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Zhai S, Tan Y, Zhu C, Zhang C, Gao Y, Mao Q, Zhang Y, Duan H, Yin Y. PepExplainer: An explainable deep learning model for selection-based macrocyclic peptide bioactivity prediction and optimization. Eur J Med Chem 2024; 275:116628. [PMID: 38944933 DOI: 10.1016/j.ejmech.2024.116628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/02/2024]
Abstract
Macrocyclic peptides possess unique features, making them highly promising as a drug modality. However, evaluating their bioactivity through wet lab experiments is generally resource-intensive and time-consuming. Despite advancements in artificial intelligence (AI) for bioactivity prediction, challenges remain due to limited data availability and the interpretability issues in deep learning models, often leading to less-than-ideal predictions. To address these challenges, we developed PepExplainer, an explainable graph neural network based on substructure mask explanation (SME). This model excels at deciphering amino acid substructures, translating macrocyclic peptides into detailed molecular graphs at the atomic level, and efficiently handling non-canonical amino acids and complex macrocyclic peptide structures. PepExplainer's effectiveness is enhanced by utilizing the correlation between peptide enrichment data from selection-based focused library and bioactivity data, and employing transfer learning to improve bioactivity predictions of macrocyclic peptides against IL-17C/IL-17 RE interaction. Additionally, PepExplainer underwent further validation for bioactivity prediction using an additional set of thirteen newly synthesized macrocyclic peptides. Moreover, it enabled the optimization of the IC50 of a macrocyclic peptide, reducing it from 15 nM to 5.6 nM based on the contribution score provided by PepExplainer. This achievement underscores PepExplainer's skill in deciphering complex molecular patterns, highlighting its potential to accelerate the discovery and optimization of macrocyclic peptides.
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Affiliation(s)
- Silong Zhai
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yahong Tan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Cheng Zhu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Chengyun Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yan Gao
- Qilu Institute of Technology, Jinan, 250200, China
| | - Qingyi Mao
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Hongliang Duan
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, 999078, 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.
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2
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Nii M, Yamaguchi K, Tojo T, Narushima N, Aoki S. Induction of Paraptotic Cell Death in Cancer Cells by Triptycene-Peptide Hybrids and the Revised Mechanism of Paraptosis II. Biochemistry 2024. [PMID: 39140188 DOI: 10.1021/acs.biochem.4c00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
In previous work, we reported on iridium(III) (Ir(III)) complex-peptide hybrids as amphiphilic conjugates (IPH-ACs) and triptycene-peptide hybrids as amphiphilic conjugates (TPH-ACs) and found that these hybrid compounds containing three cationic KK(K)GG peptide units through C6-C8 alkyl linkers induce paraptosis II, which is one of the nonapoptotic programmed cell death (PCD) types in Jurkat cells and different from previously reported paraptosis. The details of that study revealed that the paraptosis II induced by IPH-ACs (and TPH-ACs) proceeds via a membrane fusion or tethering of the endoplasmic reticulum (ER) and mitochondria, and Ca2+ transfer from the ER to mitochondria, which results in a loss of mitochondrial membrane potential (ΔΨm) in Jurkat cells. However, the detailed mechanistic studies of paraptosis II have been conducted only in Jurkat cells. In the present work, we decided to conduct mechanistic studies of paraptosis II in HeLa-S3 and A549 cells as well as in Jurkat cells to study the general mechanism of paraptosis II. Simultaneously, we designed and synthesized new TPH-ACs functionalized with peptides that contain cyclohexylalanine, which had been reported to enhance the localization of peptides to mitochondria. We found that TPH-ACs containing cyclohexylalanine promote paraptosis II processes in Jurkat, HeLa-S3 and A549 cells. The results of the experiments using fluorescence Ca2+ probes in mitochondria and cytosol, fluorescence staining agents of mitochondria and the ER, and inhibitors of paraptosis II suggest that TPH-ACs induce Ca2+ increase in mitochondria and the membrane fusion between the ER and mitochondria almost simultaneously, suggesting that our previous hypothesis on the mechanism of paraptosis II should be revised.
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Affiliation(s)
- Mayuka Nii
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan
| | - Kohei Yamaguchi
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan
| | - Toshifumi Tojo
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan
- Research Institute for Science and Technology (RIST), Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Nozomi Narushima
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan
| | - Shin Aoki
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan
- Research Institute for Science and Technology (RIST), Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Research Institute for Biomedical Sciences (RIBS), Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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3
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Feller AL, Wilke CO. Peptide-specific 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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Biological language modeling 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, able to 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.
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Affiliation(s)
- Aaron L Feller
- Interdisciplinary Life Sciences, The University of Texas, Austin
| | - Claus O Wilke
- Department of Integrative Biology, The University of Texas, Austin
- Interdisciplinary Life Sciences, The University of Texas, Austin
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4
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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.
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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
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5
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Li T, Jiang S, Li T, Xu H, Zhang X, Yan R, Wu X, Jin Y, Wang Z. Exploring the Potential of Cyclic Peptidyl Antitumor Agents Derived from Natural Macrocyclic Peptide Phakellistatin 13. J Med Chem 2024; 67:11789-11813. [PMID: 38990190 DOI: 10.1021/acs.jmedchem.4c00393] [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: 07/12/2024]
Abstract
The exploration of novel anticancer compounds based on natural cyclopeptides has emerged as a pivotal paradigm in the contemporary advancement of macrocyclic pharmaceuticals. Phakellistatin 13 is a cycloheptapeptide derived from the brown snubby sponge and exhibits remarkable antitumor activity. In this study, we have designed and synthesized a series of chiral cyclopeptides incorporating the rigid isoindolinone moiety at various sites within the natural cycloheptapeptide Phakellistatin 13, with the aim of investigating conformationally constrained cyclopeptides as potential antitumor agents. Cyclopeptide 3, comprising alternating l-/d-amino acid residues, exhibited promising antihepatocellular carcinoma effects. Detailed biological experiments have revealed that Phakellistatin 13 analogs effectively inhibit the proliferation of tumor cells and induce apoptosis and autophagy, while also causing cell cycle arrest through the modulation of the p53 and mitogen-activated protein kinase (MAPK) signaling pathway. This study not only provides valuable insights into chemical structural modifications but also contributes to a deeper understanding of the biological mechanisms underlying the development of natural cyclopeptide-based drugs.
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Affiliation(s)
- Tong Li
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Shitian Jiang
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Tingting Li
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Hongyu Xu
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Xiong Zhang
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Rui Yan
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Xiaodan Wu
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Yingxue Jin
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Zhiqiang Wang
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
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6
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Eslami SM, Padhi C, Rahman IR, van der Donk WA. Expression and Subcellular Localization of Lanthipeptides in Human Cells. ACS Synth Biol 2024; 13:2128-2140. [PMID: 38925629 PMCID: PMC11264318 DOI: 10.1021/acssynbio.4c00178] [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: 03/11/2024] [Revised: 05/19/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
Cyclic peptides, such as most ribosomally synthesized and post-translationally modified peptides (RiPPs), represent a burgeoning area of interest in therapeutic and biotechnological research because of their conformational constraints and reduced susceptibility to proteolytic degradation compared to their linear counterparts. Herein, an expression system is reported that enables the production of structurally diverse lanthipeptides and derivatives in mammalian cells. Successful targeting of lanthipeptides to the nucleus, the endoplasmic reticulum, and the plasma membrane is demonstrated. In vivo expression and targeting of such peptides in mammalian cells may allow for screening of lanthipeptide-based cyclic peptide inhibitors of native, organelle-specific protein-protein interactions in mammalian systems.
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Affiliation(s)
- Sara M. Eslami
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Chandrashekhar Padhi
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Imran R. Rahman
- Department
of Biochemistry, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Biochemistry, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
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7
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Mori T, Sumida S, Sakata K, Shirakawa S. Efficient synthetic methods for α,β-dehydroamino acids as useful and environmentally benign building blocks in biological and materials science. Org Biomol Chem 2024; 22:4625-4636. [PMID: 38804977 DOI: 10.1039/d4ob00507d] [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: 05/29/2024]
Abstract
Both natural and unnatural amino acids, peptides, and proteins are widely recognized as green and sustainable organic chemicals, not only in the field of biological sciences but also in materials science. It has been discovered that artificially designed unnatural peptides and proteins exhibit advanced properties in medical and materials science. In this context, the development of precise chemical modification methods for amino acids and peptides is acknowledged as an important research project in the field of organic synthesis. While a wide variety of modification methods for amino acid residues have been developed to artificially modify peptides and proteins, the representative methods for modifying amino acid residues have traditionally relied on the nucleophilic properties of the functionalities on the residues. In this context, the development of different modification methods using an umpolung-like approach by utilizing the electrophilic nature of amino acid derivatives appears to be very attractive. One of the promising electrophilic amino acid compounds for realizing important modification methods of amino acid derivatives is α,β-dehydroamino acids, which possess an α,β-unsaturated carbonyl structure. This review article summarizes methods for the preparation of α,β-dehydroamino acids derived from natural and unnatural amino acid derivatives. The utilities of α,β-dehydroamino acid derivatives, including peptides and proteins containing dehydroalanine units, in bioconjugations are also discussed.
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Affiliation(s)
- Taiki Mori
- Institute of Integrated Science and Technology, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
| | - Sao Sumida
- Institute of Integrated Science and Technology, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
| | - Kazuki Sakata
- Spiber Inc., 234-1 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Seiji Shirakawa
- Institute of Integrated Science and Technology, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
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8
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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.
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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
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9
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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.
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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.
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10
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Wang Y, Zhang Y, Su R, Wang Y, Qi W. Antimicrobial therapy based on self-assembling peptides. J Mater Chem B 2024; 12:5061-5075. [PMID: 38726712 DOI: 10.1039/d4tb00260a] [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: 05/30/2024]
Abstract
The emergence of drug-resistant microorganisms has threatened global health, and microbial infections have severely limited the use of medical materials. For example, the attachment and colonization of pathogenic bacteria to medical implant materials can lead to wound infections, inflammation and complications, as well as implant failure, shortening their lifespan and even resulting in patient death. In the era of antibiotic resistance, antimicrobial drug discovery needs to prioritize unconventional therapies that act on new targets or adopt new mechanisms. In this regard, supramolecular antimicrobial peptides have emerged as attractive therapeutic platforms, both as bactericides for combination antibiotics and as delivery vehicles. By taking advantage of their programmable intermolecular and intramolecular interactions, peptides can be modified to form higher-order structures (including nanofibers and nanoparticles) with unique functionality. This paper begins with an analysis of the relationship between peptide self-assembly and antimicrobial activity, describes in detail the research and development of various self-assembled antimicrobial peptides in recent years, and finally explores different combinatorial strategies for self-assembling antimicrobial peptides.
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Affiliation(s)
- Yuqi Wang
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
| | - Yexi Zhang
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
| | - Rongxin Su
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Yuefei Wang
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Wei Qi
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
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11
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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.
