1
|
Chen S, Liu M, Yi W, Li H, Yu Q. Micropeptides derived from long non-coding RNAs: Computational analysis and functional roles in breast cancer and other diseases. Gene 2025; 935:149019. [PMID: 39461573 DOI: 10.1016/j.gene.2024.149019] [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: 07/17/2024] [Revised: 10/08/2024] [Accepted: 10/16/2024] [Indexed: 10/29/2024]
Abstract
Long non-coding RNAs (lncRNAs), once thought to be mere transcriptional noise, are now revealing a hidden code. Recent advancements like ribosome sequencing have unveiled that many lncRNAs harbor small open reading frames and can potentially encode functional micropeptides. Emerging research suggests these micropeptides, not the lncRNAs themselves, play crucial roles in regulating homeostasis, inflammation, metabolism, and especially in breast cancer progression. This review delves into the rapidly evolving computational tools used to predict and validate lncRNA-encoded micropeptides. We then explore the diverse functions and mechanisms of action of these micropeptides in breast cancer pathogenesis, with a focus on their roles in various species. Ultimately, this review aims to illuminate the functional landscape of lncRNA-encoded micropeptides and their potential as therapeutic targets in cancer.
Collapse
Affiliation(s)
- Saisai Chen
- Department of Breast Surgery, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei 230031, China
| | - Mengru Liu
- Department of Infection, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Weizhen Yi
- Department of Breast Surgery, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei 230031, China
| | - Huagang Li
- Department of Breast Surgery, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei 230031, China
| | - Qingsheng Yu
- Institute of Chinese Medicine Surgery, Anhui Academy of Chinese Medicine, Hefei 230031, China.
| |
Collapse
|
2
|
Martian PC, Tertis M, Leonte D, Hadade N, Cristea C, Crisan O. Cyclic peptides: A powerful instrument for advancing biomedical nanotechnologies and drug development. J Pharm Biomed Anal 2025; 252:116488. [PMID: 39388867 DOI: 10.1016/j.jpba.2024.116488] [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: 07/18/2024] [Revised: 09/05/2024] [Accepted: 09/26/2024] [Indexed: 10/12/2024]
Abstract
Cyclic peptides have emerged as an essential tool in the advancement of biomedical nanotechnologies, offering unique structural and functional advantages over linear peptides. This review article aims to highlight the roles of cyclic peptides in the development of biomedical fields, with a particular focus on their application in drug discovery and delivery. Cyclic peptides exhibit exceptional stability, bioavailability, and binding specificity, making them ideal candidates for therapeutic and diagnostic applications. We explore the synthesis and design strategies that enable the precise control of cyclic peptide structures, leading to enhanced performance in targeting specific cellular pathways. The article also highlights recent breakthroughs in the use of cyclic peptides for creating innovative drug delivery systems, including nanoparticle conjugates and peptide-drug conjugates, which have shown promise in improving the efficacy and safety profiles of existing traditional treatments. The integration of cyclic peptides into nanotechnological frameworks holds significant promise for addressing unmet medical needs, providing a foundation for future advancements in personalized medicine and targeted drug delivery.
Collapse
Affiliation(s)
- Paul Cristian Martian
- Department of Analytical Chemistry, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 4 Pasteur Street, Cluj-Napoca 400021, Romania
| | - Mihaela Tertis
- Department of Analytical Chemistry, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 4 Pasteur Street, Cluj-Napoca 400021, Romania
| | - Denisa Leonte
- Department of Organic Chemistry, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 28 Victor Babes Street, Cluj-Napoca 400023, Romania
| | - Niculina Hadade
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babes Bolyai University, 11 Arany Janos Street, Cluj-Napoca 400028, Romania
| | - Cecilia Cristea
- Department of Analytical Chemistry, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 4 Pasteur Street, Cluj-Napoca 400021, Romania.
| | - Ovidiu Crisan
- Department of Organic Chemistry, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 28 Victor Babes Street, Cluj-Napoca 400023, Romania
| |
Collapse
|
3
|
Ullrich S, Panda B, Somathilake U, Lawes DJ, Nitsche C. Non-symmetric cysteine stapling in native peptides and proteins. Chem Commun (Camb) 2024. [PMID: 39676702 DOI: 10.1039/d4cc04995k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
Stapling rigidifies peptides through covalent linkages between amino acids. We introduce 2-chloromethyl-6-cyanopyridine for non-symmetric stapling of N-terminal and internal cysteines. This biocompatible method produces diverse peptide macrocycles with enhanced affinity, stability and inhibitory potency. It is applicable to native peptides and proteins alike, demonstrating potential for peptide drug discovery platforms.
Collapse
Affiliation(s)
- Sven Ullrich
- Research School of Chemistry, College of Science, Australian National University, Canberra 2601 ACT, Australia.
| | - Bishvanwesha Panda
- Research School of Chemistry, College of Science, Australian National University, Canberra 2601 ACT, Australia.
| | - Upamali Somathilake
- Research School of Chemistry, College of Science, Australian National University, Canberra 2601 ACT, Australia.
| | - Douglas J Lawes
- Research School of Chemistry, College of Science, Australian National University, Canberra 2601 ACT, Australia.
| | - Christoph Nitsche
- Research School of Chemistry, College of Science, Australian National University, Canberra 2601 ACT, Australia.
| |
Collapse
|
4
|
Kushwaha P, Madhavan N. A Reusable Polystyrene Support for Sustainable yet Cost-effective Octreotide Synthesis. Chemistry 2024; 30:e202402804. [PMID: 39348501 DOI: 10.1002/chem.202402804] [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: 07/25/2024] [Revised: 09/21/2024] [Accepted: 09/26/2024] [Indexed: 10/02/2024]
Abstract
The synthesis of peptide drugs has become facile with the use of supports that enable easy separation of the growing peptide. Peptide synthesis on insoluble supports typically employs excess reagents to enhance reaction efficiency and faces challenges during intramolecular cyclization. A non-crosslinked soluble polystyrene support is reported herein that improves cyclization efficiency on the support by using spacers. The support efficiency is illustrated by synthesizing octreotide drug in a scalable manner by on-support cyclization. The methodology drastically reduces the reagent waste, raw-material cost, and solvent requirement. The support can also be recovered and re-used up to 3 times making this a very sustainable method.
Collapse
Affiliation(s)
- Priyanka Kushwaha
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Nandita Madhavan
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India
| |
Collapse
|
5
|
Fang P, Pang WK, Xuan S, Chan WL, Leung KCF. Recent advances in peptide macrocyclization strategies. Chem Soc Rev 2024; 53:11725-11771. [PMID: 39560122 DOI: 10.1039/d3cs01066j] [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: 11/20/2024]
Abstract
Recently, owing to their special spatial structures, peptide-based macrocycles have shown tremendous promise and aroused great interest in multidisciplinary research ranging from potent antibiotics against resistant strains to functional biomaterials with novel properties. Besides traditional monocyclic peptides, many fascinating polycyclic and remarkable higher-order cyclic, spherical and cylindric peptidic systems have come into the limelight owing to breakthroughs in various chemical (e.g., native chemical ligation and transition metal catalysis), biological (e.g., post-translational enzymatic modification and genetic code reprogramming), and supramolecular (e.g., mechanically interlocked, metal-directed folding and self-assembly via noncovalent interactions) macrocyclization strategies developed in recent decades. In this tutorial review, diverse state-of-the-art macrocyclization methodologies and techniques for peptides and peptidomimetics are surveyed and discussed, with insights into their practical advantages and intrinsic limitations. Finally, the synthetic-technical aspects, current unresolved challenges, and outlook of this field are discussed.
Collapse
Affiliation(s)
- Pengyuan Fang
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, Fujian, P. R. China.
| | - Wing-Ka Pang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, P. R. China.
| | - Shouhu Xuan
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, Anhui 230027, P. R. China
| | - Wai-Lun Chan
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, Fujian, P. R. China.
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Ken Cham-Fai Leung
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, P. R. China.
| |
Collapse
|
6
|
Han D, Li A, Zhu L, Zhuang C, Zhao Q, Zou Y. Peptide inhibitors targeting Ras and Ras-associated protein-protein interactions. Eur J Med Chem 2024; 279:116878. [PMID: 39326269 DOI: 10.1016/j.ejmech.2024.116878] [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: 08/14/2024] [Revised: 09/04/2024] [Accepted: 09/12/2024] [Indexed: 09/28/2024]
Abstract
Peptides represent attractive molecules for targeting protein-protein interactions, and peptide drug development has made great progress during the last decades. Ras protein, the most promising target in cancer therapy, is one of the major growth drivers in various cancers. Although many small molecule inhibitors have been reported to effectively target Ras protein and some inhibitors (such as MRTX849 and AMG 510) have been translated into clinical application, just a few peptide inhibitors have been reported. Here we summarize different types of peptide inhibitors, including monocyclic peptides, bicyclic peptides, stapled peptides, and proteomimetic inhibitors, developed in recent years; emphasize the limits and achievements; and discuss the outlook and challenges associated with future research in peptide inhibitors. This review aims to provide a reference for the discovery of Ras peptide inhibitors.
Collapse
Affiliation(s)
- Dan Han
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, PR China; School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, PR China
| | - Anpeng Li
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, PR China; 92805 Military Hospital, Qingdao, PR China
| | - Lie Zhu
- Department of Burn Plastic Surgery, The Second Affiliated Hospital of Second Military Medical University, Shanghai, 200003, PR China
| | - Chunlin Zhuang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, PR China.
| | - Qingjie Zhao
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, PR China.
| | - Yan Zou
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, PR China.
| |
Collapse
|
7
|
Lamb HO, Benfield AH, Henriques ST. Peptides as innovative strategies to combat drug resistance in cancer therapy. Drug Discov Today 2024; 29:104206. [PMID: 39395530 DOI: 10.1016/j.drudis.2024.104206] [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: 07/02/2024] [Revised: 09/29/2024] [Accepted: 10/07/2024] [Indexed: 10/14/2024]
Abstract
Drug resistance is the leading cause of treatment failure in patients with cancer. Thus, innovative therapeutic strategies are required to overcome this critical challenge and improve patient outcomes. In this review, we examine the potential of peptide-based therapies to combat drug resistance in cancer. We highlight the unique strategies and mechanisms that can be explored by using peptides, including their ability to selectively target tumours, facilitate drug delivery into cancer cells, and inhibit key intracellular proteins that drive cancer progression and resistance. Peptides offer a promising approach to overcoming both intrinsic and adaptative cancer resistance against chemotherapy, targeted therapies, and biologics.
Collapse
Affiliation(s)
- Henry O Lamb
- School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Aurélie H Benfield
- School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Sónia Troeira Henriques
- School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Brisbane, QLD 4102, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia.
| |
Collapse
|
8
|
Jafari N, Addison C, Lou H, Hageman MJ. Hydroxypropyl β cyclodextrins effects on self-assembly of cyclic peptide, lanreotide acetate, in water and subsequent release rate from an in vitro emulator of subcutaneous delivery. J Pharm Sci 2024:S0022-3549(24)00538-0. [PMID: 39615879 DOI: 10.1016/j.xphs.2024.11.018] [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: 09/13/2024] [Revised: 10/29/2024] [Accepted: 11/15/2024] [Indexed: 12/19/2024]
Abstract
Most of the peptide drugs are often delivered subcutaneously. The significant barrier in this type of peptide administration is the high concentration of formulation, which can lead to self-assembly and aggregation. These phenomena can negatively impact the peptide drug's bioavailability, manufacturing, and injectability. This study investigated the self-assembly behavior of Lanreotide acetate at high concentrations in water using Hydroxypropyl β- Cyclodextrins (HPβCyD) to mitigate the self-assembly and enhance release rate during subcutaneous administration. Our finding demonstrated that the lanreotide/ HPβCyD inclusion complex effectively prevents aromatic-aromatic interactions of lanreotide, thereby controlling self-assembly. This complexation also alters the viscosity behavior of lanreotide from non-Newtonian under low shear rates to Newtonian solution. Furthermore, the lanreotide/ HPβCyD inclusion complex reduces interactions with hyaluronic acid in the subcutaneous environment, leading to significant improvement in the release rate of lanreotide acetate at high concentrations (above 3 % w/w in water).
