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Wang X, Du Z, Guo Y, Zhong J, Song K, Wang J, Yu J, Yang X, Liu CY, Shi T, Zhang J. Computer-aided molecular design and optimization of potent inhibitors disrupting APC‒Asef interaction. Acta Pharm Sin B 2024; 14:2631-2645. [PMID: 38828145 PMCID: PMC11143523 DOI: 10.1016/j.apsb.2024.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/04/2024] [Accepted: 03/14/2024] [Indexed: 06/05/2024] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer mortality worldwide. At initial diagnosis, approximately 20% of patients are diagnosed with metastatic CRC (mCRC). Although the APC‒Asef interaction is a well-established target for mCRC therapy, the discovery and development of effective and safe drugs for mCRC patients remains an urgent and challenging endeavor. In this study, we identified a novel structural scaffold based on MAI inhibitors, the first-in-class APC‒Asef inhibitors we reported previously. ONIOM model-driven optimizations of the N-terminal cap and experimental evaluations of inhibitory activity were performed, and 24-fold greater potency was obtained with the best inhibitor compared to the parental compound. In addition, the cocrystal structure validated that the two-layer π‒π stacking interactions were essential for inhibitor stabilization in the bound state. Furthermore, in vitro and in vivo studies have demonstrated that novel inhibitors suppressed lung metastasis in CRC by disrupting the APC‒Asef interaction. These results provide an intrinsic structural basis to further explore drug-like molecules for APC‒Asef-mediated CRC therapy.
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Affiliation(s)
- Xuefei Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Zeqian Du
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuegui Guo
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jie Zhong
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Kun Song
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Junyuan Wang
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Jianqiang Yu
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Xiuyan Yang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Basic Science Research Center Base (Pharmaceutical Science), Yantai University, Yantai 264005, China
| | - Chen-Ying Liu
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
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2
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Hemmati S, Behzadipour Y, Haddad M. Decoding the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for cell-penetrating peptides involved in pathogenesis or applicable as drug delivery vectors. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104474. [PMID: 32712315 PMCID: PMC7378008 DOI: 10.1016/j.meegid.2020.104474] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 01/18/2023]
Abstract
Synthetic or natural derived cell-penetrating peptides (CPPs) are vastly investigated as tools for the intracellular delivery of membrane-impermeable molecules. As viruses are intracellular obligate parasites, viral originated CPPs have been considered as suitable intracellular shuttling vectors for cargo transportation. A total of 310 CPPs were identified in the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Screening the proteome of the cause of COVID-19 reveals that SARS-CoV-2 CPPs (SCV2-CPPs) span the regions involved in replication, protein-nucleotide and protein-protein interaction, protein-metal ion interaction, and stabilization of homo/hetero-oligomers. However, to find the most appropriate peptides as drug delivery vectors, one might face several hurdles. Computational analyses showed that 94.3% of the identified SCV2-CPPs are non-toxins, and 38% are neither antigenic nor allergenic. Interestingly, 36.70% of SCV2-CPPs were resistant to all four groups of protease families. Nearly 1/3 of SCV2-CPPs had sufficient inherent or induced helix and sheet conformation leading to increased uptake efficiency. Heliquest lipid-binding discrimination factor revealed that 44.30% of the helical SCV2-CPPs are lipid-binding helices. Although Cys-rich derived CPPs of helicase (NSP13) can potentially fold into a cyclic conformation in endosomes with a higher rate of endosomal release, the most optimal SCV2-CPP candidates as vectors for drug delivery were SCV2-CPP118, SCV2-CPP119, SCV2-CPP122, and SCV2-CPP129 of NSP12 (RdRp). Ten experimentally validated viral-derived CPPs were also used as the positive control to check the scalability and reliability of our protocol in SCV2-CPP retrieval. Some peptides with a cell-penetration ability known as bioactive peptides are adopted as biotherapeutics themselves. Therefore, 59.60%, 29.63%, and 32.32% of SCV2-CPPs were identified as potential antibacterial, antiviral, and antifungals, respectively. While 63.64% of SCV2-CPPs had immuno-modulatory properties, 21.89% were recognized as anti-cancers. Conclusively, the workflow of this study provides a platform for profound screening of viral proteomes as a rich source of biotherapeutics or drug delivery carriers.
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Affiliation(s)
- Shiva Hemmati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Yasaman Behzadipour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahdi Haddad
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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3
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Tetley GJN, Murphy NP, Bonetto S, Ivanova-Berndt G, Revell J, Mott HR, Cooley RN, Owen D. The discovery and maturation of peptide biologics targeting the small G-protein Cdc42: A bioblockade for Ras-driven signaling. J Biol Chem 2020; 295:2866-2884. [PMID: 31959628 DOI: 10.1074/jbc.ra119.010077] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 12/24/2019] [Indexed: 01/10/2023] Open
Abstract
Aberrant Ras signaling drives 30% of cancers, and inhibition of the Rho family small GTPase signaling has been shown to combat Ras-driven cancers. Here, we present the discovery of a 16-mer cyclic peptide that binds to Cdc42 with nanomolar affinity. Affinity maturation of this sequence has produced a panel of derived candidates with increased affinity and modulated specificity for other closely-related small GTPases. The structure of the tightest binding peptide was solved by NMR, and its binding site on Cdc42 was determined. Addition of a cell-penetrating sequence allowed the peptides to access the cell interior and engage with their target(s), modulating signaling pathways. In Ras-driven cancer cell models, the peptides have an inhibitory effect on proliferation and show suppression of both invasion and motility. As such, they represent promising candidates for Rho-family small GTPase inhibitors and therapeutics targeting Ras-driven cancers. Our data add to the growing literature demonstrating that peptides are establishing their place in the biologics arm of drug discovery.