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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
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12
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Curcio A, Rocca R, Alcaro S, Artese A. The Histone Deacetylase Family: Structural Features and Application of Combined Computational Methods. Pharmaceuticals (Basel) 2024; 17:620. [PMID: 38794190 PMCID: PMC11124352 DOI: 10.3390/ph17050620] [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: 04/18/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Histone deacetylases (HDACs) are crucial in gene transcription, removing acetyl groups from histones. They also influence the deacetylation of non-histone proteins, contributing to the regulation of various biological processes. Thus, HDACs play pivotal roles in various diseases, including cancer, neurodegenerative disorders, and inflammatory conditions, highlighting their potential as therapeutic targets. This paper reviews the structure and function of the four classes of human HDACs. While four HDAC inhibitors are currently available for treating hematological malignancies, numerous others are undergoing clinical trials. However, their non-selective toxicity necessitates ongoing research into safer and more efficient class-selective or isoform-selective inhibitors. Computational methods have aided the discovery of HDAC inhibitors with the desired potency and/or selectivity. These methods include ligand-based approaches, such as scaffold hopping, pharmacophore modeling, three-dimensional quantitative structure-activity relationships, and structure-based virtual screening (molecular docking). Moreover, recent developments in the field of molecular dynamics simulations, combined with Poisson-Boltzmann/molecular mechanics generalized Born surface area techniques, have improved the prediction of ligand binding affinity. In this review, we delve into the ways in which these methods have contributed to designing and identifying HDAC inhibitors.
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Affiliation(s)
- Antonio Curcio
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
| | - Roberta Rocca
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
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13
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Sharma KR, Malik A, Roof RA, Boyce JP, Verma SK. New approaches for challenging therapeutic targets. Drug Discov Today 2024; 29:103942. [PMID: 38447929 PMCID: PMC10997441 DOI: 10.1016/j.drudis.2024.103942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
Despite successes with new drug approvals over the past two decades through conventional drug development approaches, many human diseases remain intractable to current therapeutic interventions. Possible barriers may be that the complexity of the target, and disease biology, are impervious to such conventional drug development approaches. The US National Institutes of Health hosted a workshop with the goal of identifying challenges and opportunities with alternative modalities for developing treatments across diseases associated with historically undruggable targets. This report highlights key issues discussed during the workshop that, if addressed, could expand the pool of therapeutic approaches for treating various diseases.
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Affiliation(s)
- Karlie R Sharma
- National Center for Advancing Translational Sciences, National Institutes of Health, 6701 Democracy Blvd, Bethesda, MD 20892, USA.
| | - Abir Malik
- National Center for Advancing Translational Sciences, National Institutes of Health, 6701 Democracy Blvd, Bethesda, MD 20892, USA
| | - Rebecca A Roof
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Jim P Boyce
- National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Sharad K Verma
- National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
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14
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Zhang C, Zhang C, Shang T, Zhu N, Wu X, Duan H. HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints. Brief Bioinform 2024; 25:bbae215. [PMID: 38706323 PMCID: PMC11070728 DOI: 10.1093/bib/bbae215] [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: 09/29/2023] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024] Open
Abstract
In recent years, cyclic peptides have emerged as a promising therapeutic modality due to their diverse biological activities. Understanding the structures of these cyclic peptides and their complexes is crucial for unlocking invaluable insights about protein target-cyclic peptide interaction, which can facilitate the development of novel-related drugs. However, conducting experimental observations is time-consuming and expensive. Computer-aided drug design methods are not practical enough in real-world applications. To tackles this challenge, we introduce HighFold, an AlphaFold-derived model in this study. By integrating specific details about the head-to-tail circle and disulfide bridge structures, the HighFold model can accurately predict the structures of cyclic peptides and their complexes. Our model demonstrates superior predictive performance compared to other existing approaches, representing a significant advancement in structure-activity research. The HighFold model is openly accessible at https://github.com/hongliangduan/HighFold.
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Affiliation(s)
- Chenhao Zhang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Chengyun Zhang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
- AI department, Shanghai Highslab Therapeutics. Inc, Shanghai, 201203, China
| | - Tianfeng Shang
- AI department, Shanghai Highslab Therapeutics. Inc, Shanghai, 201203, China
| | - Ning Zhu
- China Pharmaceutical University, Nanjing, Jiangsu, 211198, China
| | - Xinyi Wu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Hongliang Duan
- Faculty of Applied Sciences, Macao Polytechnic University, R. de Luís Gonzaga Gomes, Macao, 999078, China
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15
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Ouyang X, Chen W, Peng G, Liu H, Fan S, Li Q, Wang L, Chen L, Li L. 1,12-cyclic apelin-12 ameliorates Ang II and Apelin-13-induced cardiac hypertrophy by reducing mitochondrial oxidative damage. Chin Med J (Engl) 2024; 137:749-751. [PMID: 38321846 PMCID: PMC10950121 DOI: 10.1097/cm9.0000000000003009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Indexed: 02/08/2024] Open
Affiliation(s)
- Xueqian Ouyang
- The Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, Hengyang, Hunan 421001, China
| | - Wei Chen
- The Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, Hengyang, Hunan 421001, China
| | - Guolong Peng
- The Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, Hengyang, Hunan 421001, China
| | - Huimei Liu
- The Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, Hengyang, Hunan 421001, China
| | - Sisi Fan
- The Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, Hengyang, Hunan 421001, China
| | - Qin Li
- The Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, Hengyang, Hunan 421001, China
| | - Liwen Wang
- The Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, Hengyang, Hunan 421001, China
| | - Linxi Chen
- The Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, Hengyang, Hunan 421001, China
| | - Lanfang Li
- The Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, Hengyang, Hunan 421001, China
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16
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Zhang C, Liu F, Zhang Y, Song C. Macrocycles and macrocyclization in anticancer drug discovery: Important pieces of the puzzle. Eur J Med Chem 2024; 268:116234. [PMID: 38401189 DOI: 10.1016/j.ejmech.2024.116234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
Increasing disease-related proteins have been identified as novel therapeutic targets. Macrocycles are emerging as potential solutions, bridging the gap between conventional small molecules and biomacromolecules in drug discovery. Inspired by successful macrocyclic drugs of natural origins, macrocycles are attracting more attention for enhanced binding affinity and target selectivity. Due to the conformation constraint and structure preorganization, macrocycles can reach bioactive conformations more easily than parent acyclic compounds. Also, rational macrocyclization combined with sequent structural modification will help improve oral bioavailability and combat drug resistance. This review introduces various strategies to enhance membrane permeability in macrocyclization and subsequent modification, such as N-methylation, intramolecular hydrogen bonding modulation, isomerization, and reversible bicyclization. Several case studies highlight macrocyclic inhibitors targeting kinases, HDAC, and protein-protein interactions. Finally, some macrocyclic agents targeting tumor microenvironments are illustrated.
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Affiliation(s)
- Chao Zhang
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Fenfen Liu
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Chun Song
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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17
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Geers DWT, Gavriel K, Neumann K. Rapid, traceless and facile peptide cyclization enabled by tetrazine-thiol exchange. J Pept Sci 2024; 30:e3548. [PMID: 37779097 DOI: 10.1002/psc.3548] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/25/2023] [Accepted: 09/14/2023] [Indexed: 10/03/2023]
Abstract
Cyclic peptides offer many advantages compared to their linear counterparts, including prolonged stability within the biological environment and enhanced binding affinity. Typically, peptides are cyclized by forming an amide bond, either on-resin or in solution, through extensive use of orthogonal protecting groups or chemoselective ligation strategies, respectively. Here, we show that the chemoselective tetrazine-thiol exchange is a powerful tool for rapid in situ cyclization of peptides without the need for additional activation reagents or extensive protecting group reshuffling. The reaction between N-terminal sulfide-bearing unsymmetric tetrazines and internal cysteines occurs spontaneously within a mildly acidic environment (pH 6.5) and is of traceless nature. The rapidly available unsymmetric sulfide tetrazine building blocks can be incorporated on resin using standard solid-phase peptide synthesis protocols and are orthogonal to trifluoroacetic acid cleavage conditions. The cyclized peptides display high stability, even when incubated with a large excess of free thiols. Due to its traceless and mild nature, we expect that the tetrazine-thiol exchange will be of high value for the in situ formation of cyclic peptide libraries, thus being applicable in drug discovery and development.
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Affiliation(s)
- Daniëlle W T Geers
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Katerina Gavriel
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Kevin Neumann
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
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18
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Sakamoto K, Hirokawa T. Lipid bilayer membrane permeability mechanism of the K-Ras(G12D)-inhibitory bicyclic peptide KS-58 elucidated by molecular dynamics simulations. Bioorg Med Chem Lett 2024; 100:129649. [PMID: 38341162 DOI: 10.1016/j.bmcl.2024.129649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Peptides are mid-size molecules (700-2000 g/mol) and have attracted particular interest as therapeutic modalities as they are superior in controlling protein-protein interactions, a process that is a typical drug target category, compared with small molecules (<500 g/mol). In 2020, we identified KS-58 (1333 g/mol) as a K-Ras(G12D)-inhibitory bicyclic peptide and suggested its cell membrane permeability. However, the membrane permeability mechanism had not been elucidated. In this study, we aim to clarify the mechanism by molecular dynamics (MD) simulations. Initially, we simulated the molecular conformations of KS-58 in water (a polar solvent) and in chloroform (a non-polar solvent). The identified stable conformations were significantly different in each solvent. KS-58 behaves as a chameleon-like molecule as it alters its polar surface area (PSA) depending on the solvent environment. It was also discovered that orientation of Asp's side chain is a critical energy barrier for KS-58 altering its conformation from hydrophilic to lipophilic. Taking these properties into consideration, we simulated its lipid bilayer membrane permeability. KS-58 shifted toward the inside of the lipid bilayer membrane with altering its conformations to lipophilic. When the simulation condition was set in deionized form of that carboxy group of Asp, KS-58 traveled deeper inside the cell membrane. PSA and the depth of the membrane penetration correlated. In vitro data suggested that cell membrane permeability of KS-58 is improved in weakly acidic conditions leading to partial deionization of the carboxy group. Our data provide an example of the molecular properties of mid-size peptides with membrane accessibility and propose an effective metadynamics approach to elucidate such molecular mechanisms by MD simulations.
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Affiliation(s)
- Kotaro Sakamoto
- Research & Development Depertment, Ichimaru Pharcos Company Limited, 318-1 Asagi, Motosu, 501-0475 Gifu, Japan.
| | - Takatsugu Hirokawa
- Research & Development Depertment, Ichimaru Pharcos Company Limited, 318-1 Asagi, Motosu, 501-0475 Gifu, Japan; Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, 305-8575 Tsukuba, Japan; Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, 305-8575 Tsukuba, Japan.
