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2025] [Revised: 04/11/2025] [Accepted: 04/16/2025] [Indexed: 04/25/2025]
Abstract
An improved method for the synthesis of noncanonical cyclopropane amino acids from common laboratory reagents is described, avoiding the use of neurotoxic oxidants or precious metal catalysts. Intramolecular isocyanate trapping via a Hofmann rearrangement permits the synthesis of bicyclic carbamates in an enantioenriched and diastereopure manner. Subsequent ring-opening of these species allows access to cyclopropane amino acids which can be further functionalized via oxidation and SN2 pathways and incorporated into peptides via solid-phase peptide synthesis.
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Affiliation(s)
| | - Alex G. Edmonds
- School of Chemistry, University
of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Stephen P. Argent
- School of Chemistry, University
of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Nicholas J. Mitchell
- School of Chemistry, University
of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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29
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Ma J, Wang X, Hu Y, Ma J, Ma Y, Chen H, Han Z. Recent Advances in Augmenting the Therapeutic Efficacy of Peptide-Drug Conjugates. J Med Chem 2025; 68:9037-9056. [PMID: 40267310 PMCID: PMC12067445 DOI: 10.1021/acs.jmedchem.5c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2025] [Revised: 04/11/2025] [Accepted: 04/16/2025] [Indexed: 04/25/2025]
Abstract
There is an urgent need for the development of safe and effective modalities for the treatment of diseases owing to drug resistance, undesired side effects, and poor clinical outcomes. Combining cell-targeting and efficient cell-killing properties, peptide-drug conjugates (PDCs) have demonstrated superior efficacy compared with peptides and payloads alone. However, innovative molecular designs of PDCs are essential for further improving targeting precision, protease resistance and stability, cell permeability, and overall treatment efficacy. Several strategies have been developed to address these challenges, such as multivalency approaches, bispecific targeting, and long-acting PDCs. Other novel strategies, including overcoming biological barriers, conjugating novel functional payloads, and targeting macropinocytosis, have also shown promise. This perspective compiles the most recent strategies for enhancing PDC treatment efficacy, highlights key advancements in PDC, and provides insights on future directions for the development of novel PDCs.
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Affiliation(s)
- Jiahui Ma
- Gansu
Provincial Key Laboratory of Environmental Oncology, Department of
Tumor Center, Lanzhou University Second Hospital, Second Clinical
Medical School, Lanzhou University, Lanzhou 730000, China
| | - Xuedan Wang
- School
of Life Sciences and Engineering, Lanzhou
University of Technology, Lanzhou 730050, China
| | - Yonghua Hu
- Gansu
Provincial Key Laboratory of Environmental Oncology, Department of
Tumor Center, Lanzhou University Second Hospital, Second Clinical
Medical School, Lanzhou University, Lanzhou 730000, China
- Gansu
University of Chinese Medicine, Lanzhou 730000, China
| | - Jianping Ma
- School
of Life Sciences and Engineering, Lanzhou
University of Technology, Lanzhou 730050, China
| | - Yaping Ma
- Shenzhen
DIVBIO Pharmaceutical, Shenzhen 518057, China
| | - Hao Chen
- Gansu
Provincial Key Laboratory of Environmental Oncology, Department of
Tumor Center, Lanzhou University Second Hospital, Second Clinical
Medical School, Lanzhou University, Lanzhou 730000, China
| | - Zhijian Han
- Gansu
Provincial Key Laboratory of Environmental Oncology, Department of
Tumor Center, Lanzhou University Second Hospital, Second Clinical
Medical School, Lanzhou University, Lanzhou 730000, China
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30
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Li Q, Chao W, Qiu L. Therapeutic peptides: chemical strategies fortify peptides for enhanced disease treatment efficacy. Amino Acids 2025; 57:25. [PMID: 40338379 PMCID: PMC12062087 DOI: 10.1007/s00726-025-03454-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2024] [Accepted: 04/10/2025] [Indexed: 05/09/2025]
Abstract
Therapeutic peptides, as a unique form of medication composed of orderly arranged sequences of amino acids, are valued for their high affinity, specificity, low immunogenicity, and economical production costs. Currently, more than 100 peptides have already secured market approval. Over 150 are actively undergoing clinical trials, while an additional 400-600 are in the preclinical research stage. Despite this, their clinical application is limited by factors such as salt sensitivity, brief residence in the bloodstream, inadequate cellular uptake, and high structural flexibility. By employing suitable chemical methods to modify peptides, it is possible to regulate important physicochemical factors such as charge, hydrophobicity, conformation, amphiphilicity, and sequence that affect the physicochemical properties and biological activity of peptides. This can overcome the inherent deficiencies of peptides, enhance their pharmacokinetic properties and biological activity, and promote continuous progress in the field of research. A diverse array of modified peptides is currently being developed and investigated across numerous therapeutic fields. Drawing on the latest research, this review encapsulates the essential physicochemical factors and significant chemical modification strategies that influence the properties and biological activity of peptides as pharmaceuticals. It also assesses how physicochemical factors affect the application of peptide drugs in disease treatment and the effectiveness of chemical strategies in disease therapy. Concurrently, this review discusses the prospective advancements in therapeutic peptide development, with the goal of offering guidance for designing and optimizing therapeutic peptides and to delve deeper into the therapeutic potential of peptides for disease intervention.
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Affiliation(s)
- Qingmei Li
- Hezhou University, Hezhou, 542800, Guangxi, China
- Naval Medical University, Shanghai, 200433, China
| | - Wen Chao
- Naval Medical University, Shanghai, 200433, China
| | - Lijuan Qiu
- Naval Medical University, Shanghai, 200433, China.
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31
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Yuan R, Zhang J, Zhou J, Cong Q. Recent progress and future challenges in structure-based protein-protein interaction prediction. Mol Ther 2025; 33:2252-2268. [PMID: 40195117 DOI: 10.1016/j.ymthe.2025.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 03/05/2025] [Accepted: 04/02/2025] [Indexed: 04/09/2025] Open
Abstract
Protein-protein interactions (PPIs) play a fundamental role in cellular processes, and understanding these interactions is crucial for advances in both basic biological science and biomedical applications. This review presents an overview of recent progress in computational methods for modeling protein complexes and predicting PPIs based on 3D structures, focusing on the transformative role of artificial intelligence-based approaches. We further discuss the expanding biomedical applications of PPI research, including the elucidation of disease mechanisms, drug discovery, and therapeutic design. Despite these advances, significant challenges remain in predicting host-pathogen interactions, interactions between intrinsically disordered regions, and interactions related to immune responses. These challenges are worthwhile for future explorations and represent the frontier of research in this field.