Collapse
Affiliation(s)
- Negar Jafari
- Pharmaceutical Chemistry, University of Kansas, Lawrence, USA.
| | | | - Hao Lou
- Pharmaceutical Chemistry, University of Kansas, Lawrence, USA
| | - Michael J Hageman
- Pharmaceutical Chemistry, University of Kansas, Lawrence, USA; BIO Center, University of Kansas, Lawrence, USA.
| |
Collapse
|
9
|
Kubyshkin V, Mykhailiuk PK. Proline Analogues in Drug Design: Current Trends and Future Prospects. J Med Chem 2024; 67:20022-20055. [PMID: 39605166 DOI: 10.1021/acs.jmedchem.4c01987] [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: 11/29/2024]
Abstract
Proline analogues are versatile chemical building blocks that enable modular construction of small-molecule drugs and pharmaceutical peptides. Over the past 15 years, the FDA has approved over 15 drugs containing proline analogues in their structures, five in the last three years alone (daridorexant, trofinetide, nirmatrelvir, rezafungin, danicopan). This perspective offers an analysis of the most common types of proline analogues currently trending in drug design. We focus on examples of fluoroprolines, α-methylproline, bicyclic proline analogues, and aminoprolines, while also highlighting proline analogues that remain underrepresented. We supplement our analysis with physicochemical information regarding the specific molecular properties of these moieties. Additionally, we discuss several intriguing cases where nonproline residues were replaced with proline analogues as a strategy to eliminate unwanted hydrogen bond donor sites. In conclusion, we present some suggestions for the future exploration of this promising class of molecular entities in drug discovery.
Collapse
|
10
|
Swenson CS, Mandava G, Thomas DM, Moellering RE. Tackling Undruggable Targets with Designer Peptidomimetics and Synthetic Biologics. Chem Rev 2024; 124:13020-13093. [PMID: 39540650 DOI: 10.1021/acs.chemrev.4c00423] [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: 11/16/2024]
Abstract
The development of potent, specific, and pharmacologically viable chemical probes and therapeutics is a central focus of chemical biology and therapeutic development. However, a significant portion of predicted disease-causal proteins have proven resistant to targeting by traditional small molecule and biologic modalities. Many of these so-called "undruggable" targets feature extended, dynamic protein-protein and protein-nucleic acid interfaces that are central to their roles in normal and diseased signaling pathways. Here, we discuss the development of synthetically stabilized peptide and protein mimetics as an ever-expanding and powerful region of chemical space to tackle undruggable targets. These molecules aim to combine the synthetic tunability and pharmacologic properties typically associated with small molecules with the binding footprints, affinities and specificities of biologics. In this review, we discuss the historical and emerging platforms and approaches to design, screen, select and optimize synthetic "designer" peptidomimetics and synthetic biologics. We examine the inspiration and design of different classes of designer peptidomimetics: (i) macrocyclic peptides, (ii) side chain stabilized peptides, (iii) non-natural peptidomimetics, and (iv) synthetic proteomimetics, and notable examples of their application to challenging biomolecules. Finally, we summarize key learnings and remaining challenges for these molecules to become useful chemical probes and therapeutics for historically undruggable targets.
Collapse
Affiliation(s)
- Colin S Swenson
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Gunasheil Mandava
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Deborah M Thomas
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Raymond E Moellering
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
11
|
Kurita T, Numata K. The structural and functional impacts of rationally designed cyclic peptides on self-assembly-mediated functionality. Phys Chem Chem Phys 2024; 26:28776-28792. [PMID: 39555904 DOI: 10.1039/d4cp02759k] [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: 11/19/2024]
Abstract
Compared with their linear counterparts, cyclic peptides, characterized by their unique topologies, offer superior stability and enhanced functionality. In this review article, the rational design of cyclic peptide primary structures and their significant influence on self-assembly processes and functional capabilities are comprehensively reviewed. We emphasize how strategically modifying amino acid sequences and ring sizes critically dictate the formation and properties of peptide nanotubes (PNTs) and complex assemblies, such as rotaxanes. Adjusting the number of amino acid residues and side chains allows researchers to tailor the diameter, surface properties, and functions of PNTs precisely. In addition, we discuss the complex host-guest chemistry of cyclic peptides and their ability to form rotaxanes, highlighting their potential in the development of mechanically interlocked structures with novel functionalities. Moreover, the critical role of computational methods for accurately predicting the solution structures of cyclic peptides is also highlighted, as it enables the design of novel peptides with tailored properties for a range of applications. These insights set the stage for groundbreaking advances in nanotechnology, drug delivery, and materials science, driven by the strategic design of cyclic peptide primary structures.
Collapse
Affiliation(s)
- Taichi Kurita
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Keiji Numata
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Institute for Advanced Biosciences, Keio University, Nipponkoku 403-1, Daihouji, Tsuruoka, Yamagata 997-0017, Japan
| |
Collapse
|
12
|
Zhang S, Fan S, He H, Zhu J, Murray L, Liang G, Ran S, Zhu YZ, Cryle MJ, He HY, Zhang Y. Cyclic natural product oligomers: diversity and (bio)synthesis of macrocycles. Chem Soc Rev 2024. [PMID: 39584260 DOI: 10.1039/d2cs00909a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2024]
Abstract
Cyclic compounds are generally preferred over linear compounds for functional studies due to their enhanced bioavailability, stability towards metabolic degradation, and selective receptor binding. This has led to a need for effective cyclization strategies for compound synthesis and hence increased interest in macrocyclization mediated by thioesterase (TE) domains, which naturally boost the chemical diversity and bioactivities of cyclic natural products. Many non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) derived natural products are assembled to form cyclodimeric compounds, with these molecules possessing diverse structures and biological activities. There is significant interest in identifying the biosynthetic pathways that produce such molecules given the challenge that cyclodimerization represents from a biosynthetic perspective. In the last decade, many groups have pursued the characterization of TE domains and have provided new insights into this biocatalytic machinery: however, the enzymes involved in formation of cyclodimeric compounds have proven far more elusive. In this review we focus on natural products that involve macrocyclization in their biosynthesis and chemical synthesis, with an emphasis on the function and biosynthetic investigation on the special family of TE domains responsible for forming cyclodimeric natural products. We also introduce additional macrocyclization catalysts, including butelase and the CT-mediated cyclization of peptides, alongside the formation of cyclodipeptides mediated by cyclodipeptide synthases (CDPS) and single-module NRPSs. Due to the interdisciplinary nature of biosynthetic research, we anticipate that this review will prove valuable to synthetic chemists, drug discovery groups, enzymologists, and the biosynthetic community in general, and inspire further efforts to identify and exploit these biocatalysts for the formation of novel bioactive molecules.
Collapse
Affiliation(s)
- Songya Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Key Laboratory of Genome Manipulation and Biosynthesis, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shuai Fan
- NHC Key Laboratory of Biotechnology for Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Haocheng He
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Key Laboratory of Genome Manipulation and Biosynthesis, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jing Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Key Laboratory of Genome Manipulation and Biosynthesis, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lauren Murray
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria, 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, 3800, Australia
| | - Gong Liang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Key Laboratory of Genome Manipulation and Biosynthesis, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shi Ran
- NHC Key Laboratory of Biotechnology for Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yi Zhun Zhu
- School of Pharmacy & State Key Lab. for the Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria, 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, 3800, Australia
| | - Hai-Yan He
- NHC Key Laboratory of Biotechnology for Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- Shenzhen Key Laboratory of Genome Manipulation and Biosynthesis, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| |
Collapse
|
13
|
Feller AL, Wilke CO. Peptide-aware chemical language model successfully predicts membrane diffusion of cyclic peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607221. [PMID: 39149303 PMCID: PMC11326283 DOI: 10.1101/2024.08.09.607221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Language modeling applied to biological data has significantly advanced the prediction of membrane penetration for small molecule drugs and natural peptides. However, accurately predicting membrane diffusion for peptides with pharmacologically relevant modifications remains a substantial challenge. Here, we introduce PeptideCLM, a peptide-focused chemical language model capable of encoding peptides with chemical modifications, unnatural or non-canonical amino acids, and cyclizations. We assess this model by predicting membrane diffusion of cyclic peptides, demonstrating greater predictive power than existing chemical language models. Our model is versatile and can be extended beyond membrane diffusion predictions to other target values. Its advantages include the ability to model macromolecules using chemical string notation, a largely unexplored domain, and a simple, flexible architecture that allows for adaptation to any peptide or other macromolecule dataset.
Collapse
|
14
|
Fawaz M, Sun C, Feng Y, Qirjollari A, Josien H, DeBord D, Simone A, Williamson DL, Pearson K, Gonzalez RJ, Vasicek L, Cancilla MT, Wang W, Spellman DS, Kedia K. Leveraging High-Resolution Ion Mobility-Mass Spectrometry for Cyclic Peptide Soft Spot Identification. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2596-2607. [PMID: 38992936 DOI: 10.1021/jasms.4c00109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Cyclic peptides are an important class of molecules that gained significant attention in the field of drug discovery due to their unique pharmacological characteristics and enhanced proteolytic stability. Yet, gastrointestinal degradation remains a major hurdle in the discovery of orally bioavailable cyclic peptides. Soft spot identification (SSID) of the regions in the cyclic peptide sequence susceptible to amide hydrolysis by proteases is used in the discovery stage to guide medicinal chemistry design. SSID can be an arduous task, traditionally performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS), often resulting in complex and time-consuming manual analysis, particularly when isomeric linear peptide metabolites chromatographically coelute. Here, we present an alternative orthogonal approach that entails a high-resolution ion mobility (HRIM) system based on Structures for Lossless Ion Manipulation (SLIM) technology interfaced with quadrupole time-of-flight (QTOF) mass spectrometry to address some of the challenges associated with SSID. Two strategies were used to resolve linear isomeric peptide metabolites: labeled and label-free, both utilizing the HRIM platform. The label-free strategy leverages negative polarity to ionize the isomers which achieves better separation of the gas phase ions in the ion mobility (IM) dimension as compared to positive polarity, which is a more conventional approach when studying proteins and peptides. The second approach uses an isotope-labeled dimethyl tag on the terminal amine group, acting as a "shift reagent" to influence the mobility of isomers in the positive mode. This method resulted in baseline separation for the isomers of interest and produced unique product ions in the fragmentation spectra for unambiguous soft spot identification. Both label-free and labeled strategies demonstrated the ability to solve the challenges associated with SSID for cyclic peptides.