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19
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Ferrie RP, Fuselier T, Wimley WC. Cytosolic Delivery of Bioactive Cyclic Peptide Cargo by Spontaneous Membrane Translocating Peptides. ACS OMEGA 2024; 9:8179-8187. [PMID: 38405535 PMCID: PMC10882622 DOI: 10.1021/acsomega.3c08701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/23/2023] [Accepted: 01/18/2024] [Indexed: 02/27/2024]
Abstract
Cyclic peptides that inhibit protein-protein interactions have significant advantages over linear peptides and small molecules for modulating cellular signaling networks in cancer and other diseases. However, the permeability barrier of the plasma membrane remains a formidable obstacle to the development of cyclic peptides into applicable drugs. Here, we test the ability of a family of synthetically evolved spontaneous membrane translocating peptides (SMTPs) to deliver phalloidin, a representative bioactive cyclic peptide, to the cytosol of human cells in culture. Phalloidin does not enter cells spontaneously, but if delivered to the cytosol, it inhibits actin depolymerization. We thus use a wound-healing cell mobility assay to assess the biological activity of phalloidin conjugated to three SMTPs that we previously discovered. All three SMTPs can deliver phalloidin to the cell cytosol, and one does so at concentrations as low as 3 μM. Delivery occurs despite the fact that the SMTPs were originally selected based on membrane translocation with no cargo other than a small fluorescent dye. These results show that SMTPs are viable delivery vehicles for cyclic peptides, although their efficiency is moderate. Further, these results suggest that one additional generation of synthetic molecular evolution could be used to optimize SMTPs for the efficient delivery of any bioactive cyclic peptide into cells.
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Affiliation(s)
- Ryan P. Ferrie
- Department of Biochemistry
and Molecular Biology, Tulane University
School of Medicine, New Orleans, Louisiana 70112, United States
| | - Taylor Fuselier
- Department of Biochemistry
and Molecular Biology, Tulane University
School of Medicine, New Orleans, Louisiana 70112, United States
| | - William C. Wimley
- Department of Biochemistry
and Molecular Biology, Tulane University
School of Medicine, New Orleans, Louisiana 70112, United States
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20
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Diaz DB, Rowshanpour R, Saunders GJ, Dudding T, Yudin AK. The Role of Attractive Non-Covalent Interactions in Peptide Macrocyclization. J Org Chem 2024; 89:1483-1491. [PMID: 38217516 DOI: 10.1021/acs.joc.3c02084] [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: 01/15/2024]
Abstract
The efficiency of macrocyclization reactions relies on the appropriate conformational preorganization of a linear precursor, ensuring that reactive ends are in spatial proximity prior to ring closure. Traditional peptide cyclization approaches that reduce the extent of terminal ion pairing often disfavor cyclization-conducive conformations and can lead to undesired cyclodimerization or oligomerization side reactions, particularly when they are performed without high dilution. To address this challenge, synthetic strategies that leverage attractive noncovalent interactions, such as zwitterionic attraction between chain termini during macrocyclization, offer a potential solution by reducing the entropic penalty associated with linear peptides adopting precyclization conformations. In this study, we investigate the role of (N-isocyanoimino)triphenylphosphorane (Pinc) in facilitating the cyclization of linear peptides into conformationally rigid macrocycles. The observed moderate diastereoselectivity is consistent with the preferential Si-facial addition of Pinc, where the isocyanide adds to the E-iminium ion on the same face as the l-proline amide group. The resulting peptide chain reveals that the activated phosphonium ylide of Pinc brings the reactive ends close together, promoting cyclization by enclosing the carboxylate within the interior of the pentapeptide and preventing the formation of byproducts. For shorter peptides with modified peptide backbones, the cyclization mechanism and outcome are redirected, as nucleophilic motifs such as thiazole and imidazole can covalently trap nitrilium intermediates. The isolation of the intermediate in the unproductive macrocyclization pathway, along with nuclear magnetic resonance and density functional theory studies, provides insights into heterocycle-dependent selectivity. The Pinc-driven macrocyclization process has generated diverse collections of cyclic molecules, and our models offer a comprehensive understanding of observed trends, facilitating the development of other heterocycle-forming macrocyclization reactions.
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Affiliation(s)
- Diego B Diaz
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Rozhin Rowshanpour
- Department of Chemistry, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - George J Saunders
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Travis Dudding
- Department of Chemistry, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Andrei K Yudin
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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21
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Martinsen E, Jinnurine T, Subramani S, Rogne M. Advances in RNA therapeutics for modulation of 'undruggable' targets. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 204:249-294. [PMID: 38458740 DOI: 10.1016/bs.pmbts.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
Over the past decades, drug discovery utilizing small pharmacological compounds, fragment-based therapeutics, and antibody therapy have significantly advanced treatment options for many human diseases. However, a major bottleneck has been that>70% of human proteins/genomic regions are 'undruggable' by the above-mentioned approaches. Many of these proteins constitute essential drug targets against complex multifactorial diseases like cancer, immunological disorders, and neurological diseases. Therefore, alternative approaches are required to target these proteins or genomic regions in human cells. RNA therapeutics is a promising approach for many of the traditionally 'undruggable' targets by utilizing methods such as antisense oligonucleotides, RNA interference, CRISPR/Cas-based genome editing, aptamers, and the development of mRNA therapeutics. In the following chapter, we will put emphasis on recent advancements utilizing these approaches against challenging drug targets, such as intranuclear proteins, intrinsically disordered proteins, untranslated genomic regions, and targets expressed in inaccessible tissues.
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Affiliation(s)
| | | | - Saranya Subramani
- Pioneer Research AS, Oslo Science Park, Oslo, Norway; Department of Pharmacy, Section for Pharmacology and Pharmaceutical Biosciences, University of Oslo, Oslo, Norway
| | - Marie Rogne
- Pioneer Research AS, Oslo Science Park, Oslo, Norway; Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
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22
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Chan WJ, Li H. Recent advances in nano/micro systems for improved circulation stability, enhanced tumor targeting, penetration, and intracellular drug delivery: a review. Biomed Phys Eng Express 2024; 10:022001. [PMID: 38086099 DOI: 10.1088/2057-1976/ad14f0] [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: 05/15/2023] [Accepted: 12/12/2023] [Indexed: 01/17/2024]
Abstract
In recent years, nanoparticles (NPs) have been extensively developed as drug carriers to overcome the limitations of cancer therapeutics. However, there are several biological barriers to nanomedicines, which include the lack of stability in circulation, limited target specificity, low penetration into tumors and insufficient cellular uptake, restricting the active targeting toward tumors of nanomedicines. To address these challenges, a variety of promising strategies were developed recently, as they can be designed to improve NP accumulation and penetration in tumor tissues, circulation stability, tumor targeting, and intracellular uptake. In this Review, we summarized nanomaterials developed in recent three years that could be utilized to improve drug delivery for cancer treatments.
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Affiliation(s)
- Wei-Jen Chan
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, United States of America
| | - Huatian Li
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, United States of America
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23
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Abstract
Cyclic peptides are fascinating molecules abundantly found in nature and exploited as molecular format for drug development as well as other applications, ranging from research tools to food additives. Advances in peptide technologies made over many years through improved methods for synthesis and drug development have resulted in a steady stream of new drugs, with an average of around one cyclic peptide drug approved per year. Powerful technologies for screening random peptide libraries, and de novo generating ligands, have enabled the development of cyclic peptide drugs independent of naturally derived molecules and now offer virtually unlimited development opportunities. In this review, we feature therapeutically relevant cyclic peptides derived from nature and discuss the unique properties of cyclic peptides, the enormous technological advances in peptide ligand development in recent years, and current challenges and opportunities for developing cyclic peptides that address unmet medical needs.
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Affiliation(s)
- Xinjian Ji
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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24
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Han H, Feng X, He T, Wu Y, He T, Yue Z, Zhou W. Discussion on structure classification and regulation function of histone deacetylase and their inhibitor. Chem Biol Drug Des 2024; 103:e14366. [PMID: 37776270 DOI: 10.1111/cbdd.14366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/02/2023]
Abstract
Epigenetic regulation of genes through posttranslational regulation of proteins is a well-explored approach for disease treatment, particularly in cancer chemotherapy. Histone deacetylases have shown significant potential as effective drug targets in therapeutic studies aiming to restore epigenetic normality in oncology. Besides their role in modifying histones, histone deacetylases can also catalyze the deacetylation of various nonhistone proteins and participate in the regulation of multiple biological processes. This paper provides a review of the classification, structure, and functional characteristics of the four classes of human histone deacetylases. The increasing abundance of structural information on HDACs has led to the gradual elucidation of structural differences among subgroups and subtypes. This has provided a reasonable explanation for the selectivity of certain HDAC inhibitors. Currently, the US FDA has approved a total of six HDAC inhibitors for marketing, primarily for the treatment of various hematological tumors and a few solid tumors. These inhibitors all have a common pharmacodynamic moiety consisting of three parts: CAP, ZBG, and Linker. In this paper, the structure-effect relationship of HDAC inhibitors is explored by classifying the six HDAC inhibitors into three main groups: isohydroxamic acids, benzamides, and cyclic peptides, based on the type of inhibitor ZBG. However, there are still many questions that need to be answered in this field. In this paper, the structure-functional characteristics of HDACs and the structural information of the pharmacophore model and enzyme active region of HDAC is are considered, which can help to understand the inhibition mechanism of the compounds as well as the rational design of HDACs. This paper integrates the structural-functional characteristics of HDACs as well as the pharmacophore model of HDAC is and the structural information of the enzymatic active region, which not only contributes to the understanding of the inhibition mechanism of the compounds, but also provides a basis for the rational design of HDAC inhibitors.
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Affiliation(s)
- Han Han
- Department of Biochemistry and Molecular Biology, Shenyang Medical College, Shenyang City, P. R. China
| | - Xue Feng
- Department of Pathogen Biology, Shenyang Medical College, Shenyang City, P. R. China
| | - Ting He
- Department of Pathogen Biology, Shenyang Medical College, Shenyang City, P. R. China
| | - Yingfan Wu
- Department of Pathogen Biology, Shenyang Medical College, Shenyang City, P. R. China
| | - Tianmei He
- Department of Pathogen Biology, Shenyang Medical College, Shenyang City, P. R. China
| | - Ziwen Yue
- Department of Pathogen Biology, Shenyang Medical College, Shenyang City, P. R. China
| | - Weiqiang Zhou
- Department of Pathogen Biology, Shenyang Medical College, Shenyang City, P. R. China
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25
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Cheng J, Zhou J, Kong L, Wang H, Zhang Y, Wang X, Liu G, Chu Q. Stabilized cyclic peptides as modulators of protein-protein interactions: promising strategies and biological evaluation. RSC Med Chem 2023; 14:2496-2508. [PMID: 38107173 PMCID: PMC10718590 DOI: 10.1039/d3md00487b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/04/2023] [Indexed: 12/19/2023] Open
Abstract
Protein-protein interactions (PPIs) control many essential biological pathways which are often misregulated in disease. As such, selective PPI modulators are desirable to unravel complex functions of PPIs and thus expand the repertoire of therapeutic targets. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets for conventional drug modalities, rendering most PPIs "undruggable". Therefore, there is a growing need to discover innovative molecules that are able to modulate crucial PPIs. Peptides are ideal candidates to deliver such therapeutics attributed to their ability to closely mimic structural features of protein interfaces. However, their inherently poor proteolysis resistance and cell permeability inevitably hamper their biomedical applications. The introduction of a constraint (i.e., peptide cyclization) to stabilize peptides' secondary structure is a promising strategy to address this problem as witnessed by the rapid development of cyclic peptide drugs in the past two decades. Here, we comprehensively review the recent progress on stabilized cyclic peptides in targeting challenging PPIs. Technological advancements and emerging chemical approaches for stabilizing active peptide conformations are categorized in terms of α-helix stapling, β-hairpin mimetics and macrocyclization. To discover potent and selective ligands, cyclic peptide library technologies were updated based on genetic, biochemical or synthetic methodologies. Moreover, several advances to improve the permeability and oral bioavailability of biologically active cyclic peptides enable the de novo development of cyclic peptide ligands with pharmacological properties. In summary, the development of cyclic peptide-based PPI modulators carries tremendous promise for the next generation of therapeutic agents to target historically "intractable" PPI systems.