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Affiliation(s)
- Rongqing Yuan
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jing Zhang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jian Zhou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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32
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Motamedi M, Morshedi D, Fard NA. PQK7: A novel peptide inhibitor targeting alpha-synuclein fibrillogenesis in Parkinson's disease. Neuropeptides 2025; 111:102522. [PMID: 40339505 DOI: 10.1016/j.npep.2025.102522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Revised: 04/29/2025] [Accepted: 04/30/2025] [Indexed: 05/10/2025]
Abstract
The accumulation of alpha-synuclein (⍺-Syn) fibrils plays a central role in the progression of Parkinson's disease (PD) and related neurodegenerative disorders. In this context, the development of peptide inhibitors designed to inhibit ⍺-Syn through computational methods has emerged as a promising area of research. This study focused on developing a peptide inhibitor, PQK7, designed based on the key residues of NAC region of ⍺-Syn fibrils involved in its aggregation. Using molecular docking and dynamics simulations, PQK7 was shown to bind key residues in the NAC region of ⍺-Syn (Val-74, Ala-76, Val-77, Thr-81, Ser-87, Ile-88, and Ala-89), effectively disrupting the formation of fibrils. MD simulations indicated that the PQK7-⍺-Syn complex reaches a stable conformation, which showed increased fluctuations and reduced β-sheet content, suggests that PQK7 interferes with ⍺-Syn fibrillation at the molecular level. In vitro assays like ThT fluorescence assay, AFM imaging, CD specotroscopy, and SDS-PAGE analysis confirmed that PQK7 significantly reduces ⍺-Syn fibril formation, particularly at substoichiometric concentrations, while keeping ⍺-Syn monomers in a soluble state. Additionally, PQK7-⍺-Syn treatment in SH-SY5Y cells reduced the toxicity of ⍺-Syn aggregates, restoring normal cell cycle progression and reducing apoptosis and oxidative stress. Our findings suggest that PQK7 holds potential as a therapeutic agent for PD, acting as an anti-oligomeric inhibitor that targets early ⍺-Syn aggregates without affecting the protein's normal function.
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Affiliation(s)
- Maryam Motamedi
- Systems Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Dina Morshedi
- Bioprocess Engineering Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Najaf Allahyari Fard
- Systems Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
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33
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Chen Y, Dai C, Han J, Xing Y, Yin F, Li Z. Recent Chemical Biology Insights Towards Reversible Stapled Peptides. Chembiochem 2025; 26:e202500052. [PMID: 40011217 DOI: 10.1002/cbic.202500052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Revised: 02/25/2025] [Accepted: 02/26/2025] [Indexed: 02/28/2025]
Abstract
Peptides are increasingly recognized for their advantages over small molecules in the modulation of protein-protein interactions (PPIs), particularly in terms of potency and selectivity. "Staples" can be coupled to the amino acid residues of linear peptides to limit their conformation, improving the stability, membrane permeability, and resistance to proteolysis of peptides. However, the addition of staples can sometimes lead to the complete inactivation of the original peptide or result in extensive interactions that complicate biophysical analysis. Reversible stapled peptides provide an excellent solution to these issues. Besides, probes based on reversible stapled peptides are also indispensable tools for thoroughly investigating PPIs. Consequently, the development of diverse reversible stapling techniques for stapled peptides is crucial for broadening the applications of peptide molecules in drug discovery, drug delivery, and as tools in chemical biology research. This review aims to summarize representative chemical design strategies for reversible stapled peptides, focusing on reversible chemical stapling methods involving sulfhydryl, amino, and methylthio groups, as well as reversible modulation of the conformational states of stapled peptides. Additionally, we demonstrate some intriguing biological applications of stapled peptides and, finally, suggest future research directions in the field that will serve as references for related researchers.
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Affiliation(s)
- Ying Chen
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, P. R. China
| | - Chuan Dai
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, P. R. China
| | - Jinyan Han
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
| | - Yun Xing
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
| | - Feng Yin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, P. R. China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, P. R. China
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Fujita M, Ito T, Inokuma A, Saito K, Hirano M, Yokoo H, Demizu Y. Palindromic peptide foldamers: a strategy for structural stability and cellular uptake. Org Biomol Chem 2025. [PMID: 40314437 DOI: 10.1039/d5ob00430f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2025]
Abstract
Mid-sized peptide therapeutics have gained significant attention for their potential to overcome the limitations of small molecules and biologics. However, their clinical application is often hindered by poor stability and low cellular permeability. In this study, we designed a palindromic peptide foldamer composed of L-leucine and L-arginine residues to investigate its structural and functional properties. CD spectroscopy confirmed that the designed peptide adopts a stable α-helical conformation, even under denaturing conditions. Cellular uptake studies using LC-MS/MS and flow cytometry indicated efficient intracellular delivery, suggesting that the peptide's amphiphilic structure enhances membrane permeability. These findings provide valuable insights into the rational design of structurally stable and functionally enhanced peptide therapeutics.
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Affiliation(s)
- Minami Fujita
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Yokohama, Kanagawa 230-0045, Japan
| | - Takahito Ito
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan.
| | - Akihiko Inokuma
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Yokohama, Kanagawa 230-0045, Japan
| | - Kosuke Saito
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Motoharu Hirano
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Yokohama, Kanagawa 230-0045, Japan
| | - Hidetomo Yokoo
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan.
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushimanaka, Kita, Okayama 700-8530, Japan
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Zhang D, Wang Z, Inuzuka H, Wei W. Proximity-induced membrane protein degradation for cancer therapies. RSC Med Chem 2025:d5md00141b. [PMID: 40365034 PMCID: PMC12066958 DOI: 10.1039/d5md00141b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2025] [Accepted: 04/30/2025] [Indexed: 05/15/2025] Open
Abstract
The selective modulation of membrane proteins presents a significant challenge in drug development, particularly in cancer therapies. However, conventional small molecules and biologics often face significant hurdles in effectively targeting membrane-bound proteins, largely due to the structural complexity of these proteins and their involvement in intricate cellular processes. In light of these limitations, proximity-induced protein modulation has recently emerged as a transformative approach. It leverages molecule-induced proximity strategies to commandeer endogenous cellular machinery for precise protein manipulation. One of these modulatory strategies is protein degradation, wherein membrane-targeting degraders derived from proximity-induction approaches offer a unique therapeutic avenue by inducing the irreversible removal of key oncogenic and immune-regulatory proteins to combat cancer. This review explores the fundamental principles underlying proximity-driven membrane protein degradation, highlighting key strategies such as LYTACs, PROTABs, TransTACs, and IFLD that are reshaping targeted cancer therapy. We discuss recent technological advancements in the application of proximity-induced degraders across breast cancer, lung cancer, immunotherapy, and other malignancies, underscoring how these innovative approaches have demonstrated significant therapeutic potential. Lastly, while these emerging technologies offer significant promise, they still face substantial limitations, including drug delivery, selectivity, and resistance mechanisms that need to be addressed to achieve successful clinical translation.