Collapse
Affiliation(s)
- Maria Fawaz
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Congliang Sun
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Yu Feng
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Hubert Josien
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Daniel DeBord
- MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Ashli Simone
- MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States
| | | | - Kara Pearson
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Lisa Vasicek
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Mark T Cancilla
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Weixun Wang
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Komal Kedia
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| |
Collapse
|
15
|
Sarkar S, Chatterjee A, Kim D, Saritha C, Barman S, Jana B, Ryu JH, Das A. Host-Guest Adduct as a Stimuli-Responsive Prodrug: Enzyme-Triggered Self-Assembly Process of a Short Peptide Within Mitochondria to Induce Cell Apoptosis. Adv Healthc Mater 2024:e2403243. [PMID: 39506431 DOI: 10.1002/adhm.202403243] [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: 08/28/2024] [Revised: 10/25/2024] [Indexed: 11/08/2024]
Abstract
To address the issue of nonspecific biodistribution of a chemotherapeutic drug, stable [2]pseudorotaxane complexes (PK@CAOPP and PR@CAOPP) are used to demonstrate a proof of concept. Cationic -PPh3 + moiety in CAOPP allows specific localization of the PK@CAOPP/ PR@CAOPP in the mitochondrial membrane (MM). Electrostatic interaction between the cationic LysinePK or ArgininePR moiety and the negatively charged phosphoesterCAOPP functionality in CAOPP favours strong adduct formation. The ALP-induced hydrolytic cleavage of the phosphoester moiety in cancer cells triggers dephosphorylation and releases PK/ PR moiety from PK@CAOPP/PR@CAOPP. PK or PR, derived from the Phe-Phe dipeptide, formed fibril-like molecular aggregates in the MM to induce dysfunction, depolarization, ROS generation and apoptotic MCF7 cell death. Such phenomena were not observed in ALP-negative HEK293 normal cells. These propositions were confirmed through control studies using NBDK and PE, other guest molecules. Smaller size and inclusion of the short peptides (PK or PR) within the hydrophobic interior of CAOPP, were attributed to their stability in blood serum. Thus, we have demonstrated the use of supramolecular adducts as a potential therapeutic option for treating cancer cells without affecting healthy cells. The efficacy was also established with an in-vivo MCF7 tumour xenograft model using Balb/c nude mice.
Collapse
Affiliation(s)
- Sandip Sarkar
- Department of Chemical Sciences and Center for Advanced Functional Material, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
| | - Atin Chatterjee
- Department of Chemical Sciences and Center for Advanced Functional Material, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
| | - Dohyun Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Cevella Saritha
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar, 844102, India
| | - Surajit Barman
- Department of Chemical Sciences and Center for Advanced Functional Material, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
| | - Batakrishna Jana
- Department of Chemical Sciences and Center for Advanced Functional Material, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Ja-Hyoung Ryu
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Amitava Das
- Department of Chemical Sciences and Center for Advanced Functional Material, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
| |
Collapse
|
16
|
Nelson S, Parkinson EI. Synthetic-bioinformatic natural product-inspired peptides. Nat Prod Rep 2024. [PMID: 39479929 PMCID: PMC11525955 DOI: 10.1039/d4np00043a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Indexed: 11/02/2024]
Abstract
Covering: 2016 to 2024Natural products, particularly cyclic peptides, are a promising source of bioactive compounds. Nonribosomal peptide synthetases (NRPSs) play a key role in biosynthesizing these compounds, which include antibiotic and anticancer agents, immunosuppressants, and others. Traditional methods of discovering natural products have limitations including cryptic biosynthetic gene clusters (BGCs), low titers, and currently unculturable organisms. This has prompted the exploration of alternative approaches. Synthetic-bioinformatic natural products (syn-BNPs) are one such alternative that utilizes bioinformatics techniques to predict nonribosomal peptides (NRPs) followed by chemical synthesis of the predicted peptides. This approach has shown promise, resulting in the discovery of a variety of bioactive compounds including peptides with antibacterial, antifungal, anticancer, and proteasome-stimulating activities. Despite the success of this approach, challenges remain especially in the accurate prediction of fatty acid incorporation, tailoring enzyme modifications, and peptide release mechanisms. Further work in these areas will enable the discovery of many bioactive peptides that are currently inaccessible.
Collapse
Affiliation(s)
- Samantha Nelson
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, USA.
| | - Elizabeth I Parkinson
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, USA.
- James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, USA
| |
Collapse
|
17
|
Amifuji M, Inagaki M, Yoshida M, Doi T, Tachikawa M. Characteristics of membrane transport, metabolism, and target protein binding of cyclic depsipeptide destruxin E in HeLa cells. Drug Metab Pharmacokinet 2024; 58:101028. [PMID: 39265438 DOI: 10.1016/j.dmpk.2024.101028] [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: 05/12/2024] [Revised: 06/19/2024] [Accepted: 06/25/2024] [Indexed: 09/14/2024]
Abstract
Cyclic peptides have attracted attention as new modalities for drug development owing to their unique pharmacokinetic and pharmacodynamic properties. Destruxin E, a 19-membered cyclodepsipeptide, is a promising candidate drug for cancer therapy. The purpose of the present study was to clarify the molecular mechanisms underlying membrane transport, metabolism, and the binding for target molecules of destruxin E in human cervical carcinoma HeLa cells used as a model of cancer cells. The influx transport and the intracellular metabolism of destruxin E were non-saturable and saturable, respectively, at up to 10 μM. The intracellular amounts of destruxin E and destruxin E-diol after incubation of destruxin E with the cells significantly decreased at 4 °C compared to those at 37 °C. Destruxin E-diol, but not destruxin E, undergoes efflux transport out of cells via P-gp/MDR1/ABCB1 and BCRP/ABCG2. The epoxide hydrolase EPHX2 functions as a potent metabolizing enzyme that can convert the epoxide of destruxin E to the destruxin E-diol. Treatment with an EPHX2 inhibitor increased the intracellular destruxin E levels and enhanced the inhibitory activity of vacuolar type-H+ ATPase. These results suggest that epoxide hydrolase could be a regulatory factor for intracellular destruxin E levels and its pharmacological activity.
Collapse
Affiliation(s)
- Makoto Amifuji
- Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Sho-machi, Tokushima, 770-8505, Japan
| | - Mai Inagaki
- Graduate School of Biomedical Sciences, Tokushima University, 1-78-1 Sho-machi, Tokushima, 770-8505, Japan
| | - Masahito Yoshida
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Takayuki Doi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Masanori Tachikawa
- Graduate School of Biomedical Sciences, Tokushima University, 1-78-1 Sho-machi, Tokushima, 770-8505, Japan.
| |
Collapse
|
18
|
Roucairol M, Georgiou A, Cazenave T, Prischi F, Pardo OE. DrugSynthMC: An Atom-Based Generation of Drug-like Molecules with Monte Carlo Search. J Chem Inf Model 2024; 64:7097-7107. [PMID: 39249497 PMCID: PMC11423341 DOI: 10.1021/acs.jcim.4c01451] [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: 09/10/2024]
Abstract
A growing number of deep learning (DL) methodologies have recently been developed to design novel compounds and expand the chemical space within virtual libraries. Most of these neural network approaches design molecules to specifically bind a target based on its structural information and/or knowledge of previously identified binders. Fewer attempts have been made to develop approaches for de novo design of virtual libraries, as synthesizability of generated molecules remains a challenge. In this work, we developed a new Monte Carlo Search (MCS) algorithm, DrugSynthMC (Drug Synthesis using Monte Carlo), in conjunction with DL and statistical-based priors to generate thousands of interpretable chemical structures and novel drug-like molecules per second. DrugSynthMC produces drug-like compounds using an atom-based search model that builds molecules as SMILES, character by character. Designed molecules follow Lipinski's "rule of 5″, show a high proportion of highly water-soluble nontoxic predicted-to-be synthesizable compounds, and efficiently expand the chemical space within the libraries, without reliance on training data sets, synthesizability metrics, or enforcing during SMILES generation. Our approach can function with or without an underlying neural network and is thus easily explainable and versatile. This ease in drug-like molecule generation allows for future integration of score functions aimed at different target- or job-oriented goals. Thus, DrugSynthMC is expected to enable the functional assessment of large compound libraries covering an extensive novel chemical space, overcoming the limitations of existing drug collections. The software is available at https://github.com/RoucairolMilo/DrugSynthMC.
Collapse
Affiliation(s)
- Milo Roucairol
- LAMSADE, Université Paris-Dauphine, Pl. du Maréchal de Lattre de Tassigny, 75016 Paris, France
| | - Alexios Georgiou
- LAMSADE, Université Paris-Dauphine, Pl. du Maréchal de Lattre de Tassigny, 75016 Paris, France
| | - Tristan Cazenave
- LAMSADE, Université Paris-Dauphine, Pl. du Maréchal de Lattre de Tassigny, 75016 Paris, France
| | - Filippo Prischi
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, United Kingdom
| | - Olivier E Pardo
- Division of Cancer, Department of Surgery and Cancer, Imperial College, Du Cane Road, London W12 0NN, United Kingdom
| |
Collapse
|
19
|
Liu Z, Li H, Yu Q, Song Q, Peng B, Wang K, Li Z. Heterologous Expression Facilitates the Production and Characterization of a Class III Lanthipeptide with Coupled Labionin Cross-Links in Sponge-Associated Streptomyces rochei MB037. ACS Chem Biol 2024; 19:2060-2069. [PMID: 39145437 DOI: 10.1021/acschembio.4c00428] [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: 08/16/2024]
Abstract
Cyclic peptides, with remarkable stability, cellular permeability, and proteolysis resistance, display promising potential in pharmaceutical applications. Labionin (Lab), a unique bicyclic cross-link containing both C-C and C-S bonds, provides high rigidity and better control of conformation compared to monocyclic cross-links. To discover more Lab-containing scaffolds with highly rigid conformation for cyclic peptide drug development, herein, a cryptic class III lanthipeptide biosynthetic gene cluster (BGC) (i.e., rcs) was identified in the sponge-associated Streptomyces rochei MB037 and expressed in Escherichia coli, incorporating an N-terminal SUMO-tag on the RcsA precursor peptide to prevent proteolysis. Subsequently, a novel class III lanthipeptide, i.e., rochsin A, exhibiting a highly rigid conformation with coupled Lab cross-links crowded by bulky aromatic amino acids, was produced. Three AplP-like proteases outside the rcs BGC were proven to remove the leader peptide of rochsin A through their dual endo- and aminopeptidase activities, resulting in mature rochsin A in vitro. Ala mutation experiments revealed the C to N cyclization direction, like most class III lanthipeptides. However, RcsKC displays a high substrate breadth, enabling various ring topologies that are rarely observed in other class III lanthipeptides. Overall, the established expression system broadens the chemical diversity of cyclic peptides with unique Lab cross-links and offers a highly rigid scaffold for cyclic peptide drug development.
Collapse
Affiliation(s)
- Zhengjie Liu
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qianzhe Yu
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qianqian Song
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo Peng
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kang Wang
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| |
Collapse
|
20
|
Hurd CA, Bush JT, Powell AJ, Walport LJ. mRNA Display in Cell Lysates Enables Identification of Cyclic Peptides Targeting the BRD3 Extraterminal Domain. Angew Chem Int Ed Engl 2024; 63:e202406414. [PMID: 38899853 DOI: 10.1002/anie.202406414] [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: 04/04/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 06/21/2024]
Abstract
mRNA display is a powerful technology to screen libraries of >1012 cyclic peptides against a protein target, enabling the rapid discovery of high affinity ligands. These cyclic peptides are particularly well suited to challenging protein targets that have been difficult to drug with small molecules. However, target choice can still be limited as screens are typically performed against purified proteins which often demands the use of isolated domains and precludes the use of aggregation-prone targets. Herein, we report a method to perform mRNA display selections in mammalian cell lysates without the need for prior target purification, vastly expanding the potential target scope of mRNA display. We have applied the methodology to identify low to sub-nanomolar peptide binders for two targets: a NanoLuc subunit (LgBiT) and full-length bromodomain-containing protein 3 (BRD3). Our cyclic peptides for BRD3 were found to bind to the extraterminal (ET) domain of BRD3 and the closely related BRD proteins, BRD2 and BRD4. While many chemical probes exist for the bromodomains of BRD proteins, the ET domain is relatively underexplored, making these peptides valuable additions to the BRD toolbox.