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Affiliation(s)
- Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Junlong Zhou
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University 639 Longmian Avenue Nanjing 211198 China
| | - Lingyan Kong
- College of Food Science and Engineering, Nanjing University of Finance and Economics Nanjing 210023 China
| | - Haiying Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Yuchi Zhang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Xiaofeng Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Guangxiang Liu
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Qian Chu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University 639 Longmian Avenue Nanjing 211198 China
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University Nanjing 210009 China
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26
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Gabizon R, Tivon B, Reddi RN, van den Oetelaar MCM, Amartely H, Cossar PJ, Ottmann C, London N. A simple method for developing lysine targeted covalent protein reagents. Nat Commun 2023; 14:7933. [PMID: 38040731 PMCID: PMC10692228 DOI: 10.1038/s41467-023-42632-5] [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: 04/13/2023] [Accepted: 10/16/2023] [Indexed: 12/03/2023] Open
Abstract
Peptide-based covalent probes can target shallow protein surfaces not typically addressable using small molecules, yet there is a need for versatile approaches to convert native peptide sequences into covalent binders that can target a broad range of residues. Here we report protein-based thio-methacrylate esters-electrophiles that can be installed easily on unprotected peptides and proteins via cysteine side chains, and react efficiently and selectively with cysteine and lysine side chains on the target. Methacrylate phosphopeptides derived from 14-3-3-binding proteins irreversibly label 14-3-3σ via either lysine or cysteine residues, depending on the position of the electrophile. Methacrylate peptides targeting a conserved lysine residue exhibit pan-isoform binding of 14-3-3 proteins both in lysates and in extracellular media. Finally, we apply this approach to develop protein-based covalent binders. A methacrylate-modified variant of the colicin E9 immunity protein irreversibly binds to the E9 DNAse, resulting in significantly higher thermal stability relative to the non-covalent complex. Our approach offers a simple and versatile route to convert peptides and proteins into potent covalent binders.
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Affiliation(s)
- Ronen Gabizon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Barr Tivon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Rambabu N Reddi
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maxime C M van den Oetelaar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Hadar Amartely
- Wolfson Centre for Applied Structural Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel.
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27
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Tang X, Kokot J, Waibl F, Fernández-Quintero ML, Kamenik AS, Liedl KR. Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity. J Chem Inf Model 2023; 63:7107-7123. [PMID: 37943023 PMCID: PMC10685455 DOI: 10.1021/acs.jcim.3c01123] [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: 07/23/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023]
Abstract
We evaluated a workflow to reliably sample the conformational space of a set of 47 peptidic macrocycles. Starting from SMILES strings, we use accelerated molecular dynamics simulations to overcome high energy barriers, in particular, the cis-trans isomerization of peptide bonds. We find that our approach performs very well in polar solvents like water and dimethyl sulfoxide. Interestingly, the protonation state of a secondary amine in the ring only slightly influences the conformational ensembles of our test systems. For several of the macrocycles, determining the conformational distribution in chloroform turns out to be considerably more challenging. Especially, the choice of partial charges crucially influences the ensembles in chloroform. We address these challenges by modifying initial structures and the choice of partial charges. Our results suggest that special care has to be taken to understand the configurational distribution in apolar solvents, which is a key step toward a reliable prediction of membrane permeation of macrocycles and their chameleonic properties.
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Affiliation(s)
- Xuechen Tang
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Janik Kokot
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Franz Waibl
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, 8093 Zürich, Switzerland
| | | | - Anna S. Kamenik
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
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28
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Eslami SM, Rahman IR, van der Donk WA. Expression of Lanthipeptides in Human Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563208. [PMID: 37961259 PMCID: PMC10634679 DOI: 10.1101/2023.10.19.563208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cyclic peptides represent a burgeoning area of interest in therapeutic and biotechnological research. In opposition to their linear counterparts, cyclic peptides, such as certain ribosomally synthesized and post-translationally modified peptides (RiPPs), are more conformationally constrained and less susceptible to proteolytic degradation. The lanthipeptide RiPP cytolysin L forms a covalently enforced helical structure that may be used to disrupt helical interactions at protein-protein interfaces. Herein, an expression system is reported to produce lanthipeptides and structurally diverse cytolysin L derivatives in mammalian cells. Successful targeting of lanthipeptides to the nucleus is demonstrated. In vivo expression and targeting of such peptides in mammalian cells may allow for screening of lanthipeptide inhibitors of native protein-protein interactions.
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Affiliation(s)
- Sara M. Eslami
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Imran R. Rahman
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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29
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Karami Y, Murail S, Giribaldi J, Lefranc B, Defontaine F, Lesouhaitier O, Leprince J, de Vries S, Tufféry P. Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization. J Chem Inf Model 2023; 63:6436-6450. [PMID: 37827517 PMCID: PMC10599322 DOI: 10.1021/acs.jcim.3c00865] [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: 06/16/2023] [Indexed: 10/14/2023]
Abstract
Peptides have recently regained interest as therapeutic candidates, but their development remains confronted with several limitations including low bioavailability. Backbone head-to-tail cyclization, i.e., setting a covalent peptide bond linking the last amino acid with the first one, is one effective strategy of peptide-based drug design to stabilize the conformation of bioactive peptides while preserving peptide properties in terms of low toxicity, binding affinity, target selectivity, and preventing enzymatic degradation. Starting from an active peptide, it usually requires the design of a linker of a few amino acids to make it possible to cyclize the peptide, possibly preserving the conformation of the initial peptide and not affecting its activity. However, very little is known about the sequence-structure relationship requirements of designing linkers for peptide cyclization in a rational manner. Recently, we have shown that large-scale data-mining of available protein structures can lead to the precise identification of protein loop conformations, even from remote structural classes. Here, we transpose this approach to linkers, allowing head-to-tail peptide cyclization. First we show that given a linker sequence and the conformation of the linear peptide, it is possible to accurately predict the cyclized peptide conformation. Second, and more importantly, we show that it seems possible to elaborate on the information inferred from protein structures to propose effective candidate linker sequences constrained by length and amino acid composition, providing the first framework for the rational design of head-to-tail cyclization linkers. Finally, we illustrate this for two peptides using a limited set of amino-acids likely not to interfere with peptide function. For a linear peptide derived from Nrf2, the peptide cyclized starting from the experimental structure showed a 26-fold increase in the binding affinity. For urotensin II, a peptide already cyclized by a disulfide bond that exerts a broad array of biological activities, we were able, starting from models of the structure, to design a head-to-tail cyclized peptide, the first synthesized bicyclic 14-residue long urotensin II analogue, showing a retention of in vitro activity. Although preliminary, our results strongly suggest that such an approach has strong potential for cyclic peptide-based drug design.
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Affiliation(s)
- Yasaman Karami
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Samuel Murail
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Julien Giribaldi
- Institut
des Biomolécules Max Mousseron, UMR 5247, Université de Montpellier-CNRS, 34293 Montpellier, France
| | - Benjamin Lefranc
- Université
de Rouen Normandie, INSERM U1239 NorDiC, Neuroendocrine, Endocrine and Germinal Differentiation and Communication,
INSERM US51 HeRacLeS, F-76000 Rouen, France
| | - Florian Defontaine
- Université
de Rouen Normandie, UR CBSA, Research Unit
Bacterial Communication and Anti-infectious Strategies, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Université
de Rouen Normandie, UR CBSA, Research Unit
Bacterial Communication and Anti-infectious Strategies, 27000 Evreux, France
| | - Jérôme Leprince
- Université
de Rouen Normandie, INSERM U1239 NorDiC, Neuroendocrine, Endocrine and Germinal Differentiation and Communication,
INSERM US51 HeRacLeS, F-76000 Rouen, France
| | - Sjoerd de Vries
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Pierre Tufféry
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
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30
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Liu SX, Ou-Yang SY, Lu YF, Guo CL, Dai SY, Li C, Yu TY, Pei YH. Recent advances on cyclodepsipeptides: biologically active compounds for drug research. Front Microbiol 2023; 14:1276928. [PMID: 37849925 PMCID: PMC10577210 DOI: 10.3389/fmicb.2023.1276928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 09/12/2023] [Indexed: 10/19/2023] Open
Abstract
Cyclodepsipeptides are a large family of peptide-related natural products consisting of hydroxy and amino acids linked by amide and ester bonds. A number of cyclodepsipeptides have been isolated and characterized from fungi and bacteria. Most of them showed antitumor, antifungal, antiviral, antimalarial, and antitrypanosomal properties. Herein, this review summarizes the recent literatures (2010-2022) on the progress of cyclodepsipeptides from fungi and bacteria except for those of marine origin, in order to enrich our knowledge about their structural features and biological sources.
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Affiliation(s)
- Si-Xuan Liu
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Si-Yi Ou-Yang
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yong-Fu Lu
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Chun-Lin Guo
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Si-Yang Dai
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Chang Li
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
- Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Tian-Yi Yu
- The Third Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, China
| | - Yue-Hu Pei
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
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31
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Ghosh P, Raj N, Verma H, Patel M, Chakraborti S, Khatri B, Doreswamy CM, Anandakumar SR, Seekallu S, Dinesh MB, Jadhav G, Yadav PN, Chatterjee J. An amide to thioamide substitution improves the permeability and bioavailability of macrocyclic peptides. Nat Commun 2023; 14:6050. [PMID: 37770425 PMCID: PMC10539501 DOI: 10.1038/s41467-023-41748-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 09/06/2023] [Indexed: 09/30/2023] Open
Abstract
Solvent shielding of the amide hydrogen bond donor (NH groups) through chemical modification or conformational control has been successfully utilized to impart membrane permeability to macrocyclic peptides. We demonstrate that passive membrane permeability can also be conferred by masking the amide hydrogen bond acceptor (>C = O) through a thioamide substitution (>C = S). The membrane permeability is a consequence of the lower desolvation penalty of the macrocycle resulting from a concerted effect of conformational restriction, local desolvation of the thioamide bond, and solvent shielding of the amide NH groups. The enhanced permeability and metabolic stability on thioamidation improve the bioavailability of a macrocyclic peptide composed of hydrophobic amino acids when administered through the oral route in rats. Thioamidation of a bioactive macrocyclic peptide composed of polar amino acids results in analogs with longer duration of action in rats when delivered subcutaneously. These results highlight the potential of O to S substitution as a stable backbone modification in improving the pharmacological properties of peptide macrocycles.