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Affiliation(s)
- Dingpeng Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School Boston MA 02215 USA
| | - Zhen Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School Boston MA 02215 USA
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School Boston MA 02215 USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School Boston MA 02215 USA
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36
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Li K, Wu Y, Li Y, Guo Y, Kong Y, Wang Y, Liang Y, Fan Y, Huang L, Zhang R, Zhou F. AMPCliff: Quantitative definition and benchmarking of activity cliffs in antimicrobial peptides. J Adv Res 2025:S2090-1232(25)00292-9. [PMID: 40318764 DOI: 10.1016/j.jare.2025.04.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Revised: 04/09/2025] [Accepted: 04/29/2025] [Indexed: 05/07/2025] Open
Abstract
INTRODUCTION Activity cliff (AC) is a phenomenon that a pair of similar molecules differ by a small structural alternation but exhibit a large difference in their biochemical activities. This phenomenon affects various tasks ranging from virtual screening to lead optimization in drug development. The AC of small molecules has been extensively investigated but limited knowledge is accumulated about the AC phenomenon in pharmaceutical peptides with canonical amino acids. OBJECTIVES This study introduces a quantitative definition and benchmarking framework AMPCliff for the AC phenomenon in antimicrobial peptides (AMPs) composed by canonical amino acids. METHODS This study establishes a benchmark dataset of paired AMPs in Staphylococcus aureus from the publicly available AMP dataset GRAMPA, and conducts a rigorous procedure to evaluate various AMP AC prediction models, including nine machine learning, four deep learning algorithms, four masked language models, and four generative language models. RESULTS A comprehensive analysis of the existing AMP dataset reveals a significant prevalence of AC within AMPs. AMPCliff quantifies the activities of AMPs by the metric minimum inhibitory concentration (MIC), and defines 0.9 as the minimum threshold for the normalized BLOSUM62 similarity score between a pair of aligned peptides with at least two-fold MIC changes. Our analysis reveals that these models are capable of detecting AMP AC events and the pre-trained protein language model ESM2 demonstrates superior performance across the evaluations. The predictive performance of AMP activity cliffs remains to be further improved, considering that ESM2 with 33 layers only achieves the Spearman correlation coefficient 0.4669 for the regression task of the -log(MIC) values on the benchmark dataset. CONCLUSION Our findings highlight limitations in current deep learning-based representation models. To more accurately capture the properties of antimicrobial peptides (AMPs), it is essential to integrate atomic-level dynamic information that reflects their underlying mechanisms of action.
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Affiliation(s)
- Kewei Li
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Yuqian Wu
- School of Software, Jilin University, Changchun 130012 Jilin, China
| | - Yinheng Li
- Department of Computer Science, Columbia University, 116th and Broadway, New York City, NY 10027, United States
| | - Yutong Guo
- School of Life Sciences, Jilin University, Changchun 130012 Jilin, China
| | - Yanwen Kong
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Yan Wang
- School of Computer Engineering, Changchun University of Engineering, Changchun 130103 Jilin, China
| | - Yiyang Liang
- Changchun Wenli High School, Changchun 130062 Jilin, China
| | - Yusi Fan
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Lan Huang
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Ruochi Zhang
- School of Artificial Intelligence, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012 Jilin, China.
| | - Fengfeng Zhou
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China; School of Biology and Engineering, Guizhou Medical University, Guiyang 550025 Guizhou, China.
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37
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Krueger J, Dieskau AP, Hassfeld J, Gries J, Block O, Weinmann H, Kaufmann D, Hildbrand S, Kraft V, Moeckel R, Dehli JR, Scholz U, Nising CF. Chemical Process Development in the Pharmaceutical Industry in Europe-Insights and Perspectives from Industry Scientists. Angew Chem Int Ed Engl 2025; 64:e202420719. [PMID: 40145815 PMCID: PMC12051753 DOI: 10.1002/anie.202420719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 02/25/2025] [Accepted: 03/10/2025] [Indexed: 03/28/2025]
Abstract
Chemical process development is a critical component in the development process for active pharmaceutical ingredients (APIs). With interfaces to drug discovery and API manufacturing, chemical process development activities must deliver scalable, safe, cost-efficient, sustainable, and reliable processes for novel as well as marketed APIs. Despite its importance for the pharmaceutical industry and society, the domain of chemical process development, together with its advances and challenges, is often not well known to nonpractitioners. As industry scientists, we provide a scientific perspective on the state of affairs in chemical process development, which we believe will be of value to a broader audience, including academic researchers, students, and professionals from related fields.