Collapse
Affiliation(s)
- Catherine A Hurd
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ
- Crick-GSK Biomedical LinkLabs, The Francis Crick Institute, London, NW1 1AT
| | - Jacob T Bush
- Crick-GSK Biomedical LinkLabs, GSK, Gunnels Wood Road, Stevenage, SG1 2NY
| | - Andrew J Powell
- Crick-GSK Biomedical LinkLabs, GSK, Gunnels Wood Road, Stevenage, SG1 2NY
| | - Louise J Walport
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT
| |
Collapse
|
21
|
Cardoso Prado Martins F, Dos Reis Rocho F, Bonatto V, Jatai Batista PH, Lameira J, Leitão A, Montanari CA. Novel selective proline-based peptidomimetics for human cathepsin K inhibition. Bioorg Med Chem Lett 2024; 110:129887. [PMID: 39002936 DOI: 10.1016/j.bmcl.2024.129887] [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: 05/14/2024] [Revised: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
Human cathepsin K (CatK) stands out as a promising target for the treatment of osteoporosis, considering its role in degrading the bone matrix. Given the small and shallow S2 subsite of CatK and considering its preference for proline or hydroxyproline, we now propose the rigidification of the leucine fragment found at the P2 position in a dipeptidyl-based inhibitor, generating rigid proline-based analogs. Accordingly, with these new proline-based peptidomimetics inhibitors, we selectively inhibited CatK against other human cathepsins (B, L and S). Among these new ligands, the most active one exhibited a high affinity (pKi = 7.3 - 50.1 nM) for CatK and no inhibition over the other cathepsins. This specific inhibitor harbors two novel substituents never employed in other CatK inhibitors: the trifluoromethylpyrazole and the 4-methylproline at P3 and P2 positions. These results broaden and advance the path toward new potent and selective inhibitors for CatK.
Collapse
Affiliation(s)
- Felipe Cardoso Prado Martins
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos/SP, Brazil
| | - Fernanda Dos Reis Rocho
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos/SP, Brazil
| | - Vinícius Bonatto
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos/SP, Brazil
| | - Pedro Henrique Jatai Batista
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos/SP, Brazil
| | - Jerônimo Lameira
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos/SP, Brazil; Institute of Biological Science, Federal University of Pará, Rua Augusto Correa S/N, Belém, PA, Brazil
| | - Andrei Leitão
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos/SP, Brazil
| | - Carlos A Montanari
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos/SP, Brazil.
| |
Collapse
|
22
|
Song L, Jiang S, Yang Q, Huang W, Qiu Y, Chen Z, Sun X, Wang T, Wu S, Chen Y, Zeng H, Wang Z, Kang L. Development of a Novel Peptide-Based PET Tracer [ 68Ga]Ga-DOTA-BP1 for BCMA Detection in Multiple Myeloma. J Med Chem 2024; 67:15118-15130. [PMID: 39167092 DOI: 10.1021/acs.jmedchem.4c00759] [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: 08/23/2024]
Abstract
B-cell maturation antigen (BCMA) has emerged as a promising tumor marker for the diagnosis and treatment of multiple myeloma. The noninvasive and rapid detection of BCMA expression in vivo provides significant value in screening and evaluating multiple myeloma patients receiving BCMA-targeted therapy. We identified the BCMA-targeting peptide BP1 from a one-bead-one-compound (OBOC) peptide library using a high-throughput microarray strategy. The BCMA-targeting specificity and affinity of BP1 were assessed by surface plasmon resonance imaging (SPRi), flow cytometry, and confocal imaging. BCMA-positive (H929) and BCMA-negative (K562) subcutaneous tumor models were established and labeled with 68Ga for BP1, followed by PET imaging and biodistribution studies. PET imaging demonstrated that 68Ga-labeled BP1 has significant specific uptake in multiple myeloma, enabling rapid identification of BCMA expression and precise delineation of the disease. Thus, BP1 represents an ideal candidate for multiple myeloma imaging.
Collapse
Affiliation(s)
- Lele Song
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Sujun Jiang
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350122, China
| | - Qi Yang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Wenpeng Huang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Yongkang Qiu
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Zhao Chen
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Xinyao Sun
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Tianyao Wang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Sitong Wu
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Yongshou Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Huajie Zeng
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350122, China
| | - Zihua Wang
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350122, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Lei Kang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| |
Collapse
|
23
|
Darling WTP, Wieske LHE, Cook DT, Aliev AE, Caron L, Humphrys EJ, Figueiredo AM, Hansen DF, Erdélyi M, Tabor AB. The Influence of Disulfide, Thioacetal and Lanthionine-Bridges on the Conformation of a Macrocyclic Peptide. Chemistry 2024; 30:e202401654. [PMID: 38953277 DOI: 10.1002/chem.202401654] [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: 04/26/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/03/2024]
Abstract
Cyclisation of peptides by forming thioether (lanthionine), disulfide (cystine) or methylene thioacetal bridges between side chains is established as an important tool to stabilise a given structure, enhance metabolic stability and optimise both potency and selectivity. However, a systematic comparative study of the effects of differing bridging modalities on peptide conformation has not previously been carried out. In this paper, we have used the NMR deconvolution algorithm, NAMFIS, to determine the conformational ensembles, in aqueous solution, of three cyclic analogues of angiotensin(1-7), incorporating either disulfide, or non-reducible thioether or methylene thioacetal bridges. We demonstrate that the major solution conformations are conserved between the different bridged peptides, but the distribution of conformations differs appreciably. This suggests that subtle differences in ring size and bridging structure can be exploited to fine-tune the conformational properties of cyclic peptides, which may modulate their bioactivities.
Collapse
Affiliation(s)
- William T P Darling
- Department of Chemistry, University College London, 20, Gordon Street, London, WC1H 0AJ, UK
| | - Lianne H E Wieske
- Department of Chemistry-BMC, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Declan T Cook
- Department of Chemistry, University College London, 20, Gordon Street, London, WC1H 0AJ, UK
| | - Abil E Aliev
- Department of Chemistry, University College London, 20, Gordon Street, London, WC1H 0AJ, UK
| | - Laurent Caron
- Biosynth Laboratories Ltd (formerly Cambridge Research Biochemicals Ltd), 17-18 Belasis Court, Belasis Hall Technology Park, Billingham, TS23 4AZ, UK
| | - Emily J Humphrys
- Biosynth Laboratories Ltd (formerly Cambridge Research Biochemicals Ltd), 17-18 Belasis Court, Belasis Hall Technology Park, Billingham, TS23 4AZ, UK
| | - Angelo Miguel Figueiredo
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, UCL Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - D Flemming Hansen
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, UCL Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Máté Erdélyi
- Department of Chemistry-BMC, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Alethea B Tabor
- Department of Chemistry, University College London, 20, Gordon Street, London, WC1H 0AJ, UK
| |
Collapse
|
24
|
Bohley M, Leroux J. Gastrointestinal Permeation Enhancers Beyond Sodium Caprate and SNAC - What is Coming Next? ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400843. [PMID: 38884149 PMCID: PMC11434117 DOI: 10.1002/advs.202400843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/13/2024] [Indexed: 06/18/2024]
Abstract
Oral peptide delivery is trending again. Among the possible reasons are the recent approvals of two oral peptide formulations, which represent a huge stride in the field. For the first time, gastrointestinal (GI) permeation enhancers (PEs) are leveraged to overcome the main limitation of oral peptide delivery-low permeability through the intestinal epithelium. Despite some success, the application of current PEs, such as salcaprozate sodium (SNAC), sodium caprylate (C8), and sodium caprate (C10), is generally resulting in relatively low oral bioavailabilities (BAs)-even for carefully selected therapeutics. With several hundred peptide-based drugs presently in the pipeline, there is a huge unmet need for more effective PEs. Aiming to provide useful insights for the development of novel PEs, this review summarizes the biological hurdles to oral peptide delivery with special emphasis on the epithelial barrier. It describes the concepts and action modes of PEs and mentions possible new targets. It further states the benchmark that is set by current PEs, while critically assessing and evaluating emerging PEs regarding translatability, safety, and efficacy. Additionally, examples of novel PEs under preclinical and clinical evaluation and future directions are discussed.
Collapse
Affiliation(s)
- Marilena Bohley
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH ZurichZurich8093Switzerland
| | - Jean‐Christophe Leroux
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH ZurichZurich8093Switzerland
| |
Collapse
|
25
|
Tang X, Hou K, Chen X, Fan W, Wu H, Lu C, He GX. Discovery of macrocyclic covalent inhibitors for severe acute respiratory syndrome coronavirus 2 3CL protease. Bioorg Med Chem 2024; 111:117846. [PMID: 39106653 DOI: 10.1016/j.bmc.2024.117846] [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: 06/04/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/09/2024]
Abstract
The coronavirus disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spread worldwide for more than 3 years. Although the hospitalization rate and mortality have decreased dramatically due to wide vaccination effort and improved treatment options, the disease is still a global health issue due to constant viral mutations, causing negative impact on social and economic activities. In addition, long COVID and complications arising from COVID-19 weeks after infection have become a concern for public health experts. Therefore, better treatments for COVID-19 are still needed. Herein, we describe a class of macrocyclic peptidomimetic compounds that are potent inhibitors of SARS-Cov-2 3CL protease (3CLpro). Significantly, some of the compounds showed a higher stability against human liver microsomes (HLM t1/2 > 180 min) and may be suitable for oral administration without the need for a pharmacokinetic (PK) boosting agent such as ritonavir.
Collapse
Affiliation(s)
- Xiubo Tang
- Shanghai CureGene Pharmaceutical Co., Ltd, 2nd floor, Building C1, No. 1976 middle Gaoke Road, ZhangJiang Hitech Park, Pudong, Shanghai 201210, China.
| | - Kai Hou
- Shanghai CureGene Pharmaceutical Co., Ltd, 2nd floor, Building C1, No. 1976 middle Gaoke Road, ZhangJiang Hitech Park, Pudong, Shanghai 201210, China
| | - Xiaowu Chen
- Shanghai CureGene Pharmaceutical Co., Ltd, 2nd floor, Building C1, No. 1976 middle Gaoke Road, ZhangJiang Hitech Park, Pudong, Shanghai 201210, China
| | - Wenyuan Fan
- Shanghai CureGene Pharmaceutical Co., Ltd, 2nd floor, Building C1, No. 1976 middle Gaoke Road, ZhangJiang Hitech Park, Pudong, Shanghai 201210, China
| | - Hao Wu
- Shanghai CureGene Pharmaceutical Co., Ltd, 2nd floor, Building C1, No. 1976 middle Gaoke Road, ZhangJiang Hitech Park, Pudong, Shanghai 201210, China
| | - Changliang Lu
- Shanghai CureGene Pharmaceutical Co., Ltd, 2nd floor, Building C1, No. 1976 middle Gaoke Road, ZhangJiang Hitech Park, Pudong, Shanghai 201210, China
| | - Gong-Xin He
- Shanghai CureGene Pharmaceutical Co., Ltd, 2nd floor, Building C1, No. 1976 middle Gaoke Road, ZhangJiang Hitech Park, Pudong, Shanghai 201210, China
| |
Collapse
|
26
|
Matsuda K. Macrocyclizing-thioesterases in bacterial non-ribosomal peptide biosynthesis. J Nat Med 2024:10.1007/s11418-024-01841-y. [PMID: 39214926 DOI: 10.1007/s11418-024-01841-y] [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: 05/30/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Macrocyclization of peptides reduces conformational flexibilities, potentially leading to improved drug-like properties. However, side reactions such as epimerization and oligomerization often pose synthetic challenges. Peptide-cyclizing biocatalysts in the biosynthesis of non-ribosomal peptides (NRPs) have remarkable potentials as chemoenzymatic tools to facilitate more straightforward access to complex macrocycles. This review highlights the biocatalytic potentials of NRP cyclases, especially those of cis-acting thioesterases, the most general cyclizing machinery in NRP biosynthesis. Growing insights into penicillin-binding protein-type thioesterases, a relatively new group of trans-acting thioesterases, are also summarized.