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Affiliation(s)
- Pritha Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Nishant Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Hitesh Verma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Monika Patel
- Neuroscience & Ageing Biology, CSIR-CDRI, Lucknow, 226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sohini Chakraborti
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Chandrashekar M Doreswamy
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - S R Anandakumar
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - Srinivas Seekallu
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - M B Dinesh
- Central Animal Facility, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Gajanan Jadhav
- Eurofins Advinus Biopharma Services India Pvt. Ltd., Bangalore, 560058, Karnataka, India
| | - Prem Narayan Yadav
- Neuroscience & Ageing Biology, CSIR-CDRI, Lucknow, 226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India.
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32
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Román T, Acosta G, de la Torre BG, Cárdenas C, Guzmán F, Albericio F. Improving 2-Chlorotrityl Chloride (2-CTC) Resin Activation. Methods Protoc 2023; 6:82. [PMID: 37736965 PMCID: PMC10514796 DOI: 10.3390/mps6050082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Abstract
Used in solid-phase peptide synthesis (SPPS) for peptides with an acid termination, the 2-chlorotrityl chloride (2-CTC) resin is highly susceptible to moisture, leading to reduced resin loading and lower synthetic yields. It is therefore recommended that the resin be activated with thionyl chloride (SOCl2) before peptide assembly. Here we present an optimized procedure for resin activation that minimizes the use of SOCl2 as the activation reagent and reduces the activation time. Additionally, we demonstrate the feasibility of reusing the 2-CTC resin when following the activation protocol, achieving comparable results to the first usage of the resin. Moreover, we achieved different degrees of resin activation by varying the amount of SOCl2. For instance, the use of 2% SOCl2 in anhydrous dichloromethane (DCM) allowed up to 44% activation of the resin, thereby making it suitable for the synthesis of longer peptides. Alternatively, employing 25% SOCl2 in anhydrous DCM resulted in up to 80% activation with a reaction time of only 5 min in both cases.
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Affiliation(s)
- Tanya Román
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile; (T.R.); (C.C.); (F.G.)
- Doctorado en Biotecnología, Pontificia Universidad Católica de Valparaíso, Universidad Técnica Federico Santa María, Valparaíso 2373223, Chile
- Department of Organic Chemistry and CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, University of Barcelona, 08028 Barcelona, Spain;
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Gerardo Acosta
- Department of Organic Chemistry and CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, University of Barcelona, 08028 Barcelona, Spain;
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Beatriz G. de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa;
| | - Constanza Cárdenas
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile; (T.R.); (C.C.); (F.G.)
| | - Fanny Guzmán
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile; (T.R.); (C.C.); (F.G.)
| | - Fernando Albericio
- Department of Organic Chemistry and CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, University of Barcelona, 08028 Barcelona, Spain;
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
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33
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Liu T, Gao C, Wang J, Song J, Chen X, Chen H, Zhao X, Tang H, Gu D. Peptide aptamer-based time-resolved fluoroimmunoassay for CHIKV diagnosis. Virol J 2023; 20:166. [PMID: 37501131 PMCID: PMC10375649 DOI: 10.1186/s12985-023-02132-w] [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: 03/29/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023] Open
Abstract
BACKGROUND Chikungunya virus (CHIKV) and Dengue virus (DENV) have similar clinical symptoms, which often induce misdiagnoses. Therefore, an antigen detection diagnostic system that can clearly identify these two viruses is desirable. METHODS In this study, we developed a novel peptide with high affinity and specificity to CHIKV, and further constructed peptide aptamer-based TRFIA assay to efficiently detect CHIKV. Peptide aptamer B2 (ITPQSSTTEAEL) and B3 (DTQGSNWI) were obtained through computer-aided design and selected as CHIKV-specific peptide aptamers based on their high binding affinity, strong hydrogen bonding, and RMSD of molecular docking. Then, a sandwich-Time-Resolved Fluoroimmunoassay (TRFIA) was successfully constructed for the detection of the interaction between peptide aptamers and viruses. RESULTS When using B2 as the detection element, highly specific detection of CHIKV E2 was achieved with detection limits of 8.5 ng/ml in PBS solution. Variation coefficient between inter-assay showed the disturbances received from the detection of clinical fluid specimens (including serum and urine), were also within acceptable limits. The detection limits for 10-fold dilution serum and urine were 57.8 ng/mL and 147.3 ng/mL, respectively. The fluorescent signal intensity exhibited a good linear correlation with E2 protein concentration in the range of 0-1000 ng/mL, indicating the potential for quantitative detection of E2 protein. CONCLUSIONS These results demonstrate that the construction of peptide aptamers with high affinity and specificity provides an excellent method for rapid diagnostic element screening, and the developed peptide aptamer B2 contributed to better detection of CHIKV viral particles compared to traditional antibodies.
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Affiliation(s)
- Tonggong Liu
- Department of Laboratory Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, 518035, Shenzhen, China
- School of Public Health, Dongguan Key Laboratory of Environmental Medicine, Guangdong Medical University, 523808, Guangdong, China
| | - Cheng Gao
- Department of Laboratory Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, 518035, Shenzhen, China
| | - Jingzhe Wang
- Department of Laboratory Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, 518035, Shenzhen, China
| | - Jianning Song
- Guangzhou Medical University, 510182, Guangzhou, China
| | - Xi Chen
- School of Public Health, Dongguan Key Laboratory of Environmental Medicine, Guangdong Medical University, 523808, Guangdong, China
| | - Hongfang Chen
- School of Public Health, Dongguan Key Laboratory of Environmental Medicine, Guangdong Medical University, 523808, Guangdong, China
| | - Xiaona Zhao
- Guangxi University of Chinese Medicine, 530004, Nanning, China
| | - Huanwen Tang
- School of Public Health, Dongguan Key Laboratory of Environmental Medicine, Guangdong Medical University, 523808, Guangdong, China.
| | - Dayong Gu
- Department of Laboratory Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, 518035, Shenzhen, China.
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Alboreggia G, Udompholkul P, Baggio C, Pellecchia M. Mixture-Based Screening of Focused Combinatorial Libraries by NMR: Application to the Antiapoptotic Protein hMcl-1. J Med Chem 2023. [PMID: 37464766 PMCID: PMC10388297 DOI: 10.1021/acs.jmedchem.3c01073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
We report on an innovative ligand discovery strategy based on protein NMR-based screening of a combinatorial library of ∼125,000 compounds that was arranged in 96 distinct mixtures. Using sensitive solution protein NMR spectroscopy and chemical perturbation-based screening followed by an iterative synthesis, deconvolutions, and optimization strategy, we demonstrate that the approach could be useful in the identification of initial binding molecules for difficult drug targets, such as those involved in protein-protein interactions. As an application, we will report novel agents targeting the Bcl-2 family protein hMcl-1. The approach is of general applicability and could be deployed as an effective screening strategy for de novo identification of ligands, particularly when tackling targets involved in protein-protein interactions.
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Affiliation(s)
- Giulia Alboreggia
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Parima Udompholkul
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Carlo Baggio
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Maurizio Pellecchia
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
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Tang SJ, Shao CX, Yang Y, Ren R, Jin L, Hu D, Wu SL, Lei P, He YL, Xu J. The antitumor effect of mycelia extract of the medicinal macrofungus Inonotus hispidus on HeLa cells via the mitochondrial-mediated pathway. JOURNAL OF ETHNOPHARMACOLOGY 2023; 311:116407. [PMID: 37001769 DOI: 10.1016/j.jep.2023.116407] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/09/2023] [Accepted: 03/18/2023] [Indexed: 06/19/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Inonotus hispidus (I. hispidus), known as shaggy bracket, has been used extensively in China and some East Asian countries as a traditional medicinal macrofungus to treat difficult diseases, such as diabetes, gout, and arthritis. Modern pharmacological research has shown that I. hispidus has an important application value in antitumor treatment. However, the main anti-cervical cancer activity substances from its mycelia and its mechanisms are still not clear. AIMS OF THE STUDY To enrich the germplasm resources of I. hispidus, to reveal the antitumor activity of the extract from the mycelium of I. hispidus against cervical cancer, and to preliminarily analyze its action mechanism. MATERIALS AND METHODS The SH3 strain was isolated from wild fruiting bodies and identified by morphology and molecular biology. The antitumor active component from the mycelium of I. hispidus was isolated and identified with liquid chromatography-tandem mass spectrometry. The cell viability was assessed by MTT assay. The cell cycle distribution, apoptotic cell detection, and mitochondrial membrane potential were detected by flow cytometer. The expression of apoptosis-related proteins was assessed by Western blotting. The inhibition of tumor growth in vivo was assessed by a mouse xenograft model. RESULTS The SH3 strain was isolated and identified as a new strain of I. hispidus. The antitumor active component containing cyclic peptides from the mycelium of I. hispidus (CCM) was isolated for the first time. In addition, we found that CCM had a strong inhibitory effect on HeLa proliferation in vitro and in vivo. Mechanically, the CCM blocked the cell cycle at the G0/G1 phase, decreased the mitochondrial membrane potential, and eventually promoted apoptosis of HeLa cells through the mitochondria-mediated pathway by upregulating the expression levels of Bax, cytochrome C, cleaved caspase-9, and cleaved caspase-3 and downregulating the expression level of Bcl-2. CONCLUSIONS Our study not only enriches the strain resources of I. hispidus but also confirms that the mycelium of this strain has active components that can inhibit cervical cancer. This is highly significant for the development of active drugs and drug lead molecules for treating cervical cancer.
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Affiliation(s)
- Shao-Jun Tang
- Hunan Institute of Microbiology, 81 Xinkaipu Road, Changsha, 410009, China
| | - Chen-Xia Shao
- Hunan Institute of Microbiology, 81 Xinkaipu Road, Changsha, 410009, China
| | - Yi Yang
- Hunan Institute of Microbiology, 81 Xinkaipu Road, Changsha, 410009, China
| | - Rui Ren
- Hunan Institute of Microbiology, 81 Xinkaipu Road, Changsha, 410009, China
| | - Lei Jin
- Hunan Institute of Microbiology, 81 Xinkaipu Road, Changsha, 410009, China
| | - Dan Hu
- Hunan Institute of Microbiology, 81 Xinkaipu Road, Changsha, 410009, China
| | - Shen-Lian Wu
- Hunan Institute of Microbiology, 81 Xinkaipu Road, Changsha, 410009, China
| | - Pin Lei
- Hunan Institute of Microbiology, 81 Xinkaipu Road, Changsha, 410009, China
| | - Yue-Lin He
- Hunan Institute of Microbiology, 81 Xinkaipu Road, Changsha, 410009, China
| | - Jun Xu
- Hunan Institute of Microbiology, 81 Xinkaipu Road, Changsha, 410009, China.