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Affiliation(s)
- Joachim Krueger
- Pharmaceuticals CMC & TechnologyBayer AGD‐42096WuppertalGermany
| | | | - Jorma Hassfeld
- Pharmaceuticals CMC & TechnologyBayer AGD‐42096WuppertalGermany
| | - Joerg Gries
- Pharmaceuticals CMC & TechnologyBayer AGD‐42096WuppertalGermany
| | - Oliver Block
- Global CMC DevelopmentMerck Healthcare KGaAD‐64293DarmstadtGermany
| | - Hilmar Weinmann
- Chemical Process R&DJohnson & Johnson Innovative MedicineBeerseB‐2340Belgium
| | - Daniel Kaufmann
- Chemical & Analytical DevelopmentNovartis AGBaselCH‐4056Switzerland
| | - Stefan Hildbrand
- Process Chemistry & CatalysisF. Hoffmann‐La Roche LtdBaselCH‐4070Switzerland
| | - Volker Kraft
- R&D Global CMC Development SyntheticsSanofi‐Aventis Deutschland GmbHD‐65926FrankfurtGermany
| | - Robert Moeckel
- Chemical DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KGD‐55216Ingelheim am RheinGermany
| | - Juan R. Dehli
- Chemical DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KGD‐55216Ingelheim am RheinGermany
| | - Ulrich Scholz
- Chemical DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KGD‐55216Ingelheim am RheinGermany
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Balde A, Kim SK, Nazeer RA. A review on microneedle patch as a delivery system for proteins/peptides and their applications in transdermal inflammation suppression. Int J Biol Macromol 2025; 307:141963. [PMID: 40086558 DOI: 10.1016/j.ijbiomac.2025.141963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Revised: 02/27/2025] [Accepted: 03/09/2025] [Indexed: 03/16/2025]
Abstract
Transdermal delivery is one of the most recent modes of administration studied due to several shortfalls observed for intra-venous, and oral drug administrations. Among, microneedle-based transdermal delivery is the popular choice due to non-invasive procedure and minimal toxicological effects. Microneedle devices consist of micron scaled needle patch entrapped with the target specific drug molecules. Due to body's immune response and occasional pathogen attack, various inflammatory diseases are developed such as psoriasis, dermatitis, rashes, rheumatoid arthritis, gouty arthritis, and fibrosis. These inflammatory conditions can be treated by microneedle assisted transdermal delivery. Moreover, for localized suppression of pain and inflammation, various therapeutic peptides and proteins have been investigated. Although, these therapeutic agents can show reduced activity and undergo enzymatic degradation when administered orally or intra-venously. Hence, a microneedle-based delivery system can be used as an effective way to localize these peptides/proteins and reduce the inflammation. Herein, this review includes various microneedle fabrication methods for enhancing drug delivery for suppression of inflammation. Moreover, recent development in microneedle devices of peptide and protein delivery applications are discoursed. At last, future scope and challenges endured for preparing an efficient microneedle patch for peptide and protein delivery are also elaborated.
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Affiliation(s)
- Akshad Balde
- Biopharmaceuticals Lab, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chennai 603203, Tamilnadu, India
| | - Se-Kwon Kim
- Department of Marine Science and Convergence Engineering, Hanyang University, Ansan 11558, Gyeonggi-do, South Korea
| | - Rasool Abdul Nazeer
- Biopharmaceuticals Lab, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chennai 603203, Tamilnadu, India.
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39
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Prashar N, Mohammed SB, Raja NS, Mohideen HS. Rerouting therapeutic peptides and unlocking their potential against SARS-CoV2. 3 Biotech 2025; 15:116. [PMID: 40191455 PMCID: PMC11971104 DOI: 10.1007/s13205-025-04270-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2025] [Accepted: 03/10/2025] [Indexed: 04/09/2025] Open
Abstract
The COVID-19 pandemic highlighted the potential of peptide-based therapies as an alternative to traditional pharmaceutical treatments for SARS-CoV-2 and its variants. Our review explores the role of therapeutic peptides in modulating immune responses, inhibiting viral entry, and disrupting replication. Despite challenges such as stability, bioavailability, and the rapid mutation of the virus, ongoing research and clinical trials show that peptide-based treatments are increasingly becoming integral to future viral outbreak responses. Advancements in computational modelling methods in combination with artificial intelligence will enable mass screening of therapeutic peptides and thereby, comprehending a peptide repurposing strategy similar to the small molecule repurposing. These findings suggest that peptide-based therapies play a critical and promising role in future pandemic preparedness and outbreak management.
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Affiliation(s)
- Namrata Prashar
- Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Chennai, Tamil Nadu 603203 India
| | - Saharuddin Bin Mohammed
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - N. S. Raja
- Deparmtent of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Chennai, Tamil Nadu 603203 India
| | - Habeeb Shaik Mohideen
- Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Chennai, Tamil Nadu 603203 India
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40
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Zhu C, Cao S, Shang T, Guo J, Su A, Li C, Duan H. Predicting the structures of cyclic peptides containing unnatural amino acids by HighFold2. Brief Bioinform 2025; 26:bbaf202. [PMID: 40350698 PMCID: PMC12066415 DOI: 10.1093/bib/bbaf202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2025] [Revised: 03/25/2025] [Accepted: 04/09/2025] [Indexed: 05/14/2025] Open
Abstract
Cyclic peptides containing unnatural amino acids possess many excellent properties and have become promising candidates in drug discovery. Therefore, accurately predicting the 3D structures of cyclic peptides containing unnatural residues will significantly advance the development of cyclic peptide-based therapeutics. Although deep learning-based structural prediction models have made tremendous progress, these models still cannot predict the structures of cyclic peptides containing unnatural amino acids. To address this gap, we introduce a novel model, HighFold2, built upon the AlphaFold-Multimer framework. HighFold2 first extends the pre-defined rigid groups and their initial atomic coordinates from natural amino acids to unnatural amino acids, thus enabling structural prediction for these residues. Then, it incorporates an additional neural network to characterize the atom-level features of peptides, allowing for multi-scale modeling of peptide molecules while enabling the distinction between various unnatural amino acids. Besides, HighFold2 constructs a relative position encoding matrix for cyclic peptides based on different cyclization constraints. Except for training using spatial structures with unnatural amino acids, HighFold2 also parameterizes the unnatural amino acids to relax the predicted structure by energy minimization for clash elimination. Extensive empirical experiments demonstrate that HighFold2 can accurately predict the 3D structures of cyclic peptide monomers containing unnatural amino acids and their complexes with proteins, with the median RMSD for Cα reaching 1.891 Å. All these results indicate the effectiveness of HighFold2, representing a significant advancement in cyclic peptide-based drug discovery.