Collapse
Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
| |
Collapse
|
27
|
Sarkar R, Adhikary K, Banerjee A, Ganguly K, Sarkar R, Mohanty S, Dhua R, Bhattacharya K, Ahuja D, Pal S, Maiti R. Novel targets and improved immunotherapeutic techniques with an emphasis on antimycosal drug resistance for the treatment and management of mycosis. Heliyon 2024; 10:e35835. [PMID: 39224344 PMCID: PMC11367498 DOI: 10.1016/j.heliyon.2024.e35835] [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: 06/19/2024] [Revised: 08/04/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Infections due to pathogenic fungi are endemic in particular area with increased morbidity and mortality. More than a thousand people are infected per year and the way of treatment is of high demand having a significant impact on the population health. Medical practitioners confront various troublesome analytic and therapeutical challenges in the administration of immunosuppressed sufferer at high danger of expanding fungal infections. An upgraded antimycosal treatment is fundamental for a fruitful result while treating intrusive mycoses. A collection of antimycosal drugs keeps on developing with their specific antifungal targets including cell membrane, mitochondria, cell wall, and deoxyribonucleic acid (DNA)/ribonucleic acid (RNA) or protein biosynthesis. Some fundamental classes of ordinarily directed medications are the polyenes, amphotericin B, syringomycin, allylamines, honokiol, azoles, flucytosine, echinocandins etc. However, few immunotherapy processes and vaccinations are being developed to mark this need, although one presently can't seem to arrive at the conclusion. In this review article, there has been a trial to give details upgradation about the current immune therapeutic techniques and vaccination strategies against prevention or treatment of mycosis as well as the difficulties related with their turn of events. There has been also a visualization in the mentioned review paper about the various assorted drugs and their specific target analysis along with therapeutic interventions.
Collapse
Affiliation(s)
- Riya Sarkar
- Department of Medical Lab Technology and Biotechnology, Paramedical College Durgapur, West Bengal, 713212, India
| | - Krishnendu Adhikary
- Department of Medical Lab Technology and Biotechnology, Paramedical College Durgapur, West Bengal, 713212, India
| | - Arundhati Banerjee
- Department of Medical Lab Technology and Biotechnology, Paramedical College Durgapur, West Bengal, 713212, India
| | - Krishnendu Ganguly
- Department of Medical Lab Technology and Biotechnology, Paramedical College Durgapur, West Bengal, 713212, India
| | - Riya Sarkar
- Department of Medical Laboratory Technology, Dr. B. C. Roy Academy of Professional Courses, Durgapur, West Bengal, 713206, India
| | - Satyajit Mohanty
- Department of Advanced Pharmacology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Rumpa Dhua
- Department of Nutrition, Bankura Sammilani College, Kenduadihi, Bankura, West Bengal, 722102, India
| | - Koushik Bhattacharya
- School of Paramedics and Allied Health Sciences, Centurion University of Technology and Management, Jatni, Bhubaneswar, Odisha, 752050, India
| | - Deepika Ahuja
- School of Paramedics and Allied Health Sciences, Centurion University of Technology and Management, Jatni, Bhubaneswar, Odisha, 752050, India
| | - Suchandra Pal
- Department of Biotechnology, National Institute of Technology, Durgapur, West Bengal, 713209, India
| | - Rajkumar Maiti
- Department of Physiology, Bankura Christian College, Bankura, West Bengal, 722101, India
| |
Collapse
|
28
|
Koch NG, Budisa N. Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion. Chem Rev 2024; 124:9580-9608. [PMID: 38953775 PMCID: PMC11363022 DOI: 10.1021/acs.chemrev.4c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024]
Abstract
Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific archaea. Our Review provides an overview of how the once obscure pyrrolysyl-tRNA synthetase (PylRS) tRNA pair, originally responsible for accurately translating enzymes crucial in methanogenic metabolic pathways, laid the foundation for the burgeoning field of genetic code expansion. Our primary focus is the discussion of how to successfully engineer the PylRS to recognize new substrates and exhibit higher in vivo activity. We have compiled a comprehensive list of ncAAs incorporable with the PylRS system. Additionally, we also summarize recent successful applications of the PylRS system in creating innovative therapeutic solutions, such as new antibody-drug conjugates, advancements in vaccine modalities, and the potential production of new antimicrobials.
Collapse
Affiliation(s)
- Nikolaj G. Koch
- Department
of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Nediljko Budisa
- Biocatalysis
Group, Institute of Chemistry, Technische
Universität Berlin, 10623 Berlin, Germany
- Chemical
Synthetic Biology Chair, Department of Chemistry, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| |
Collapse
|
29
|
Ivachtchenko AV, Khvat AV, Shkil DO. Development and Prospects of Furin Inhibitors for Therapeutic Applications. Int J Mol Sci 2024; 25:9199. [PMID: 39273149 PMCID: PMC11394684 DOI: 10.3390/ijms25179199] [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: 07/22/2024] [Revised: 08/17/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
Furin, a serine protease enzyme located in the Golgi apparatus of animal cells, plays a crucial role in cleaving precursor proteins into their mature, active forms. It is ubiquitously expressed across various tissues, including the brain, lungs, gastrointestinal tract, liver, pancreas, and reproductive organs. Since its discovery in 1990, furin has been recognized as a significant therapeutic target, leading to the active development of furin inhibitors for potential use in antiviral, antibacterial, anticancer, and other therapeutic applications. This review provides a comprehensive overview of the progress in the development and characterization of furin inhibitors, encompassing peptides, linear and macrocyclic peptidomimetics, and non-peptide compounds, highlighting their potential in the treatment of both infectious and non-infectious diseases.
Collapse
|
30
|
West AC, Harpur CM, Le Page MA, Lam M, Hodges C, Ely LK, Gearing AJ, Tate MD. Harnessing Endogenous Peptide Compounds as Potential Therapeutics for Severe Influenza. J Infect Dis 2024; 230:e384-e394. [PMID: 38060822 PMCID: PMC11326819 DOI: 10.1093/infdis/jiad566] [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: 07/18/2023] [Accepted: 12/05/2023] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND Excessive pulmonary inflammation and damage are characteristic features of severe influenza virus infections. LAT8881 is a synthetic 16-amino acid cyclic peptide form of a naturally occurring C-terminal fragment of human growth hormone with therapeutic efficacy against influenza. Shorter linear peptides are typically easier to manufacture and formulate for delivery than larger cyclic peptides. A 6-amino acid linear peptide fragment of LAT8881, LAT9997, was investigated as a potential influenza therapy. METHODS LAT9997 was evaluated for its potential to limit disease in a preclinical mouse model of severe influenza infection. RESULTS Intranasal treatment of mice with either LAT8881 or LAT9997 from day 1 following influenza infection significantly improved survival outcomes. Initiating LAT9997 treatment at the onset of severe disease also significantly improved disease severity. Greater disease resistance in LAT9997-treated mice correlated with reduced lung immunopathology, damage markers, vascular leak, and epithelial cell death. Treatment reduced viral loads, cytokines, and neutrophil infiltration in the airways yet maintained protective alveolar macrophages in a dose-dependent manner. Sequential trimming of N- and C-terminal amino acids from LAT9997 revealed a structure-activity relationship. CONCLUSIONS These findings provide preclinical evidence that therapeutic LAT9997 treatment limits viral burden and characteristic features of severe influenza, including hyperinflammation and lung damage. SUMMARY Excessive pulmonary inflammation and damage are characteristic features of severe influenza virus infections. LAT9997 is a linear peptide fragment derived from human growth hormone. This study provides preclinical evidence that therapeutic LAT9997 treatment limits viral burden, hyperinflammation, and lung damage.
Collapse
Affiliation(s)
- Alison C West
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research
- Department of Molecular and Translational Sciences, Monash University, Clayton
| | - Christopher M Harpur
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research
- Department of Molecular and Translational Sciences, Monash University, Clayton
| | - Mélanie A Le Page
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research
- Department of Molecular and Translational Sciences, Monash University, Clayton
| | - Maggie Lam
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research
- Department of Molecular and Translational Sciences, Monash University, Clayton
| | - Christopher Hodges
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research
- Department of Molecular and Translational Sciences, Monash University, Clayton
| | | | | | - Michelle D Tate
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research
- Department of Molecular and Translational Sciences, Monash University, Clayton
| |
Collapse
|
31
|
Yu Y, Gu M, Guo H, Deng Y, Chen D, Wang J, Wang C, Liu X, Yan W, Huang J. MuCoCP: a priori chemical knowledge-based multimodal contrastive learning pre-trained neural network for the prediction of cyclic peptide membrane penetration ability. Bioinformatics 2024; 40:btae473. [PMID: 39067027 PMCID: PMC11315609 DOI: 10.1093/bioinformatics/btae473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/04/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024] Open
Abstract
MOTIVATION There has been a burgeoning interest in cyclic peptide therapeutics due to their various outstanding advantages and strong potential for drug formation. However, it is undoubtedly costly and inefficient to use traditional wet lab methods to clarify their biological activities. Using artificial intelligence instead is a more energy-efficient and faster approach. MuCoCP aims to build a complete pre-trained model for extracting potential features of cyclic peptides, which can be fine-tuned to accurately predict cyclic peptide bioactivity on various downstream tasks. To maximize its effectiveness, we use a novel data augmentation method based on a priori chemical knowledge and multiple unsupervised training objective functions to greatly improve the information-grabbing ability of the model. RESULTS To assay the efficacy of the model, we conducted validation on the membrane-permeability of cyclic peptides which achieved an accuracy of 0.87 and R-squared of 0.503 on CycPeptMPDB using semi-supervised training and obtained an accuracy of 0.84 and R-squared of 0.384 using a model with frozen parameters on an external dataset. This result has achieved state-of-the-art, which substantiates the stability and generalization capability of MuCoCP. It means that MuCoCP can fully explore the high-dimensional information of cyclic peptides and make accurate predictions on downstream bioactivity tasks, which will serve as a guide for the future de novo design of cyclic peptide drugs and promote the development of cyclic peptide drugs. AVAILABILITY AND IMPLEMENTATION All code used in our proposed method can be found at https://github.com/lennonyu11234/MuCoCP.