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36
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Lee ML, Farag S, Del Cid JS, Bashore C, Hallenbeck KK, Gobbi A, Cunningham CN. Identification of Macrocyclic Peptide Families from Combinatorial Libraries Containing Noncanonical Amino Acids Using Cheminformatics and Bioinformatics Inspired Clustering. ACS Chem Biol 2023; 18:1425-1434. [PMID: 37220419 PMCID: PMC10278063 DOI: 10.1021/acschembio.3c00159] [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: 03/16/2023] [Accepted: 05/10/2023] [Indexed: 05/25/2023]
Abstract
In the past decade, macrocyclic peptides gained increasing interest as a new therapeutic modality to tackle intracellular and extracellular therapeutic targets that had been previously classified as "undruggable". Several technological advances have made discovering macrocyclic peptides against these targets possible: 1) the inclusion of noncanonical amino acids (NCAAs) into mRNA display, 2) increased availability of next generation sequencing (NGS), and 3) improvements in rapid peptide synthesis platforms. This type of directed-evolution based screening can produce large numbers of potential hit sequences given that DNA sequencing is the functional output of this platform. The current standard for selecting hit peptides from these selections for downstream follow-up relies on the frequency counting and sorting of unique peptide sequences which can result in the generation of false negatives due to technical reasons including low translation efficiency or other experimental factors. To overcome our inability to detect weakly enriched peptide sequences among our large data sets, we wanted to develop a clustering method that would enable the identification of peptide families. Unfortunately, utilizing traditional clustering algorithms, such as ClustalW, is not possible for this technology due to the incorporation of NCAAs in these libraries. Therefore, we developed a new atomistic clustering method with a Pairwise Aligned Peptide (PAP) chemical similarity metric to perform sequence alignments and identify macrocyclic peptide families. With this method, low enriched peptides, including isolated sequences (singletons), can now be clustered into families providing a comprehensive analysis of NGS data resulting from macrocycle discovery selections. Additionally, upon identification of a hit peptide with the desired activity, this clustering algorithm can be used to identify derivatives from the initial data set for structure-activity relationship (SAR) analysis without requiring additional selection experiments.
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Affiliation(s)
- Man-Ling Lee
- Discovery
Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sherif Farag
- Discovery
Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Joselyn S. Del Cid
- Peptide
Therapeutics, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Charlene Bashore
- Biological
Chemistry, Genentech Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Kenneth K. Hallenbeck
- Peptide
Therapeutics, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Alberto Gobbi
- Discovery
Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Peptide
Therapeutics, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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37
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Blackwell DJ, Smith AN, Do T, Gochman A, Schmeckpeper J, Hopkins CR, Akers WS, Johnston JN, Knollmann BC. In Vivo Pharmacokinetic and Pharmacodynamic Properties of the Antiarrhythmic Molecule ent-Verticilide. J Pharmacol Exp Ther 2023; 385:205-213. [PMID: 36894328 PMCID: PMC10201578 DOI: 10.1124/jpet.122.001455] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/19/2023] [Accepted: 02/24/2023] [Indexed: 03/11/2023] Open
Abstract
The unnatural verticilide enantiomer (ent-verticilide) is a selective and potent inhibitor of cardiac ryanodine receptor (RyR2) calcium release channels and exhibits antiarrhythmic activity in a murine model of catecholaminergic polymorphic ventricular tachycardia (CPVT). To determine verticilide's pharmacokinetic and pharmacodynamic properties in vivo, we developed a bioassay to measure nat- and ent-verticilide in murine plasma and correlated plasma concentrations with antiarrhythmic efficacy in a mouse model of CPVT. nat-Verticilide rapidly degraded in plasma in vitro, showing >95% degradation within 5 minutes, whereas ent-verticilide showed <1% degradation over 6 hours. Plasma was collected from mice following intraperitoneal administration of ent-verticilide at two doses (3 mg/kg, 30 mg/kg). Peak C max and area under the plasma-concentration time curve (AUC) scaled proportionally to dose, and the half-life was 6.9 hours for the 3-mg/kg dose and 6.4 hours for the 30-mg/kg dose. Antiarrhythmic efficacy was examined using a catecholamine challenge protocol at time points ranging from 5 to 1440 minutes after intraperitoneal dosing. ent-Verticilide inhibited ventricular arrhythmias as early as 7 minutes after administration in a concentration-dependent manner, with an estimated potency (IC50) of 266 ng/ml (312 nM) and an estimated maximum inhibitory effect of 93.5%. Unlike the US Food and Drug Administration-approved pan-RyR blocker dantrolene, the RyR2-selective blocker ent-verticilide (30 mg/kg) did not reduce skeletal muscle strength in vivo. We conclude that ent-verticilide has favorable pharmacokinetic properties and reduces ventricular arrhythmias with an estimated potency in the nanomolar range, warranting further drug development. SIGNIFICANCE STATEMENT: ent-Verticilide has therapeutic potential to treat cardiac arrhythmias, but little is known about its pharmacological profile in vivo. The primary purpose of this study is to determine the systemic exposure and pharmacokinetics of ent-verticilide in mice and estimate its efficacy and potency in vivo. The current work suggests ent-verticilide has favorable pharmacokinetic properties and reduces ventricular arrhythmias with an estimated potency in the nanomolar range, warranting further drug development.
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Affiliation(s)
- Daniel J Blackwell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee (D.J.B., J.S., B.C.K.); Departments of Chemistry (A.N.S., J.N.J.) and Pharmacology (A.G., W.S.A), and Vanderbilt Institute of Chemical Biology (A.N.S., J.N.J.), Vanderbilt University, Nashville, Tennessee; Pharmaceutical Sciences Research Center, Lipscomb University, Nashville, Tennessee (T.D., W.S.A); and Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska (C.R.H.)
| | - Abigail N Smith
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee (D.J.B., J.S., B.C.K.); Departments of Chemistry (A.N.S., J.N.J.) and Pharmacology (A.G., W.S.A), and Vanderbilt Institute of Chemical Biology (A.N.S., J.N.J.), Vanderbilt University, Nashville, Tennessee; Pharmaceutical Sciences Research Center, Lipscomb University, Nashville, Tennessee (T.D., W.S.A); and Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska (C.R.H.)
| | - Tri Do
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee (D.J.B., J.S., B.C.K.); Departments of Chemistry (A.N.S., J.N.J.) and Pharmacology (A.G., W.S.A), and Vanderbilt Institute of Chemical Biology (A.N.S., J.N.J.), Vanderbilt University, Nashville, Tennessee; Pharmaceutical Sciences Research Center, Lipscomb University, Nashville, Tennessee (T.D., W.S.A); and Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska (C.R.H.)
| | - Aaron Gochman
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee (D.J.B., J.S., B.C.K.); Departments of Chemistry (A.N.S., J.N.J.) and Pharmacology (A.G., W.S.A), and Vanderbilt Institute of Chemical Biology (A.N.S., J.N.J.), Vanderbilt University, Nashville, Tennessee; Pharmaceutical Sciences Research Center, Lipscomb University, Nashville, Tennessee (T.D., W.S.A); and Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska (C.R.H.)
| | - Jeffrey Schmeckpeper
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee (D.J.B., J.S., B.C.K.); Departments of Chemistry (A.N.S., J.N.J.) and Pharmacology (A.G., W.S.A), and Vanderbilt Institute of Chemical Biology (A.N.S., J.N.J.), Vanderbilt University, Nashville, Tennessee; Pharmaceutical Sciences Research Center, Lipscomb University, Nashville, Tennessee (T.D., W.S.A); and Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska (C.R.H.)
| | - Corey R Hopkins
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee (D.J.B., J.S., B.C.K.); Departments of Chemistry (A.N.S., J.N.J.) and Pharmacology (A.G., W.S.A), and Vanderbilt Institute of Chemical Biology (A.N.S., J.N.J.), Vanderbilt University, Nashville, Tennessee; Pharmaceutical Sciences Research Center, Lipscomb University, Nashville, Tennessee (T.D., W.S.A); and Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska (C.R.H.)
| | - Wendell S Akers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee (D.J.B., J.S., B.C.K.); Departments of Chemistry (A.N.S., J.N.J.) and Pharmacology (A.G., W.S.A), and Vanderbilt Institute of Chemical Biology (A.N.S., J.N.J.), Vanderbilt University, Nashville, Tennessee; Pharmaceutical Sciences Research Center, Lipscomb University, Nashville, Tennessee (T.D., W.S.A); and Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska (C.R.H.)
| | - Jeffrey N Johnston
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee (D.J.B., J.S., B.C.K.); Departments of Chemistry (A.N.S., J.N.J.) and Pharmacology (A.G., W.S.A), and Vanderbilt Institute of Chemical Biology (A.N.S., J.N.J.), Vanderbilt University, Nashville, Tennessee; Pharmaceutical Sciences Research Center, Lipscomb University, Nashville, Tennessee (T.D., W.S.A); and Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska (C.R.H.)
| | - Bjorn C Knollmann
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee (D.J.B., J.S., B.C.K.); Departments of Chemistry (A.N.S., J.N.J.) and Pharmacology (A.G., W.S.A), and Vanderbilt Institute of Chemical Biology (A.N.S., J.N.J.), Vanderbilt University, Nashville, Tennessee; Pharmaceutical Sciences Research Center, Lipscomb University, Nashville, Tennessee (T.D., W.S.A); and Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska (C.R.H.)
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38
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Lu Q, Regan DP, Barlow DE, Fears KP. Antimicrobial efficacy of cyclic α- and β-peptides incorporated in polyurethane coatings. Biointerphases 2023; 18:031008. [PMID: 37289032 DOI: 10.1116/6.0002515] [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: 01/23/2023] [Accepted: 05/12/2023] [Indexed: 06/09/2023] Open
Abstract
Microbial growth on surfaces poses health concerns and can accelerate the biodegradation of engineered materials and coatings. Cyclic peptides are promising agents to combat biofouling because they are more resistant to enzymatic degradation than their linear counterparts. They can also be designed to interact with extracellular targets and intracellular targets and/or self-assemble into transmembrane pores. Here, we determine the antimicrobial efficacy of two pore-forming cyclic peptides, α-K3W3 and β-K3W3, against bacterial and fungal liquid cultures and their capacity to inhibit biofilm formation on coated surfaces. These peptides display identical sequences, but the additional methylene group in the peptide backbone of β-amino acids results in a larger diameter and an enhancement in the dipole moment. In liquid cultures, β-K3W3 exhibited lower minimum inhibitory concentration values and greater microbicidal power in reducing the number of colony forming units (CFUs) when exposed to a gram-positive bacterium, Staphylococcus aureus, and two fungal strains, Naganishia albida and Papiliotrema laurentii. To evaluate the efficacy against the formation of fungal biofilms on painted surfaces, cyclic peptides were incorporated into polyester-based thermoplastic polyurethane. The formation of N. albida and P. laurentii microcolonies (105 per inoculation) for cells extracted from coatings containing either peptide could not be detected after a 7-day exposure. Moreover, very few CFUs (∼5) formed after 35 days of repeated depositions of freshly cultured P. laurentii every 7 days. In contrast, the number of CFUs for cells extracted from the coating without cyclic peptides was >8 log CFU.