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Affiliation(s)
- Cheng Zhu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Chaowang Road, Gongshu District, Hangzhou 310014, China
| | - Sen Cao
- Faculty of Applied Sciences, Macao Polytechnic University, R. de Luís Gonzaga Gomes, Macao 999078, China
| | - Tianfeng Shang
- Artificial Intelligence Department, Shenzhen Highslab Therapeutics. Inc, Guangke 1st Road, Pingshan District, Shenzhen 518000, China
| | - Jingjing Guo
- Faculty of Applied Sciences, Macao Polytechnic University, R. de Luís Gonzaga Gomes, Macao 999078, China
| | - An Su
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Chaowang Road, Gongshu District, Hangzhou 310014, China
| | - Chengxi Li
- College of Chemical and Biological Engineering, Zhejiang University, Yuhangtang Road, Xihu District, Hangzhou 310027, China
| | - Hongliang Duan
- Faculty of Applied Sciences, Macao Polytechnic University, R. de Luís Gonzaga Gomes, Macao 999078, China
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Overby C, Abraham B, Adjei-Sowah E, March A, Ling K, Basu S, Benoit DSW. A Rapid Manual Solid Phase Peptide Synthesis Method for High-Throughput Peptide Production. J Biomed Mater Res A 2025; 113:e37922. [PMID: 40312963 DOI: 10.1002/jbm.a.37922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2025] [Revised: 04/18/2025] [Accepted: 04/22/2025] [Indexed: 05/03/2025]
Abstract
Solid phase peptide synthesis (SPPS) techniques are critical for developing and using peptides in various biomedical applications. However, typical synthesis routes used in SPPS are either resource-intensive (e.g., with automated synthesis or commercial services) or time-consuming (e.g., with manual benchtop synthesis). Here, a rapid manual synthesis method was developed to produce up to 8 peptides with fast cycle times simultaneously. Peptides synthesized manually were of equivalent or superior quality to those produced by in-house microwave-assisted automated peptide synthesis, with higher average crude purity of 70% compared to 50%. The method significantly reduced synthesis time, enabling the parallel coupling of up to 8 amino acids simultaneously in 15-20 min, as opposed to traditional benchtop peptide synthesis, which requires 80-150 min per amino acid. This approach offers an intermediate throughput between milligram-scale libraries and gram-scale single peptide synthesis, enabling rapid iteration for novel peptide designs without the need for expensive automated systems. As a result, peptide modifications, including incorporation of unnatural amino acids, can be explored, accelerating the development of peptides for a wide range of applications.
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Affiliation(s)
- Clyde Overby
- Department of Biomedical Engineering, University of Rochester, Rochester, New York, USA
- Center for Musculoskeletal Research, University of Rochester, Rochester, New York, USA
| | - Brittany Abraham
- Department of Biomedical Engineering, University of Rochester, Rochester, New York, USA
- Center for Musculoskeletal Research, University of Rochester, Rochester, New York, USA
| | - Emmanuella Adjei-Sowah
- Department of Biomedical Engineering, University of Rochester, Rochester, New York, USA
- Center for Musculoskeletal Research, University of Rochester, Rochester, New York, USA
| | - Alyson March
- Department of Biomedical Engineering, University of Rochester, Rochester, New York, USA
- Center for Musculoskeletal Research, University of Rochester, Rochester, New York, USA
| | - Kevin Ling
- Department of Biomedical Engineering, University of Rochester, Rochester, New York, USA
- Center for Musculoskeletal Research, University of Rochester, Rochester, New York, USA
| | - Sayantani Basu
- Department of Biomedical Engineering, University of Rochester, Rochester, New York, USA
- Center for Musculoskeletal Research, University of Rochester, Rochester, New York, USA
| | - Danielle S W Benoit
- Department of Biomedical Engineering, University of Rochester, Rochester, New York, USA
- Center for Musculoskeletal Research, University of Rochester, Rochester, New York, USA
- Department of Chemical Engineering, University of Rochester, Rochester, New York, USA
- Materials Science Program, University of Rochester, Rochester, New York, USA
- Department of Bioengineering, Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon, USA
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42
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Jayakody T, Budagoda DK, Mendis K, Dilshan WD, Bethmage D, Dissasekara R, Dawe GS. Biased agonism in peptide-GPCRs: A structural perspective. Pharmacol Ther 2025; 269:108806. [PMID: 39889970 DOI: 10.1016/j.pharmthera.2025.108806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 12/13/2024] [Accepted: 01/15/2025] [Indexed: 02/03/2025]
Abstract
G protein-coupled receptors (GPCRs) are dynamic membrane receptors that transduce extracellular signals to the cell interior by forming a ligand-receptor-effector (ternary) complex that functions via allosterism. Peptides constitute an important class of ligands that interact with their cognate GPCRs (peptide-GPCRs) to form the ternary complex. "Biased agonism", a therapeutically relevant phenomenon exhibited by GPCRs owing to their allosteric nature, has also been observed in peptide-GPCRs, leading to the development of selective therapeutics with fewer side effects. In this review, we have focused on the structural basis of signalling bias at peptide-GPCRs of classes A and B, and reviewed the therapeutic relevance of bias at peptide-GPCRs, with the hope of contributing to the discovery of novel biased peptide drugs.
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Affiliation(s)
- Tharindunee Jayakody
- Department of Chemistry, University of Colombo, P.O. Box 1490, Colombo 00300, Sri Lanka
| | | | - Krishan Mendis
- Department of Chemistry, University of Colombo, P.O. Box 1490, Colombo 00300, Sri Lanka
| | | | - Duvindu Bethmage
- Department of Chemistry, University of Colombo, P.O. Box 1490, Colombo 00300, Sri Lanka
| | - Rashmi Dissasekara
- Department of Chemistry, University of Colombo, P.O. Box 1490, Colombo 00300, Sri Lanka; The Graduate School, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Gavin Stewart Dawe
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Neurobiology Programme, Life Sciences Institute, National University of Singapore, Singapore; Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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Yu YJ, Rahman MU, Balakrishnan R, Kim JM, Kim JH, Choi DK. The novel peptide DBCH reduces LPS-stimulated NF-κB/MAPK signaling in BV-2 microglia and ameliorates cognitive impairment in scopolamine-treated mice by modulating BDNF/CREB. Neurochem Int 2025; 185:105946. [PMID: 39971241 DOI: 10.1016/j.neuint.2025.105946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 02/05/2025] [Accepted: 02/10/2025] [Indexed: 02/21/2025]
Abstract
Microglial-mediated neuroinflammation significantly impacts cognitive impairment, and modulating neuroinflammatory responses has emerged as a promising target for treatment. However, the specific role of microglial-mediated neuroinflammation in cognitive impairment associated with Alzheimer's disease (AD) remains unclear. In our continuous endeavors to seek potent anti-Alzheimer's agents, we recently synthesized and developed a series of peptidomimetic compounds, including dipeptide-68 bis-cyclohexylpropyl histidinamide (DBCH), derived from a caryopsis-1 peptide that has demonstrated anti-inflammatory and anti-microbial properties in various infectious diseases. Among the bioactive peptides synthesized, DBCH exhibited good neuroprotective and anti-inflammatory activity and high potency. Therefore, in this study, the neuroprotective and anti-inflammatory effects of DBCH were assessed in lipopolysaccharide (LPS)-stimulated BV-2 microglial cells and a scopolamine-induced C57BL/6 N amnesic mouse model. In the in vitro study, DBCH effectively suppressed the production and expression of nitric oxide (NO) and proinflammatory cytokines in BV-2 microglial cells stimulated with LPS. Furthermore, it effectively inhibited the LPS-triggered phosphorylation and activation of NF-κB/MAPK signaling and modulated inflammatory mediators, including iNOS and COX-2, in BV-2 microglial cells. In vivo results showed that DBCH administration of 5 or 10 mg/kg improved spatial memory learning and cognitive function in scopolamine-induced amnesic mice. Furthermore, DBCH treatment upregulated phosphorylated cAMP-response element-binding protein (p-CREB) and brain-derived neurotrophic factor (BDNF) levels and downregulated the inflammatory response. Overall, DBCH effectively prevented both scopolamine-induced cognitive impairment and neuroinflammation. Our research findings suggest that DBCH may serve as a medication for cognitive decline associated with AD.