Collapse
Affiliation(s)
- Yunxiang Yu
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Mengyun Gu
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Hai Guo
- The Second Hospital Clinical Medical School, Lanzhou University, Lanzhou, 730000, China
| | - Yabo Deng
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Danna Chen
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
- The Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, China
- Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, 510180, China
| | - Jianwei Wang
- Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, 510180, China
| | - Caixia Wang
- Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, 510180, China
| | - Xia Liu
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Wenjin Yan
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jinqi Huang
- The Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, China
- Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, 510180, China
| |
Collapse
|
32
|
Xiao Y, Zhou H, Liu H, Li X. Trifluoroacetic Acid Mediated Additive-Free Late-Stage Native Peptide Cyclization to Form Disulfide Mimetics via Thioketalization with Ketones. Org Lett 2024; 26:6512-6517. [PMID: 39046909 DOI: 10.1021/acs.orglett.4c02464] [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: 07/27/2024]
Abstract
Peptide cyclization is often used to introduce conformational rigidity and to enhance the physiological stability of the peptide. This study presents a novel late-stage cyclization method for creating thioketal cyclic peptides from bis-cysteine peptides and drugs. Symmetrical cyclic ketones and acetone were found to react with bis-cysteine unprotected peptides efficiently to form thioketal linkages in trifluoroacetic acid (TFA) without any other additive. The attractive features of this method include high chemoselectivity, operational simplicity, and robustness. In addition, TFA as the reaction solvent can dissolve any unprotected peptide. As a showcase, the dimethyl thioketal versions of lanreotide and octreotide were prepared and evaluated, both of which showed much improved reductive stability and comparable activity.
Collapse
Affiliation(s)
- Yisa Xiao
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Haiyan Zhou
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
- Chemistry and Chemical Engineering Guangdong Laboratory, Shantou, Guangdong Province 515063, People's Republic of China
| | - Han Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| |
Collapse
|
33
|
Lefin N, Herrera-Belén L, Farias JG, Beltrán JF. Review and perspective on bioinformatics tools using machine learning and deep learning for predicting antiviral peptides. Mol Divers 2024; 28:2365-2374. [PMID: 37626205 DOI: 10.1007/s11030-023-10718-3] [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: 05/02/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023]
Abstract
Viruses constitute a constant threat to global health and have caused millions of human and animal deaths throughout human history. Despite advances in the discovery of antiviral compounds that help fight these pathogens, finding a solution to this problem continues to be a task that consumes time and financial resources. Currently, artificial intelligence (AI) has revolutionized many areas of the biological sciences, making it possible to decipher patterns in amino acid sequences that encode different functions and activities. Within the field of AI, machine learning, and deep learning algorithms have been used to discover antimicrobial peptides. Due to their effectiveness and specificity, antimicrobial peptides (AMPs) hold excellent promise for treating various infections caused by pathogens. Antiviral peptides (AVPs) are a specific type of AMPs that have activity against certain viruses. Unlike the research focused on the development of tools and methods for the prediction of antimicrobial peptides, those related to the prediction of AVPs are still scarce. Given the significance of AVPs as potential pharmaceutical options for human and animal health and the ongoing AI revolution, we have reviewed and summarized the current machine learning and deep learning-based tools and methods available for predicting these types of peptides.
Collapse
Affiliation(s)
- Nicolás Lefin
- Department of Chemical Engineering, Faculty of Engineering and Science, University of La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Lisandra Herrera-Belén
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Temuco, Chile
| | - Jorge G Farias
- Department of Chemical Engineering, Faculty of Engineering and Science, University of La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Jorge F Beltrán
- Department of Chemical Engineering, Faculty of Engineering and Science, University of La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
| |
Collapse
|
34
|
Hamers SMWR, Abendstein L, Boyle AL, Jongkees SAK, Sharp TH. Selection and characterization of a peptide-based complement modulator targeting C1 of the innate immune system. RSC Chem Biol 2024; 5:787-799. [PMID: 39092440 PMCID: PMC11289891 DOI: 10.1039/d4cb00081a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/24/2024] [Indexed: 08/04/2024] Open
Abstract
The human complement pathway plays a pivotal role in immune defence, homeostasis, and autoimmunity regulation, and complement-based therapeutics have emerged as promising interventions, with both antagonistic and agonistic approaches being explored. The classical pathway of complement is initiated when the C1 complex binds to hexameric antibody platforms. Recent structural data revealed that C1 binds to small, homogeneous interfaces at the periphery of the antibody platforms. Here, we have developed a novel strategy for complement activation using macrocyclic peptides designed to mimic the interface between antibodies and the C1 complex. In vitro selection utilizing the RaPID system identified a cyclic peptide (cL3) that binds to the C1 complex via the globular head domains of C1q. Notably, when immobilized on surfaces, cL3 effectively recruits C1 from human serum, activates C1s proteases, and induces lysis of cell-mimetic lipid membranes. This represents the first instance of a peptide capable of activating complement by binding C1 when immobilized. Further characterization and synthesis of deletion mutants revealed a critical cycle size of cL3 essential for C1 binding and efficient complement activation. Importantly, cL3 also demonstrated the ability to inhibit complement-mediated lysis without affecting C1 binding, highlighting its potential as a therapeutic modality to prevent complement-dependent cytotoxicity whilst promoting cellular phagocytosis and cell clearance. In summary, this study introduces the concept of "Peptactins" - peptide-based activators of complement - and underscores the potential of macrocyclic peptides for complement modulation, offering potential advantages over traditional biologicals in terms of size, production, and administration.
Collapse
Affiliation(s)
- Sebastiaan M W R Hamers
- Department of Cell and Chemical Biology, Leiden University Medical Centre 2300 RC Leiden The Netherlands
| | - Leoni Abendstein
- Department of Cell and Chemical Biology, Leiden University Medical Centre 2300 RC Leiden The Netherlands
| | - Aimee L Boyle
- Leiden Institute of Chemistry, Leiden University 2333 CC Leiden The Netherlands
- School of Chemistry, University of Bristol Bristol BS8 1QU UK
| | - Seino A K Jongkees
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam 1081 HV Amsterdam The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Centre 2300 RC Leiden The Netherlands
- School of Biochemistry, University of Bristol Bristol BS8 1TD UK
| |
Collapse
|
35
|
Qutub SS, Bhat IA, Maatouk BI, Moosa B, Fakim A, Nawaz K, Diaz-Galicia E, Lin W, Grünberg R, Arold ST, Khashab NM. An Amphiphilic Cell-Penetrating Macrocycle for Efficient Cytosolic Delivery of Proteins, DNA, and CRISPR Cas9. Angew Chem Int Ed Engl 2024; 63:e202403647. [PMID: 38752721 DOI: 10.1002/anie.202403647] [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: 02/21/2024] [Indexed: 07/02/2024]
Abstract
The discovery of safe platforms that can circumvent the endocytic pathway is of great significance for biological therapeutics that are usually degraded during endocytosis. Here we show that a self-assembled and dynamic macrocycle can passively diffuse through the cell membrane and deliver a broad range of biologics, including proteins, CRISPR Cas9, and ssDNA, directly to the cytosol while retaining their bioactivity. Cell-penetrating macrocycle CPM can be easily prepared from the room temperature condensation of diketopyrrolopyrrole lactams with diamines. We attribute the high cellular permeability of CPM to its amphiphilic nature and chameleonic properties. It adopts conformations that partially bury polar groups and expose hydrophobic side chains, thus self-assembling into micellar-like structures. Its superior fluorescence makes CPM trackable inside cells where it follows the endomembrane system. CPM outperformed commercial reagents for biologics delivery and showed high RNA knockdown efficiency of CRISPR Cas9. We envisage that this macrocycle will be an ideal starting point to design and synthesize biomimetic macrocyclic tags that can readily facilitate the interaction and uptake of biomolecules and overcome endosomal digestion.
Collapse
Affiliation(s)
- Somayah S Qutub
- Smart Hybrid Materials (SHMs) Laboratory, Chemistry Program, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Imtiyaz Ahmad Bhat
- Smart Hybrid Materials (SHMs) Laboratory, Chemistry Program, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Current Address: Department of Chemistry, Islamic University of Science and Technology, Awantipora, 192122, Jammu and Kashmir, India
| | - Batoul I Maatouk
- Smart Hybrid Materials (SHMs) Laboratory, Chemistry Program, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Basem Moosa
- Smart Hybrid Materials (SHMs) Laboratory, Chemistry Program, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Aliyah Fakim
- Smart Hybrid Materials (SHMs) Laboratory, Chemistry Program, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Kashif Nawaz
- The Coral Symbiomics Lab, Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Escarlet Diaz-Galicia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Weibin Lin
- Smart Hybrid Materials (SHMs) Laboratory, Chemistry Program, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Raik Grünberg
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Stefan T Arold
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Niveen M Khashab
- Smart Hybrid Materials (SHMs) Laboratory, Chemistry Program, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| |
Collapse
|
36
|
Li J, Yanagisawa K, Akiyama Y. CycPeptMP: enhancing membrane permeability prediction of cyclic peptides with multi-level molecular features and data augmentation. Brief Bioinform 2024; 25:bbae417. [PMID: 39210505 PMCID: PMC11361855 DOI: 10.1093/bib/bbae417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 07/23/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Cyclic peptides are versatile therapeutic agents that boast high binding affinity, minimal toxicity, and the potential to engage challenging protein targets. However, the pharmaceutical utility of cyclic peptides is limited by their low membrane permeability-an essential indicator of oral bioavailability and intracellular targeting. Current machine learning-based models of cyclic peptide permeability show variable performance owing to the limitations of experimental data. Furthermore, these methods use features derived from the whole molecule that have traditionally been used to predict small molecules and ignore the unique structural properties of cyclic peptides. This study presents CycPeptMP: an accurate and efficient method to predict cyclic peptide membrane permeability. We designed features for cyclic peptides at the atom-, monomer-, and peptide-levels and seamlessly integrated these into a fusion model using deep learning technology. Additionally, we applied various data augmentation techniques to enhance model training efficiency using the latest data. The fusion model exhibited excellent prediction performance for the logarithm of permeability, with a mean absolute error of $0.355$ and correlation coefficient of $0.883$. Ablation studies demonstrated that all feature levels contributed and were relatively essential to predicting membrane permeability, confirming the effectiveness of augmentation to improve prediction accuracy. A comparison with a molecular dynamics-based method showed that CycPeptMP accurately predicted peptide permeability, which is otherwise difficult to predict using simulations.
Collapse
Affiliation(s)
- Jianan Li
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo 1528550, Japan
| | - Keisuke Yanagisawa
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo 1528550, Japan
- Middle-Molecule ITbased Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, Tokyo 1528550, Japan
| | - Yutaka Akiyama
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo 1528550, Japan
- Middle-Molecule ITbased Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, Tokyo 1528550, Japan
| |
Collapse
|
37
|
Benny A, Scanlan EM. Synthesis of macrocyclic thiolactone peptides via photochemical intramolecular radical acyl thiol-ene ligation. Chem Commun (Camb) 2024; 60:7950-7953. [PMID: 38985027 DOI: 10.1039/d4cc02442g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
A photochemical acyl thiol-ene reaction can be used to rapidly cyclise fully unprotected peptides bearing both a thioacid and alkene to form peptide thiolactones. This strategy represents the first reported synthesis of peptide thiolactones under radical-mediated conditions.