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Affiliation(s)
- Qin Lu
- Chemistry Division, U.S. Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375
| | - Daniel P Regan
- Chemistry Division, U.S. Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375
| | - Daniel E Barlow
- Chemistry Division, U.S. Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375
| | - Kenan P Fears
- Chemistry Division, U.S. Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375
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39
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Li A, Li X, Zou J, Zhuo X, Chen S, Chai X, Gai C, Xu W, Zhao Q, Zou Y. SOS1-inspired hydrocarbon-stapled peptide as a pan-Ras inhibitor. Bioorg Chem 2023; 135:106500. [PMID: 37003134 DOI: 10.1016/j.bioorg.2023.106500] [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: 02/24/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023]
Abstract
Blocking the interaction between Ras and Son of Sevenless homolog 1 (SOS1) has been an attractive therapeutic strategy for treating cancers involving oncogenic Ras mutations. K-Ras mutation is the most common in Ras-driven cancers, accounting for 86%, with N-Ras mutation and H-Ras mutation accounting for 11% and 3%, respectively. Here, we report the design and synthesis of a series of hydrocarbon-stapled peptides to mimic the alpha-helix of SOS1 as pan-Ras inhibitors. Among these stapled peptides, SSOSH-5 was identified to maintain a well-constrained alpha-helical structure and bind to H-Ras with high affinity. SSOSH-5 was furthermore validated to bind with Ras similarly to the parent linear peptide through structural modeling analysis. This optimized stapled peptide was proven to be capable of effectively inhibiting the proliferation of pan-Ras-mutated cancer cells and inducing apoptosis in a dose-dependent manner by modulating downstream kinase signaling. Of note, SSOSH-5 exhibited a high capability of crossing cell membranes and strong proteolytic resistance. We demonstrated that the peptide stapling strategy is a feasible approach for developing peptide-based pan-Ras inhibitors. Furthermore, we expect that SSOSH-5 can be further characterized and optimized for the treatment of Ras-driven cancers.
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Affiliation(s)
- Anpeng Li
- School of Pharmacy, Naval Medical University, Shanghai, PR China; 92805 Military Hospital, Qingdao, PR China
| | - Xiang Li
- School of Pharmacy, Naval Medical University, Shanghai, PR China
| | - Jihua Zou
- School of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, PR China
| | - Xiaobin Zhuo
- School of Pharmacy, Naval Medical University, Shanghai, PR China
| | - Shuai Chen
- School of Pharmacy, Naval Medical University, Shanghai, PR China
| | - Xiaoyun Chai
- School of Pharmacy, Naval Medical University, Shanghai, PR China
| | - Conghao Gai
- School of Pharmacy, Naval Medical University, Shanghai, PR China
| | - Weiheng Xu
- School of Pharmacy, Naval Medical University, Shanghai, PR China.
| | - Qingjie Zhao
- School of Pharmacy, Naval Medical University, Shanghai, PR China.
| | - Yan Zou
- School of Pharmacy, Naval Medical University, Shanghai, PR China.
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40
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Lee KY, Lee BJ. Dynamics-Based Regulatory Switches of Type II Antitoxins: Insights into New Antimicrobial Discovery. Antibiotics (Basel) 2023; 12:antibiotics12040637. [PMID: 37106997 PMCID: PMC10135005 DOI: 10.3390/antibiotics12040637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Type II toxin-antitoxin (TA) modules are prevalent in prokaryotes and are involved in cell maintenance and survival under harsh environmental conditions, including nutrient deficiency, antibiotic treatment, and human immune responses. Typically, the type II TA system consists of two protein components: a toxin that inhibits an essential cellular process and an antitoxin that neutralizes its toxicity. Antitoxins of type II TA modules typically contain the structured DNA-binding domain responsible for TA transcription repression and an intrinsically disordered region (IDR) at the C-terminus that directly binds to and neutralizes the toxin. Recently accumulated data have suggested that the antitoxin's IDRs exhibit variable degrees of preexisting helical conformations that stabilize upon binding to the corresponding toxin or operator DNA and function as a central hub in regulatory protein interaction networks of the type II TA system. However, the biological and pathogenic functions of the antitoxin's IDRs have not been well discussed compared with those of IDRs from the eukaryotic proteome. Here, we focus on the current state of knowledge about the versatile roles of IDRs of type II antitoxins in TA regulation and provide insights into the discovery of new antibiotic candidates that induce toxin activation/reactivation and cell death by modulating the regulatory dynamics or allostery of the antitoxin.
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Affiliation(s)
- Ki-Young Lee
- College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Pocheon-si 11160, Republic of Korea
| | - Bong-Jin Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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41
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Ono T, Tabata KV, Noji H, Morimoto J, Sando S. Each side chain of cyclosporin A is not essential for high passive permeability across lipid bilayers. RSC Adv 2023; 13:8394-8397. [PMID: 36922944 PMCID: PMC10010161 DOI: 10.1039/d3ra01358h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
We compared the passive permeability of cyclosporin A (CsA) derivatives with side chain deletions across lipid bilayers. CsA maintained passive permeability after losing any one of the side chains, which suggests that the propensity of the backbone of CsA is an important component for high passive permeability.
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Affiliation(s)
- Takahiro Ono
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Kazuhito V Tabata
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan.,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Jumpei Morimoto
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Shinsuke Sando
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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42
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Menke AJ, Gloor CJ, Claton LE, Mekhail MA, Pan H, Stewart MD, Green KN, Reibenspies JH, Pavan GM, Capelli R, Simanek EE. A Model for the Rapid Assessment of Solution Structures for 24-Atom Macrocycles: The Impact of β-Branched Amino Acids on Conformation. J Org Chem 2023; 88:2692-2702. [PMID: 36780253 PMCID: PMC10903118 DOI: 10.1021/acs.joc.2c01984] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Experiment and computation are used to develop a model to rapidly predict solution structures of macrocycles sharing the same Murcko framework. These 24-atom triazine macrocycles result from the quantitative dimerization of identical monomers presenting a hydrazine group and an acetal tethered to an amino acid linker. Monomers comprising glycine and the β-branched amino acids threonine, valine, and isoleucine yield macrocycles G-G, T-T, V-V, and I-I, respectively. Elements common to all members of the framework include the efficiency of macrocyclization (quantitative), the solution- and solid-state structures (folded), the site of protonation (opposite the auxiliary dimethylamine group), the geometry of the hydrazone (E), the C2 symmetry of the subunits (conserved), and the rotamer state adopted. In aggregate, the data reveal metrics predictive of the three-dimensional solution structure that derive from the fingerprint region of the 1D 1H spectrum and a network of rOes from a single resonance. The metrics also afford delineation of more nuanced structural features that allow subpopulations to be identified among the members of the framework. Well-tempered metadynamics provides free energy surfaces and population distributions of these macrocycles. The areas of the free energy surface decrease with increasing steric bulk (G-G > V-V ∼ T-T > I-I). In addition, the surfaces are increasingly isoenergetic with decreasing steric bulk (G-G > V-V ∼ T-T > I-I).
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Affiliation(s)
- Alexander J Menke
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Camryn J Gloor
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Liam E Claton
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Magy A Mekhail
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Hongjun Pan
- Department of Chemistry, University of North Texas, Denton, Texas 76203, United States
| | - Mikaela D Stewart
- Department of Biology, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Kayla N Green
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Joseph H Reibenspies
- Department of Chemistry, Texas A&M University, College Station, Texas 77845, United States
| | - Giovanni M Pavan
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Viganello, 6962 Lugano, Switzerland
- Department of Applied Science and Technology, Politecnico di Torino, 10129 Torino, Italy
| | - Riccardo Capelli
- Department of Biosciences, Université degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Eric E Simanek
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
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43
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Mazibuko M, Jeena V. Synthesis of 2,4,5-Trisubstituted Oxazoles from Copper-Mediated Benzylic sp 3 C-H Aerobic Oxidative Annulation of Ketones and Amines via a Cascade Reaction. J Org Chem 2023; 88:1227-1234. [PMID: 36575054 DOI: 10.1021/acs.joc.2c02148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The functionalization of sp3 carbons is deemed challenging in synthetic organic chemistry yet has tremendous potential in producing potent organic compounds. A facile synthesis of 2,4,5-trisubstituted oxazoles through an oxidative, copper-catalyzed, and solvent-free annulation is described. Various arylated oxazoles were efficaciously synthesized at a mild temperature from readily available substrates under a molecular oxygen atmosphere. Preliminary mechanistic studies suggested that the reaction proceeds via an anionic-type mechanism and indicated the formation of a keto-imine intermediate. The reaction is notable for the abstraction of six hydrogen atoms, the functionalization of one sp2 carbon and two sp3 carbons, and the formation of C-O and C-N bonds.