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Affiliation(s)
- Ye-Ji Yu
- Department of Applied Life Sciences, Graduate School, BK21 Program, Konkuk University, Chungju, 27478, South Korea
| | - Mujeeb Ur Rahman
- Department of Applied Life Sciences, Graduate School, BK21 Program, Konkuk University, Chungju, 27478, South Korea
| | - Rengasamy Balakrishnan
- Department of Biotechnology, College of Biomedical and Health Science, Research Institute of Inflammatory Disease (RID), Konkuk University, Chungju, 27478, South Korea
| | - Jong-Min Kim
- Division of R&D, WellPep Co., LTD, 172, Dolma-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Jae Ho Kim
- Division of R&D, WellPep Co., LTD, 172, Dolma-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Dong-Kug Choi
- Department of Applied Life Sciences, Graduate School, BK21 Program, Konkuk University, Chungju, 27478, South Korea; Department of Biotechnology, College of Biomedical and Health Science, Research Institute of Inflammatory Disease (RID), Konkuk University, Chungju, 27478, South Korea.
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44
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Malhotra S, Lijnse T, Cearbhaill EO, Brayden DJ. Devices to overcome the buccal mucosal barrier to administer therapeutic peptides. Adv Drug Deliv Rev 2025; 220:115572. [PMID: 40174726 DOI: 10.1016/j.addr.2025.115572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 03/21/2025] [Accepted: 03/24/2025] [Indexed: 04/04/2025]
Abstract
Peptide therapeutics are important in healthcare owing to their high target specificity, therapeutic efficacy, and relatively low side effect profile. Injections of these agents have improved thetreatment of chronic diseases including autoimmune, metabolic disorders, and cancer. However, their administration via injections can prove a barrier to patient acceptability of treatments. While oral delivery of these molecules is preferable, oral peptide formulations are associated with limited bioavailability due to degradation in the intestine and low epithelial permeability. Buccal administration of peptides is a potential alternative to injections and oral formulations. Similar to the oral route, the buccal route can promote better patient adherence to dosing regimens, along with the added advantages of not requiring restriction on food or drink consumption before and after administration, as well as avoidance of the liver first-pass metabolism. However, like oral, effective buccal absorption of peptides is still challenging due to the high epithelial permeability barrier. We present a multidisciplinary approach to understanding the buccal physiological barrier to macromolecule permeation and discuss how engineered devices may overcome it. Selected examples of buccal devices can facilitate fast and efficient macromolecule absorption through multiple mechanisms including physical disruption of epithelia, convection-based mass transfer, and a combination of physicochemical strategies. Importantly, minimally invasive devices can be self-applied and are associated with the maintenance of the barrier after exposure. We analysed the critical attributes that are required forthe clinical translation of buccal peptide administration devices. These include performance-driven device development, manufacturing features, patient acceptability, and commercial viability.
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Affiliation(s)
- Sahil Malhotra
- UCD School of Medicine, University College Dublin (UCD), -Belfield, Dublin 4, Ireland; Research Ireland-CÚRAM Centre for Medical Devices, UCD, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, UCD-Belfield, Dublin 4, Ireland
| | - Thomas Lijnse
- Research Ireland-CÚRAM Centre for Medical Devices, UCD, Ireland; School of Mechanical and Materials Engineering, UCD, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, UCD-Belfield, Dublin 4, Ireland
| | - Eoin O' Cearbhaill
- Research Ireland-CÚRAM Centre for Medical Devices, UCD, Ireland; School of Mechanical and Materials Engineering, UCD, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, UCD-Belfield, Dublin 4, Ireland
| | - David J Brayden
- Research Ireland-CÚRAM Centre for Medical Devices, UCD, Ireland; UCD School of Veterinary Medicine, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, UCD-Belfield, Dublin 4, Ireland.
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45
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Schuermans S, Quanico J, Kestens C, Vandendriessche S, Slowikowski E, Crijns ML, Pörtner N, Berghmans N, Baggerman G, Mattos MS, Proost P, Marques PE. Degradation rather than disassembly of necrotic debris is essential to enhance recovery after acute liver injury. Cell Mol Life Sci 2025; 82:190. [PMID: 40301163 PMCID: PMC12040799 DOI: 10.1007/s00018-025-05720-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Revised: 04/15/2025] [Accepted: 04/17/2025] [Indexed: 05/01/2025]
Abstract
Necrotic cell death causes loss of membrane integrity, release of intracellular contents and deposition of necrotic cell debris. Effective clearance of this debris is crucial for resolving inflammation and promoting tissue recovery. While leukocyte phagocytosis plays a major role, soluble factors in the bloodstream also contribute to debris removal. Our study examined whether enzymatic degradation or disassembly of necrotic debris enhances clearance and improves outcomes in a mouse model of drug-induced liver injury. Using intravital microscopy and on-tissue spatially-resolved microproteomics, we demonstrated that necrotic debris is more complex than anticipated, containing DNA, filamentous actin, histones, complement C3, fibrin(ogen) and plasmin(ogen), among many other components. DNase 1 treatment facilitated recovery significantly by enhancing the clearance of DNA from necrotic areas, reducing circulating nucleosomes and actin, and lowering the associated inflammatory response. However, its effect on actin and other damage-associated molecular patterns in necrotic regions was limited. Treatment with short synthetic peptides, specifically 20-amino acid-long positively charged poly L-lysine (PLK) and negatively charged poly L-glutamic acid (PLE), which displace histones from debris in vitro, did not inhibit liver injury or promote recovery. Moreover, activating plasmin to disrupt fibrin encapsulation via tissue plasminogen activator (tPa) led to increased circulating actin levels and worsening of injury parameters. These findings suggest that fibrin encapsulation is important for containing necrotic debris and that enzymatic degradation of necrotic debris is a more effective strategy to enhance tissue recovery than targeting debris disassembly.