Collapse
Affiliation(s)
- Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
| |
Collapse
|
38
|
Shao C, Tang B, Chu JCH, Lau KM, Wong WT, Che CM, Tai WCS, Wong WT, Wong CTT. Macrophage-engaging peptidic bispecific antibodies (pBsAbs) for immunotherapy via a facile bioconjugation strategy. Chem Sci 2024; 15:11272-11278. [PMID: 39055004 PMCID: PMC11268508 DOI: 10.1039/d4sc00851k] [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: 02/06/2024] [Accepted: 04/29/2024] [Indexed: 07/27/2024] Open
Abstract
Bispecific antibodies are artificial molecules that fuse two different antigen-binding sites of monoclonal antibodies into one single entity. They have emerged as a promising next-generation anticancer treatment. Despite the fascinating applications of bispecific antibodies, the design and production of bispecific antibodies remain tedious and challenging, leading to a long R&D process and high production costs. We herein report an unprecedented strategy to cyclise and conjugate tumour-targeting peptides on the surface of a monoclonal antibody to form a novel type of bispecific antibody, namely the peptidic bispecific antibody (pBsAb). Such design combines the merits of highly specific monoclonal antibodies and serum-stable cyclic peptides that endows an additional tumour-targeting ability to the monoclonal antibody for binding with two different antigens. Our results show that the novel pBsAb, which comprises EGFR-binding cyclic peptides and an anti-SIRP-α monoclonal antibody, could serve as a macrophage-engaging bispecific antibody to initiate enhanced macrophage-cancer cell interaction and block the "don't eat me" signal between CD47-SIRP-α, as well as promoting antibody-dependent cellular phagocytosis and 3D cell spheroid infiltration. These findings give rise to a new type of bispecific antibody and a new platform for the rapid generation of new bispecific antibodies for research and potential therapeutic uses.
Collapse
Affiliation(s)
- Chihao Shao
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Bo Tang
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Jacky C H Chu
- Laboratory for Synthetic Chemistry and Chemical Biology Limited Units 1503-1511, 15/F, Building 17W, Hong Kong Science Park New Territories Hong Kong China
| | - Kwai Man Lau
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Wai-Ting Wong
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Chi-Ming Che
- Laboratory for Synthetic Chemistry and Chemical Biology Limited Units 1503-1511, 15/F, Building 17W, Hong Kong Science Park New Territories Hong Kong China
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - William C S Tai
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Wing-Tak Wong
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Clarence T T Wong
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| |
Collapse
|
39
|
Ding Y, Pedersen SS, Wang H, Xiang B, Wang Y, Yang Z, Gao Y, Morosan E, Jones MR, Xiao H, Ball ZT. Selective Macrocyclization of Unprotected Peptides with an Ex Situ Gaseous Linchpin Reagent. Angew Chem Int Ed Engl 2024; 63:e202405344. [PMID: 38753429 DOI: 10.1002/anie.202405344] [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: 03/18/2024] [Indexed: 07/16/2024]
Abstract
Peptide cyclization has dramatic effects on a variety of important properties, enhancing metabolic stability, limiting conformational flexibility, and altering cellular entry and intracellular localization. The hydrophilic, polyfunctional nature of peptides creates chemoselectivity challenges in macrocyclization, especially for natural sequences without biorthogonal handles. Herein, we describe a gaseous sulfonyl chloride derived reagent that achieves amine-amine, amine-phenol, and amine-aniline crosslinking through a minimalist linchpin strategy that affords macrocyclic urea or carbamate products. The cyclization reaction is metal-mediated and involves a novel application of sulfine species that remains unexplored in aqueous or biological contexts. The aqueous method delivers unique cyclic or bicyclic topologies directly from a variety of natural bioactive peptides without the need for protecting-group strategies.
Collapse
Affiliation(s)
- Yuxuan Ding
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Simon S Pedersen
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
- Carbon Dioxide Activation Center (CADIAC), Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Haofan Wang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Baorui Xiang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Yixian Wang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Zhi Yang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Yuxiang Gao
- Department of Physics and Astronomy, Rice University, Houston, Texas, 77005, United States
| | - Emilia Morosan
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
- Department of Physics and Astronomy, Rice University, Houston, Texas, 77005, United States
| | - Matthew R Jones
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Han Xiao
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Zachary T Ball
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| |
Collapse
|
40
|
Song L, Liu H, Li M, Yang Y, Dong H, Li J, Shao J, Zhi L, Sun H, Li Z, Sui H, Zhang Y, Wu C, Yin Y. Ribosomal Incorporation of Lithocholic Acid into Peptides for the De Novo Discovery Of Peptide-Lithocholic Acid Hybrid Macrocyclic Peptides. ACS Chem Biol 2024; 19:1440-1446. [PMID: 38901034 DOI: 10.1021/acschembio.4c00298] [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: 06/22/2024]
Abstract
Peptide-bile acid hybrids offer promising drug candidates due to enhanced pharmacological properties, such as improved protease resistance and oral bioavailability. However, it remains unknown whether bile acids can be incorporated into peptide chains by the ribosome to produce a peptide-bile acid hybrid macrocyclic peptide library for target-based de novo screening. In this study, we achieved the ribosomal incorporation of lithocholic acid (LCA)-d-tyrosine into peptide chains. This led to the construction of a peptide-LCA hybrid macrocyclic peptide library, which enabled the identification of peptides TP-2C-4L3 (targeting Trop2) and EP-2C-4L5 (targeting EphA2) with strong binding affinities. Notably, LCA was found to directly participate in binding to EphA2 and confer on the peptides improved stability and resistance to proteases. Cell staining experiments confirmed the high specificity of the peptides for targeting Trop2 and EphA2. This study highlights the benefits of LCA in peptides and paves the way for de novo discovery of stable peptide-LCA hybrid drugs.
Collapse
Affiliation(s)
- Lulu Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Hongtan Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Maolin Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yawen Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Huilei Dong
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Jinjing Li
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Jiaqi Shao
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lixu Zhi
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Sun
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhifeng Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Haiyan Sui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Chuanliu Wu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
- Shandong Research Institute of Industrial Technology, Jinan 250101, China
| |
Collapse
|
41
|
Lamartina CW, Chartier CA, Hirano JM, Shah NH, Rovis T. Crafting Unnatural Peptide Macrocycles via Rh(III)-Catalyzed Carboamidation. J Am Chem Soc 2024. [PMID: 39024122 DOI: 10.1021/jacs.4c05248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Contemporary developments in the field of peptide macrocyclization methodology are imperative for enabling the advance of drug design in medicinal chemistry. This report discloses a Rh(III)-catalyzed macrocyclization via carboamidation, reacting acryloyl-peptide-dioxazolone precursors and arylboronic acids to form complex cyclic peptides with concomitant incorporation of noncanonical α-amino acids. The diverse and modular technology allows for expedient access to a wide variety of cyclic peptides from 4 to 15 amino acids in size and features simultaneous formation of unnatural phenylalanine and tyrosine derivatives with up to >20:1 diastereoselectivity. The reaction showcases an expansive substrate scope with 45 examples and is compatible with the majority of standard protected amino acids used in Fmoc-solid phase peptide synthesis. The methodology is applied to the synthesis of multiple peptidomimetic macrocyclic analogs, including derivatives of cyclosomatostatin and gramicidin S.
Collapse
Affiliation(s)
| | - Cassandra A Chartier
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jillian M Hirano
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| |
Collapse
|
42
|
Xiao Y, Zhou H, Shi P, Zhao X, Liu H, Li X. Clickable tryptophan modification for late-stage diversification of native peptides. SCIENCE ADVANCES 2024; 10:eadp9958. [PMID: 38985871 PMCID: PMC11235173 DOI: 10.1126/sciadv.adp9958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/10/2024] [Indexed: 07/12/2024]
Abstract
As the least abundant residue in proteins, tryptophan widely exists in peptide drugs and bioactive natural products and contributes to drug-target interactions in multiple ways. We report here a clickable tryptophan modification for late-stage diversification of native peptides, via catalyst-free C2-sulfenylation with 8-quinoline thiosulfonate reagents in trifluoroacetic acid (TFA). A wide range of groups including trifluoromethylthio (SCF3), difluoromethylthio (SCF2H), (ethoxycarbonyl)difluoromethylthio (SCF2CO2Et), alkylthio, and arylthio were readily incorporated. The rapid reaction kinetics of Trp modification and full tolerance with other 19 proteinogenic amino acids, as well as the super dissolving capability of TFA, render this method suitable for all kinds of Trp-containing peptides without limitations from sequences, hydrophobicity, and aggregation propensity. The late-stage modification of 15 therapeutic peptides (1.0 to 7.6 kilodaltons) and the improved bioactivity and serum stability of SCF3- and SCF2H-modified melittin analogs illustrated the effectiveness of this method and its potential in pharmacokinetic property improvement.
Collapse
Affiliation(s)
- Yisa Xiao
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Haiyan Zhou
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
- Chemistry and Chemical Engineering Guangdong Laboratory, Shantou, Guangdong Province 515063, P. R. China
| | - Pengfei Shi
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Xueqian Zhao
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, P. R. China
| | - Han Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| |
Collapse
|
43
|
Hu L, Lin J, Qin F, Xu L, Luo L. Exploring Sources, Biological Functions, and Potential Applications of the Ubiquitous Marine Cyclic Dipeptide: A Concise Review of Cyclic Glycine-Proline. Mar Drugs 2024; 22:271. [PMID: 38921582 PMCID: PMC11205142 DOI: 10.3390/md22060271] [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: 05/14/2024] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
Cyclic glycine-proline (cGP), a prevalent marine cyclic dipeptide, possesses a distinct pyrrolidine-2,5-dione scaffold, which contributes to the chemical diversity and broad bioactivities of cGP. The diverse sources from marine-related, endogenous biological, and synthetic pathways and the in vitro and in vivo activities of cGP are reviewed. The potential applications for cGP are also explored. In particular, the pivotal roles of cGP in regulating insulin-like growth factor-1 homeostasis, enhancing neuroprotective effects, and improving neurotrophic function in central nervous system diseases are described. The potential roles of this endogenous cyclic peptide in drug development and healthcare initiatives are also highlighted. This review underscores the significance of cGP as a fundamental building block in drug discovery with exceptional drug-like properties and safety. By elucidating the considerable value of cGP, this review aims to reignite interest in cGP-related research within marine medicinal chemistry and synthetic biology.
Collapse
Affiliation(s)
- Lei Hu
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Jing Lin
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Fei Qin
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Li Xu
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Lianzhong Luo
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| |
Collapse
|
44
|
Bak-Sypien I, Pawlak T, Paluch P, Wroblewska A, Dolot R, Pawlowicz A, Szczesio M, Wielgus E, Kaźmierski S, Górecki M, Pawlowska R, Chworos A, Potrzebowski MJ. Influence of heterochirality on the structure, dynamics, biological properties of cyclic(PFPF) tetrapeptides obtained by solvent-free ball mill mechanosynthesis. Sci Rep 2024; 14:12825. [PMID: 38834643 DOI: 10.1038/s41598-024-63552-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
Cyclic tetrapeptides c(Pro-Phe-Pro-Phe) obtained by the mechanosynthetic method using a ball mill were isolated in a pure stereochemical form as a homochiral system (all L-amino acids, sample A) and as a heterochiral system with D configuration at one of the stereogenic centers of Phe (sample B). The structure and stereochemistry of both samples were determined by X-ray diffraction studies of single crystals. In DMSO and acetonitrile, sample A exists as an equimolar mixture of two conformers, while only one is monitored for sample B. The conformational space and energetic preferences for possible conformers were calculated using DFT methods. The distinctly different conformational flexibility of the two samples was experimentally proven by Variable Temperature (VT) and 2D EXSY NMR measurements. Both samples were docked to histone deacetylase HDAC8. Cytotoxic studies proved that none of the tested cyclic peptide is toxic.