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Affiliation(s)
- Mncedisi Mazibuko
- School of Chemistry and Physics, University of KwaZulu-Natal, Scottsville, Pietermaritzburg 3209, South Africa
| | - Vineet Jeena
- School of Chemistry and Physics, University of KwaZulu-Natal, Scottsville, Pietermaritzburg 3209, South Africa
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44
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Abstract
In the design and development of therapeutic agents, macromolecules with restricted structures have stronger competitive edges than linear biological entities since cyclization can overcome the limitations of linear structures. The common issues of linear peptides include susceptibility to degradation of the peptidase enzyme, off-target effects, and necessity of routine dosing, leading to instability and ineffectiveness. The unique conformational constraint of cyclic peptides provides a larger surface area to interact with the target at the same time, improving the membrane permeability and in vivo stability compared to their linear counterparts. Currently, cyclic peptides have been reported to possess various activities, such as antifungal, antiviral and antimicrobial activities. To date, there is emerging interest in cyclic peptide therapeutics, and increasing numbers of clinically approved cyclic peptide drugs are available on the market. In this review, the medical significance of cyclic peptides in the defence against viral infections will be highlighted. Except for chikungunya virus, which lacks specific antiviral treatment, all the viral diseases targeted in this review are those with effective treatments yet with certain limitations to date. Thus, strategies and approaches to optimise the antiviral effect of cyclic peptides will be discussed along with their respective outcomes. Apart from isolated naturally occurring cyclic peptides, chemically synthesized or modified cyclic peptides with antiviral activities targeting coronavirus, herpes simplex viruses, human immunodeficiency virus, Ebola virus, influenza virus, dengue virus, five main hepatitis viruses, termed as type A, B, C, D and E and chikungunya virus will be reviewed herein. Graphical Abstract
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45
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Zhang H, Kang Y, Qi X, Wu J, Liu D, Fan A, Huang J, Lin W. Versicotide G suppresses osteoclastogenesis and prevents osteolysis. Bioorg Chem 2022; 129:106114. [PMID: 36087552 DOI: 10.1016/j.bioorg.2022.106114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022]
Abstract
Excessive formation and function of osteoclasts cause various osteolytic bone diseases. Natural products are a potential source for the discovery of new therapeutic candidates to treat bone destruction diseases. In this study, chemical informatics and bioassay guided examination of the marine-derived Aspergillus versicolor F77 fungus chemically resulted in the isolation of seven cyclopeptides, of which versicotides G-J (1-4) are new cyclohexapeptides. Their structures were identified by spectroscopic data in association with Marfey method and single crystal X-ray diffraction data for configurational assignments. Bioassay revealed that versicotide G (1, VG) is the most active among the analogs to suppress the receptor activator of nuclear factor-KB ligand (RANKL)-induced osteoclastogenesis in bone marrow derived monocytes (BMMs) without affecting BMMs viability. VG also suppressed RANKL-induced actin-ring formation and resorbing function of osteoclast dose-dependently. Mechanistically, VG attenuated RANKL-induced intracellular calcium elevation by inhibiting PLCγ1 phosphorylation and blocking the activation of downstream phosphatase calcineurin. In addition, VG abrogated the expression and translocation of nuclear factor of activated T cells cytoplasmic-1 (NFATc1), leading to the downregulation of the expression of osteoclast-specific genes and the abolishment of the osteoclast formation. In the in vivo test, VG suppressed osteoclast formation and bone loss in Ti-induced calvarial osteolytic mouse model.These findings imply that VG is a promising candidate for the remedy of bone destruction-related diseases.
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Affiliation(s)
- He Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, PR China
| | - Ying Kang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, PR China
| | - Xinyi Qi
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, PR China
| | - Jingshuai Wu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, PR China
| | - Dong Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, PR China
| | - Aili Fan
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, PR China
| | - Jian Huang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, PR China.
| | - Wenhan Lin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, PR China; Institute of Ocean Research, Ningbo Institute of Marine Medicine, Peking University, Beijing 100191, PR China.
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46
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Maemoto T, Kitai Y, Takahashi R, Shoji H, Yamada S, Takei S, Ito D, Muromoto R, Kashiwakura JI, Handa H, Hashimoto A, Hashimoto S, Ose T, Oritani K, Matsuda T. A peptide derived from adaptor protein STAP-2 inhibits tumor progression by downregulating epidermal growth factor receptor signaling. J Biol Chem 2022; 299:102724. [PMID: 36410436 PMCID: PMC9800302 DOI: 10.1016/j.jbc.2022.102724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/20/2022] Open
Abstract
Signal-transducing adaptor family member-2 (STAP-2) is an adaptor protein that regulates various intracellular signals. We previously demonstrated that STAP-2 binds to epidermal growth factor receptor (EGFR) and facilitates its stability and activation of EGFR signaling in prostate cancer cells. Inhibition of this interaction may be a promising direction for cancer treatment. Here, we found that 2D5 peptide, a STAP-2-derived peptide, blocked STAP-2-EGFR interactions and suppressed EGFR-mediated proliferation in several cancer cell lines. 2D5 peptide inhibited tumor growth of human prostate cancer cell line DU145 and human lung cancer cell line A549 in murine xenograft models. Additionally, we determined that EGFR signaling and its stability were decreased by 2D5 peptide treatment during EGF stimulation. In conclusion, our study shows that 2D5 peptide is a novel anticancer peptide that inhibits STAP-2-mediated activation of EGFR signaling and suppresses prostate and lung cancer progression.
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Affiliation(s)
- Taiga Maemoto
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yuichi Kitai
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan,For correspondence: Yuichi Kitai; Tadashi Matsuda
| | - Runa Takahashi
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Haruka Shoji
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Shunsuke Yamada
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Shiho Takei
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Daiki Ito
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ryuta Muromoto
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Jun-ichi Kashiwakura
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Haruka Handa
- Department of Molecular Biology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ari Hashimoto
- Department of Molecular Biology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Shigeru Hashimoto
- Division of Molecular Psychoimmunology, Graduate School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Toyoyuki Ose
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kenji Oritani
- Department of Hematology, International University of Health and Welfare, Narita, Chiba, Japan
| | - Tadashi Matsuda
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan,For correspondence: Yuichi Kitai; Tadashi Matsuda
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47
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Yang J, Zhu Q, Wu Y, Qu X, Liu H, Jiang B, Ge D, Song X. Utilization of macrocyclic peptides to target protein-protein interactions in cancer. Front Oncol 2022; 12:992171. [PMID: 36465350 PMCID: PMC9714258 DOI: 10.3389/fonc.2022.992171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/24/2022] [Indexed: 07/30/2023] Open
Abstract
Protein-protein interactions (PPIs) play vital roles in normal cellular processes. Dysregulated PPIs are involved in the process of various diseases, including cancer. Thus, these PPIs may serve as potential therapeutic targets in cancer treatment. However, despite rapid advances in small-molecule drugs and biologics, it is still hard to target PPIs, especially for those intracellular PPIs. Macrocyclic peptides have gained growing attention for their therapeutic properties in targeting dysregulated PPIs. Macrocyclic peptides have some unique features, such as moderate sizes, high selectivity, and high binding affinities, which make them good drug candidates. In addition, some oncology macrocyclic peptide drugs have been approved by the US Food and Drug Administration (FDA) for clinical use. Here, we reviewed the recent development of macrocyclic peptides in cancer treatment. The opportunities and challenges were also discussed to inspire new perspectives.
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Affiliation(s)
- Jiawen Yang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Qiaoliang Zhu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yifan Wu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojuan Qu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haixia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Di Ge
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaoling Song
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
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48
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Saunders GJ, Yudin AK. A focus on the discovery of potent and selective cyclic peptide scaffolds for drug development. Chem Sci 2022; 13:12942-12944. [PMID: 36425493 PMCID: PMC9667955 DOI: 10.1039/d2sc90214a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024] Open
Abstract
In the past, cyclic peptide drugs were commonly discovered by isolation of natural products. However, recent efforts predominantly use high-throughput synthetic or genetically encoded libraries to find potent and selective hits against a range of challenging therapeutic targets. Kawamura et al. (Chem. Sci., 2022, 13, 3256-3262, https://doi.org/10.1039/D1SC06844J) developed a new workflow that can be applied to mRNA display, using high-throughput clustering, SAR investigations and in silico structural studies. This led to the discovery of nanomolar, serum-stable cyclic peptides against the human glucose-dependent insulinotropic peptide receptor (hGIP-R).
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Affiliation(s)
- George J Saunders
- Davenport Research Laboratories, University of Toronto 80 St. George St Toronto M5S 3H6 Ontario Canada
| | - Andrei K Yudin
- Davenport Research Laboratories, University of Toronto 80 St. George St Toronto M5S 3H6 Ontario Canada
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49
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Wills R, Adebomi V, Spancake C, Cohen RD, Raj M. Synthesis of L-cyclic tetrapeptides by backbone amide activation CyClick strategy. Tetrahedron 2022; 126:133071. [PMID: 37994371 PMCID: PMC10664817 DOI: 10.1016/j.tet.2022.133071] [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] [Indexed: 10/31/2022]
Abstract
Cyclic tetrapeptides exhibit high cellular permeability and a wide range of biological properties and thus have gained great interest in the field of medicinal chemistry. We synthesized highly strained 12-membered head to tail cyclic peptides with varying reactive amino acids, without oligomerization using the exclusively intramolecular CyClick chemistry. This occurs by a two-step process involving the low-energy formation of a 15 atom-containing cyclic imine, followed by a chemoselective ring contraction of the peptide backbone generating a highly strained 12 atom-containing cyclic tetrapeptide. This reaction exhibited high substrate scope and generated head to tail cyclic tetrapeptides with varying amino acids at the N-terminus, showing chemoselectivity without the need for side group protection.
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Affiliation(s)
- Rachel Wills
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Victor Adebomi
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | | | | | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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50
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Zhang M, Xu B, Li N, Zhang R, Zhang Q, Chen D, Rizvi SFA, Xu K, Shi Y, Yu B, Fang Q. OFP011 Cyclic Peptide as a Multifunctional Agonist for Opioid/Neuropeptide FF Receptors with Improved Blood-Brain Barrier Penetration. ACS Chem Neurosci 2022; 13:3078-3092. [PMID: 36262082 DOI: 10.1021/acschemneuro.2c00442] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Mounting evidence indicates that the neuropeptide FF (NPFF) system is involved in the side effects of opioid usage, including antinociceptive tolerance, hyperalgesia, abuse, constipation, and respiratory depression. Our group recently discovered that the multitarget opioid/NPFF receptor agonist DN-9 exhibits peripheral antinociceptive activity. To improve its metabolic stability, antinociceptive potency, and duration, in this study, we designed and synthesized a novel cyclic disulfide analogue of DN-9, OFP011, and examined its bioactivity through in vitro cyclic adenosine monophosphate (cAMP) functional assays and in vivo behavioral experiments. OFP011 exhibited multifunctional agonistic effects at the μ-opioid and the NPFF1 and NPFF2 receptors and partial agonistic effects at the δ- and κ-opioid in vitro, as determined via the cAMP functional assays. Pharmacokinetic and pharmacological experiments revealed improvement in its blood-brain barrier permeability after systemic administration. In addition, subcutaneous OFP011 exhibited potent and long-lasting antinociceptive activity via the central μ- and κ-opioid receptors, as observed in different physiological and pathological pain models. At the highest antinociceptive doses, subcutaneous OFP011 exhibited limited tolerance, gastrointestinal transit, motor coordination, addiction, reward, and respiration depression. Notably, OFP011 exhibited potent oral antinociceptive activities in mouse models of acute, inflammatory, and neuropathic pain. These results suggest that the multifunctional opioid/NPFF receptor agonists with improved blood-brain barrier penetration are a promising strategy for long-term treatment of moderate to severe nociceptive and pathological pain with fewer side effects.
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Affiliation(s)
- Mengna Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, and State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, P. R. China
| | - Biao Xu
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, and State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, P. R. China
| | - Ning Li
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, and State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, P. R. China
| | - Run Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, and State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, P. R. China
| | - Qinqin Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, and State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, P. R. China
| | - Dan Chen
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, and State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, P. R. China
| | - Syed Faheem Askari Rizvi
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, and State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, P. R. China
| | - Kangtai Xu
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, and State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, P. R. China
| | - Yonghang Shi
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, and State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, P. R. China
| | - Bowen Yu
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, and State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, P. R. China
| | - Quan Fang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, and State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, P. R. China
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