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Affiliation(s)
- Sara Schuermans
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Jusal Quanico
- Centre for Proteomics (CfP), UAntwerpen, Antwerpen, Belgium
| | - Caine Kestens
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Sofie Vandendriessche
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Emily Slowikowski
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Maria-Laura Crijns
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Noëmie Pörtner
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Nele Berghmans
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Matheus Silvério Mattos
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Pedro Elias Marques
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
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46
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Jadhav K, Abhang A, Kole EB, Gadade D, Dusane A, Iyer A, Sharma A, Rout SK, Gholap AD, Naik J, Verma RK, Rojekar S. Peptide-Drug Conjugates as Next-Generation Therapeutics: Exploring the Potential and Clinical Progress. Bioengineering (Basel) 2025; 12:481. [PMID: 40428099 PMCID: PMC12108627 DOI: 10.3390/bioengineering12050481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2025] [Revised: 04/20/2025] [Accepted: 04/24/2025] [Indexed: 05/29/2025] Open
Abstract
Peptide-drug conjugates (PDCs) have emerged as a next-generation therapeutic platform, combining the target specificity of peptides with the pharmacological potency of small-molecule drugs. As an evolution beyond antibody-drug conjugates (ADCs), PDCs offer distinct advantages, including enhanced cellular permeability, improved drug selectivity, and versatile design flexibility. This review provides a comprehensive analysis of the fundamental components of PDCs, including homing peptide selection, linker engineering, and payload optimization, alongside strategies to address their inherent challenges, such as stability, bioactivity, and clinical translation barriers. Therapeutic applications of PDCs span oncology, infectious diseases, metabolic disorders, and emerging areas like COVID-19, with several conjugates advancing in clinical trials and achieving regulatory milestones. Innovations, including bicyclic peptides, supramolecular architectures, and novel linker technologies, are explored as promising avenues to enhance PDC design. Additionally, this review examines the clinical trajectory of PDCs, emphasizing their therapeutic potential and highlighting ongoing trials that exemplify their efficacy. By addressing limitations and leveraging emerging advancements, PDCs hold immense promise as targeted therapeutics capable of addressing complex disease states and driving progress in precision medicine.
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Affiliation(s)
- Krishna Jadhav
- Institute of Nano Science and Technology (INST), Knowledge City, Sector-81, Sahibzada Ajit Singh Nagar, Mohali 140306, Punjab, India; (K.J.); (R.K.V.)
| | - Ashwin Abhang
- Department of Pharmaceutical Sciences, University of Connecticut School of Pharmacy, Storrs, CT 06269, USA;
| | - Eknath B. Kole
- Department of Pharmaceutical Technology, University Institute of Chemical Technology, KBC North Maharashtra University, Jalgaon 425001, Maharashtra, India; (E.B.K.); (J.N.)
| | - Dipak Gadade
- Department of Pharmaceutical Sciences, Delhi Skill and Entrepreneurship University, Dwarka Campus, Sector 9 Dwarka, New Delhi 110077, Delhi, India;
| | - Apurva Dusane
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA 52242, USA;
| | - Aditya Iyer
- Biopharmaceutics Department, Biocon Bristol-Myers Squibb R&D Center (BBRC), Bangalore 560099, Karnataka, India;
| | | | - Saroj Kumar Rout
- Research and Development, LNK International Inc., New York, NY 11788, USA;
| | - Amol D. Gholap
- Department of Pharmaceutics, St. John Institute of Pharmacy and Research, Palghar 401404, Maharashtra, India;
| | - Jitendra Naik
- Department of Pharmaceutical Technology, University Institute of Chemical Technology, KBC North Maharashtra University, Jalgaon 425001, Maharashtra, India; (E.B.K.); (J.N.)
| | - Rahul K. Verma
- Institute of Nano Science and Technology (INST), Knowledge City, Sector-81, Sahibzada Ajit Singh Nagar, Mohali 140306, Punjab, India; (K.J.); (R.K.V.)
| | - Satish Rojekar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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47
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Sadeeq M, Li Y, Wang C, Hou F, Zuo J, Xiong P. Unlocking the power of antimicrobial peptides: advances in production, optimization, and therapeutics. Front Cell Infect Microbiol 2025; 15:1528583. [PMID: 40365533 PMCID: PMC12070195 DOI: 10.3389/fcimb.2025.1528583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Accepted: 03/19/2025] [Indexed: 05/15/2025] Open
Abstract
Antimicrobial peptides (AMPs) are critical effectors of innate immunity, presenting a compelling alternative to conventional antibiotics amidst escalating antimicrobial resistance. Their broad-spectrum efficacy and inherent low resistance development are countered by production challenges, including limited yields and proteolytic degradation, which restrict their clinical translation. While chemical synthesis offers precise structural control, it is often prohibitively expensive and complex for large-scale production. Heterologous expression systems provide a scalable, cost-effective platform, but necessitate optimization. This review comprehensively examines established and emerging AMP production strategies, encompassing fusion protein technologies, molecular engineering approaches, rational peptide design, and post-translational modifications, with an emphasis on maximizing yield, bioactivity, stability, and safety. Furthermore, we underscore the transformative role of artificial intelligence, particularly machine learning algorithms, in accelerating AMP discovery and optimization, thereby propelling their expanded therapeutic application and contributing to the global fight against drug-resistant infections.
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Affiliation(s)
| | | | | | | | - Jia Zuo
- Biosynthesis and Bio Transformation Center, School of Life Sciences and Medicine,
Shandong University of Technology (SDUT), Zibo, China
| | - Peng Xiong
- Biosynthesis and Bio Transformation Center, School of Life Sciences and Medicine,
Shandong University of Technology (SDUT), Zibo, China
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48
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Delgado JAC, Amaral J, Penteado PS, Ferreira AG, da Silva MFF, König B, Paixão MW. Selective Native N (in)-H Bond Activation in Peptides with Metallaphotocatalysis. JACS AU 2025; 5:2040-2046. [PMID: 40313804 PMCID: PMC12042047 DOI: 10.1021/jacsau.5c00119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Revised: 03/12/2025] [Accepted: 03/14/2025] [Indexed: 05/03/2025]
Abstract
The development of chemical methods enabling site-selective incorporation of noncanonical amino acids into peptide backbones with precise functional tailoring remains a critical challenge. Particularly compelling is the use of underexplored endogenous amino acid hotspots, such as the N (in) of tryptophan, as versatile anchors for diversification. Herein, we report a chemoselective N(sp2)-H bond activation strategy targeting native tryptophan residues within peptide frameworks, exemplified by GLP-1 (7-37), using nickel metallaphotocatalysis under postsynthetic solid-phase conditions. This selective N (in)-arylation reaction proceeds efficiently within 3 h of light irradiation in highly functionalized heterogeneous environments, employing minimal excesses of electrophile and base, alongside catalytic quantities of nickel, ligand, and photocatalyst. The method affords homogeneous peptide products with high chemoselectivity and operational simplicity. We envision that this strategy could contribute to advancing the design of the next-generation long-acting class II G protein-coupled receptor agonist therapeutics.