Collapse
Affiliation(s)
- Irena Bak-Sypien
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Piotr Paluch
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aneta Wroblewska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Rafał Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aleksandra Pawlowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 St., 61-704, Poznan, Poland
| | - Małgorzata Szczesio
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116 St., 90-924, Lodz, Poland
| | - Ewelina Wielgus
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Sławomir Kaźmierski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224, Warsaw, Poland
| | - Roza Pawlowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marek J Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland.
| |
Collapse
|
45
|
Matsuda K, Wakimoto T. Penicillin-binding protein-type thioesterases: An emerging family of non-ribosomal peptide cyclases with biocatalytic potentials. Curr Opin Chem Biol 2024; 80:102465. [PMID: 38759287 DOI: 10.1016/j.cbpa.2024.102465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/19/2024]
Abstract
Macrocyclization of peptides reduces conformational flexibilities, potentially leading to improved drug-like properties, such as target specificities and metabolic stabilities. As chemical methodologies often allow side reactions like epimerization and oligomerization, keen attention has been directed toward enzymatic peptide cyclization using peptide cyclases from specialized metabolic pathways. Penicillin-binding protein-type thioesterases (PBP-type TEs) are a recently identified family of peptide cyclases involved in the biosynthesis of non-ribosomal peptides in actinobacteria. PBP-type TEs have undergone intensive investigation due to their outstanding potential as biocatalysts. This review summarizes the rapidly growing knowledge on PBP-type TEs, with special emphasis on their functions, scopes, and structures, and efforts towards their biocatalytic applications.
Collapse
Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.
| |
Collapse
|
46
|
Zuo Q, Li Y, Lai X, Bao G, Chen L, He Z, Song X, E R, Wang P, Shi Y, Luo H, Sun W, Wang R. Cysteine-Specific Multifaceted Bioconjugation of Peptides and Proteins Using 5-Substituted 1,2,3-Triazines. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308491. [PMID: 38466927 DOI: 10.1002/advs.202308491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/08/2024] [Indexed: 03/13/2024]
Abstract
Peptide and protein postmodification have gained significant attention due to their extensive impact on biomolecule engineering and drug discovery, of which cysteine-specific modification strategies are prominent due to their inherent nucleophilicity and low abundance. Herein, the study introduces a novel approach utilizing multifunctional 5-substituted 1,2,3-triazine derivatives to achieve multifaceted bioconjugation targeting cysteine-containing peptides and proteins. On the one hand, this represents an inaugural instance of employing 1,2,3-triazine in biomolecular-specific modification within a physiological solution. On the other hand, as a powerful combination of precision modification and biorthogonality, this strategy allows for the one-pot dual-orthogonal functionalization of biomolecules utilizing the aldehyde group generated simultaneously. 1,2,3-Triazine derivatives with diverse functional groups allow conjugation to peptides or proteins, while bi-triazines enable peptide cyclization and dimerization. The examination of the stability of bi-triazines revealed their potential for reversible peptide modification. This work establishes a comprehensive platform for identifying cysteine-selective modifications, providing new avenues for peptide-based drug development, protein bioconjugation, and chemical biology research.
Collapse
Affiliation(s)
- 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, Xian Nong Tan Street, Beijing, 100050, P. R. China
| | - Yiping Li
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, Lanzhou University, 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China
| | - Xuanliang Lai
- 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, Xian Nong Tan Street, Beijing, 100050, P. R. China
| | - Guangjun Bao
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, Lanzhou University, 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China
| | - Lu Chen
- 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, Xian Nong Tan Street, Beijing, 100050, P. R. China
| | - Zeyuan He
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, Lanzhou University, 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China
| | - Xinyi Song
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, Lanzhou University, 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China
| | - Ruiyao E
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, Lanzhou University, 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China
| | - Pengxin Wang
- 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, Xian Nong Tan Street, Beijing, 100050, P. R. China
| | - Yuntao Shi
- 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, Xian Nong Tan Street, Beijing, 100050, P. R. China
| | - Huixin Luo
- 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, Xian Nong Tan Street, Beijing, 100050, P. R. China
| | - Wangsheng Sun
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, Lanzhou University, 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China
| | - Rui Wang
- 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, Xian Nong Tan Street, Beijing, 100050, P. R. China
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, Lanzhou University, 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China
| |
Collapse
|
47
|
Min P, Li Y, Wang C, Fan J, Liu S, Chen X, Tang Y, Han F, Zhang A, Feng L. Cyclopeptide moroidin inhibits vasculogenic mimicry formed by glioblastoma cells via regulating β-catenin activation and EMT pathways. J Biomed Res 2024; 38:322-333. [PMID: 38807414 PMCID: PMC11300521 DOI: 10.7555/jbr.38.20240015] [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: 01/19/2024] [Revised: 04/30/2024] [Accepted: 05/10/2024] [Indexed: 05/30/2024] Open
Abstract
Glioblastoma (GBM) is a highly vascularized malignant brain tumor with poor clinical outcomes. Vasculogenic mimicry (VM) formed by aggressive GBM cells is an alternative approach for tumor blood supply and contributes to the failure of anti-angiogenic therapy. To date, there is still a lack of effective drugs that target VM formation in GBM. In the present study, we evaluated the effects of the plant cyclopeptide moroidin on VM formed by GBM cells and investigated its underlying molecular mechanisms. Moroidin significantly suppressed cell migration, tube formation, and the expression levels of α-smooth muscle actin and matrix metalloproteinase-9 in human GBM cell lines at sublethal concentrations. The RNA sequencing data suggested the involvement of the epithelial-mesenchymal transition (EMT) pathway in the mechanism of moroidin. Exposure to moroidin led to a concentration-dependent decrease in the expression levels of the EMT markers N-cadherin and vimentin in GBM cells. Moreover, moroidin significantly reduced the level of phosphorylated extracellular signal-regulated protein kinase (p-ERK) and inhibited the activation of β-catenin. Finally, we demonstrated that the plant cyclopeptide moroidin inhibited VM formation by GBM cells through inhibiting the ERK/β-catenin-mediated EMT. Therefore, our study indicates a potential application of moroidin as an anti-VM agent in the treatment of GBM.
Collapse
Affiliation(s)
- Pengxiang Min
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yingying Li
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Cuirong Wang
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Junting Fan
- Department of Pharmaceutical Analysis, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Shangming Liu
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xiang Chen
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yamin Tang
- Department of Analysis and Testing Center, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Feng Han
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Institute of Brain Science, the Affiliated Brain Hospital of Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Aixia Zhang
- Department of Clinical Pharmacology, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Lili Feng
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| |
Collapse
|
48
|
Fan XZ, Song JQ, Zhang LJ, Wang R, Liu T, Bai WJ, Kong XQ, Huang YS, Liang H, Liao HB. Picrachinentins A-F, 14-Membered Cyclopeptide Alkaloid-Type Burpitides with Uncommon N-Terminal Modifications from Picrasma chinensis and Their Neuroprotective Activity. Org Lett 2024. [PMID: 38787765 DOI: 10.1021/acs.orglett.4c01390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Picrachinentins A-F (1-6, respectively), six novel cyclopeptide alkaloid-type burpitides (CPABs), were isolated and fully elucidated from the EtOH extract of the stems and leaves of Picrasma chinensis. Structurally, compounds 1-6 have a 14-membered paracyclophane ring system that was closed through an ether bond between the β-hydroxy amino acid and tyrosine and modified with a 4,5-methylenedioxybenzoyloxy (MDBz, 3 and 5) or hexanoyl (Hexa, 1, 2, 4, and 6) group at the N-terminus. Interestingly, this is the first report on the isolation and characterization of CPABs from plants of the Simaroubaceae family. In addition, all compounds showed a neuroprotective effect against H2O2-damaged SH-SY5Y cells. Compound 1 was further investigated for its neuroprotective activities using a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced Parkinson's disease animal model, and it dramatically improved MPTP-impaired motor behavioral performance. Biochemical analysis revealed compound 1 restored the tyrosine hydroxylase expression in the striatum of the MPTP-damaged mouse brain, which demonstrates its protective effect on dopaminergic neurons.
Collapse
Affiliation(s)
- Xian-Zhe Fan
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Jia-Qi Song
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Li-Jun Zhang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Rong Wang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Ting Liu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Wen-Jing Bai
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiang-Qian Kong
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Ya-Si Huang
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Hong Liang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Hai-Bing Liao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| |
Collapse
|
49
|
Bruce A, Adebomi V, Czabala P, Palmer J, McFadden WM, Lorson ZC, Slack RL, Bhardwaj G, Sarafianos SG, Raj M. A Tag-Free Platform for Synthesis and Screening of Cyclic Peptide Libraries. Angew Chem Int Ed Engl 2024; 63:e202320045. [PMID: 38529717 PMCID: PMC11254100 DOI: 10.1002/anie.202320045] [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: 12/26/2023] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
In the realm of high-throughput screening (HTS), macrocyclic peptide libraries traditionally necessitate decoding tags, essential for both library synthesis and identifying hit peptide sequences post-screening. Our innovation introduces a tag-free technology platform for synthesizing cyclic peptide libraries in solution and facilitates screening against biological targets to identify peptide binders through unconventional intramolecular CyClick and DeClick chemistries (CCDC) discovered through our research. This combination allows for the synthesis of diverse cyclic peptide libraries, the incorporation of various amino acids, and facile linearization and decoding of cyclic peptide binder sequences. Our sensitivity-enhancing derivatization method, utilized in tandem with nano LC-MS/MS, enables the sequencing of peptides even at exceedingly low picomolar concentrations. Employing our technology platform, we have successfully unearthed novel cyclic peptide binders against a monoclonal antibody and the first cyclic peptide binder of HIV capsid protein responsible for viral infections as validated by microscale thermal shift assays (TSA), biolayer interferometry (BLI) and functional assays.
Collapse
Affiliation(s)
- Angele Bruce
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
| | - Victor Adebomi
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States, 98195
| | - Patrick Czabala
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
| | - Jonathan Palmer
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States, 98195
| | - William M McFadden
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA, 30322, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - Zachary C Lorson
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA, 30322, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - Ryan L Slack
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA, 30322, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - Gaurav Bhardwaj
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States, 98195
| | - Stefan G Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA, 30322, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
| |
Collapse
|
50
|
Saunders GJ, Spring SA, Jayawant E, Wilkening I, Roesner S, Clarkson GJ, Dixon AM, Notman R, Shipman M. Synthesis and Functionalization of Azetidine-Containing Small Macrocyclic Peptides. Chemistry 2024; 30:e202400308. [PMID: 38488326 DOI: 10.1002/chem.202400308] [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: 02/25/2024] [Indexed: 04/11/2024]
Abstract
Cyclic peptides are increasingly important structures in drugs but their development can be impeded by difficulties associated with their synthesis. Here, we introduce the 3-aminoazetidine (3-AAz) subunit as a new turn-inducing element for the efficient synthesis of small head-to-tail cyclic peptides. Greatly improved cyclizations of tetra-, penta- and hexapeptides (28 examples) under standard reaction conditions are achieved by introduction of this element within the linear peptide precursor. Post-cyclization deprotection of the amino acid side chains with strong acid is realized without degradation of the strained four-membered azetidine. A special feature of this chemistry is that further late-stage modification of the resultant macrocyclic peptides can be achieved via the 3-AAz unit. This is done by: (i) chemoselective deprotection and substitution at the azetidine nitrogen, or by (ii) a click-based approach employing a 2-propynyl carbamate on the azetidine nitrogen. In this way, a range of dye and biotin tagged macrocycles are readily produced. Structural insights gained by XRD analysis of a cyclic tetrapeptide indicate that the azetidine ring encourages access to the less stable, all-trans conformation. Moreover, introduction of a 3-AAz into a representative cyclohexapeptide improves stability towards proteases compared to the homodetic macrocycle.
Collapse
Affiliation(s)
- George J Saunders
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Sam A Spring
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Eleanor Jayawant
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Ina Wilkening
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Stefan Roesner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Guy J Clarkson
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Ann M Dixon
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Rebecca Notman
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Michael Shipman
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
- The Palatine Centre, Stockton Road, Durham, DH1 3LE, U.K
| |
Collapse
|