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Affiliation(s)
- José A. C. Delgado
- Laboratory
for Sustainable Organic Synthesis and Catalysis, Department of Chemistry, Federal University of São Carlos − UFSCar, Rodovia Washington Luís,
km 235 - SP-310, São Carlos, São Paulo 13565-905, Brazil
| | - Jéssica
C. Amaral
- Department
of Plant Pathology and Nematology, University
of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, Piracicaba, São Paulo 13418-900, Brazil
- Department
of Chemistry, Federal University of São
Carlos − UFSCar, Rodovia Washington Luís, km 235 - SP-310, São Carlos, São Paulo 13565-905, Brazil
| | - Paula S. Penteado
- Department
of Chemistry, Federal University of São
Carlos − UFSCar, Rodovia Washington Luís, km 235 - SP-310, São Carlos, São Paulo 13565-905, Brazil
| | - Antonio G. Ferreira
- Department
of Chemistry, Federal University of São
Carlos − UFSCar, Rodovia Washington Luís, km 235 - SP-310, São Carlos, São Paulo 13565-905, Brazil
| | - Maria Fátima
G. F. da Silva
- Department
of Chemistry, Federal University of São
Carlos − UFSCar, Rodovia Washington Luís, km 235 - SP-310, São Carlos, São Paulo 13565-905, Brazil
| | - Burkhard König
- Institute
of Organic Chemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Márcio W. Paixão
- Laboratory
for Sustainable Organic Synthesis and Catalysis, Department of Chemistry, Federal University of São Carlos − UFSCar, Rodovia Washington Luís,
km 235 - SP-310, São Carlos, São Paulo 13565-905, Brazil
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49
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Ali M, Oduro-Kwateng E, Kehinde IO, Parinandi NL, Soliman MES. A Computational Approach for Designing a Peptide-Based Acetyl-CoA Synthetase 2 Inhibitor: A New Horizon for Anticancer Development. Cell Biochem Biophys 2025:10.1007/s12013-025-01729-y. [PMID: 40287570 DOI: 10.1007/s12013-025-01729-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2025] [Indexed: 04/29/2025]
Abstract
Acetyl-CoA Synthetase 2 (ACSS2) has emerged as a new target for anticancer development owing to its high expression in various tumours and its enhancement of malignancy. Stressing the growing interest in peptide-derived drugs featuring better selectivity and efficacy, a computational protocol was applied to design a peptide inhibitor for ACSS2. Herein, 3600 peptide sequences derived from ACSS2 nucleotide motif were generated by classifying the 20 amino acids into six physiochemical groups. De novo modeling maintained essential binding interactions, and a refined library of 16 peptides was derived using Support Vector Machine filters to ensure proper bioavailability, toxicity, and therapeutic relevance. Structural and folding predictions, along with molecular docking, identified the top candidate, Pep16, which demonstrated significantly higher binding affinity (91.1 ± 1.6 kcal/mol) compared to a known inhibitor (53.7 ± 0.7 kcal/mol). Further molecular dynamics simulations and binding free energy calculations revealed that Pep16 enhances ACSS2 conformational variability, occupies a larger binding interface, and achieved firm binding. MM/GBSA analysis highlighted key electrostatic interactions with specific ACSS2 residues, including ARG 373, ARG 526, ARG 628, ARG 631, and LYS 632. Overall, Pep16 appears to lock the ACSS2 nucleotide pocket into a compact, rigid conformation, potentially blocking ATP binding and catalytic activity, and may serve as a novel specific ACSS2 inhibitor. Though, we urge further research to confirm and compare its therapeutic potential to existing inhibitors. We also believe that this systematic methodology would represent an indispensable tool for prospective peptide-based drug discovery.
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Affiliation(s)
- Musab Ali
- Molecular Bio-Computation and Drug Design Research Group, School of Health Sciences, University of KwaZulu Natal, Westville Campus, Durban, South Africa
| | - Ernest Oduro-Kwateng
- Molecular Bio-Computation and Drug Design Research Group, School of Health Sciences, University of KwaZulu Natal, Westville Campus, Durban, South Africa
| | - Ibrahim Oluwatobi Kehinde
- Molecular Bio-Computation and Drug Design Research Group, School of Health Sciences, University of KwaZulu Natal, Westville Campus, Durban, South Africa
| | - Narasimham L Parinandi
- Division of Pulmonary, Critical Care and Sleep Medicine Department of Medicine, Davis Heart and Lung Research Institute, The Ohio State University, Weber Medical Center, Columbus, OH, USA
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Research Group, School of Health Sciences, University of KwaZulu Natal, Westville Campus, Durban, South Africa.
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50
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Bordignon F, Scarso A, Angelini A. Challenges and Achievements of Peptide Synthesis in Aqueous and Micellar Media. Chembiochem 2025:e2500099. [PMID: 40289017 DOI: 10.1002/cbic.202500099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Revised: 04/17/2025] [Accepted: 04/24/2025] [Indexed: 04/29/2025]
Abstract
Peptides are being increasingly explored for drug development as well as other applications, ranging from research tools to food additives. This growing interest in peptides has led to the need to develop new sustainable synthetic approaches for this class of molecules. The present review article focuses on the synthesis of peptides in aqueous media to drastically reduce organic solvent use and its consequent environmental impact. After some pioneering investigations about solid-phase peptide synthesis in water, the field is experiencing a renaissance also for the synthesis in solution spurred by increasing applications enabled by micellar catalysis. In this contribution, the challenges and opportunities offered by using aqueous and micellar media in the chemical synthesis of peptides are critically discussed.
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Affiliation(s)
- Francesca Bordignon
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, via Torino 155, 30172, Mestre Venezia, Italy
| | - Alessandro Scarso
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, via Torino 155, 30172, Mestre Venezia, Italy
| | - Alessandro Angelini
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, via Torino 155, 30172, Mestre Venezia, Italy
- European Centre for Living Technology (ECLT), Ca' Bottacin, Dorsoduro 3911, Calle Crosera, 30123, Venezia, Italy
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