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Affiliation(s)
- George J N Tetley
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd., Cambridge CB2 1GA, United Kingdom
| | - Natasha P Murphy
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd., Cambridge CB2 1GA, United Kingdom
| | - Stephane Bonetto
- Isogenica Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Gabriela Ivanova-Berndt
- Isogenica Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Jefferson Revell
- MedImmune, Sir Aaron Klug Building, Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Helen R Mott
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd., Cambridge CB2 1GA, United Kingdom.
| | - R Neil Cooley
- Isogenica Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Darerca Owen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd., Cambridge CB2 1GA, United Kingdom.
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4
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Hirasawa S, Kitahara Y, Okamatsu Y, Fujii T, Nakayama A, Ueno S, Ijichi C, Futaki F, Nakata K, Taki M. Facile and Efficient Chemoenzymatic Semisynthesis of Fc-Fusion Compounds for Half-Life Extension of Pharmaceutical Components. Bioconjug Chem 2019; 30:2323-2331. [PMID: 31038930 DOI: 10.1021/acs.bioconjchem.9b00235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The formation of Fc-fusions, in which biologically active molecules and the Fc fragment of antibodies are linked to each other, is one of the most efficient and successful half-life extension technologies to be developed and applied to peptide and protein pharmaceuticals thus far. Fc-fusion compounds are generally produced by recombinant methods. However, these cannot be applied to artificial middle molecules, such as peptides with non-natural amino acids, unnatural cyclic peptides, or pharmaceutical oligonucleotides. Here, we developed a simple, efficient, semisynthetic method for Fc-fusion production involving our previously developed enzymatic N-terminal extension reaction (i.e., NEXT-A reaction) and strain-promoted azide-alkyne cycloaddition, achieving quantitative conversion and high selectivity for the N-terminus of the Fc protein. An Fc-fusion compound prepared by this method showed comparable biological activity to that of the original peptide and a long-circulating plasma half-life. Thus, the proposed method is potentially applicable for the conjugation of a wide range of pharmaceutical components.
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Affiliation(s)
- Shigeo Hirasawa
- Department of Engineering Science, Graduate School of Informatics and Engineering , The University of Electro-Communications (UEC) , 1-5-1 Chofugaoka , Chofu , Tokyo 182-8585 , Japan
| | | | | | | | | | | | | | | | | | - Masumi Taki
- Department of Engineering Science, Graduate School of Informatics and Engineering , The University of Electro-Communications (UEC) , 1-5-1 Chofugaoka , Chofu , Tokyo 182-8585 , Japan
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5
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Ni S, Garrido-Castro AF, Merchant RR, de Gruyter JN, Schmitt DC, Mousseau JJ, Gallego GM, Yang S, Collins MR, Qiao JX, Yeung KS, Langley DR, Poss MA, Scola PM, Qin T, Baran PS. A General Amino Acid Synthesis Enabled by Innate Radical Cross-Coupling. Angew Chem Int Ed Engl 2018; 57:14560-14565. [PMID: 30212610 PMCID: PMC6352899 DOI: 10.1002/anie.201809310] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Indexed: 01/21/2023]
Abstract
The direct union of primary, secondary, and tertiary carboxylic acids with a chiral glyoxylate-derived sulfinimine provides rapid access into a variety of enantiomerically pure α-amino acids (>85 examples). Characterized by operational simplicity, this radical-based reaction enables the modular assembly of exotic α-amino acids, including both unprecedented structures and those of established industrial value. The described method performs well in high-throughput library synthesis, and has already been implemented in three distinct medicinal chemistry campaigns.
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Affiliation(s)
- Shengyang Ni
- Scripps Research, North Torrey Pines Road, La Jolla, CA, 92037, USA
| | | | - Rohan R Merchant
- Scripps Research, North Torrey Pines Road, La Jolla, CA, 92037, USA
| | | | - Daniel C Schmitt
- Pfizer Medicinal Sciences, Eastern Point Road, Groton, CT, 06340, USA
| | - James J Mousseau
- Pfizer Medicinal Sciences, Eastern Point Road, Groton, CT, 06340, USA
| | - Gary M Gallego
- Department of Chemistry, La Jolla Laboratories, Pfizer, 10770 Science Center Drive, San Diego, CA, 92121, USA
| | - Shouliang Yang
- Department of Chemistry, La Jolla Laboratories, Pfizer, 10770 Science Center Drive, San Diego, CA, 92121, USA
| | - Michael R Collins
- Department of Chemistry, La Jolla Laboratories, Pfizer, 10770 Science Center Drive, San Diego, CA, 92121, USA
| | - Jennifer X Qiao
- Department of Discovery Chemistry, Bristol-Myers Squibb Company, Research and Development, P.O. Box 4000, Princeton, NJ, 08543, USA
| | - Kap-Sun Yeung
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT, 06492, USA
| | - David R Langley
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT, 06492, USA
| | - Michael A Poss
- Department of Discovery Chemistry, Bristol-Myers Squibb Company, Research and Development, P.O. Box 4000, Princeton, NJ, 08543, USA
| | - Paul M Scola
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT, 06492, USA
| | - Tian Qin
- Scripps Research, North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Phil S Baran
- Scripps Research, North Torrey Pines Road, La Jolla, CA, 92037, USA
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6
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Ni S, Garrido-Castro AF, Merchant RR, de Gruyter JN, Schmitt DC, Mousseau JJ, Gallego GM, Yang S, Collins MR, Qiao JX, Yeung KS, Langley DR, Poss MA, Scola PM, Qin T, Baran PS. A General Amino Acid Synthesis Enabled by Innate Radical Cross-Coupling. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809310] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shengyang Ni
- Scripps Research; North Torrey Pines Road La Jolla CA 92037 USA
| | | | | | | | | | | | - Gary M. Gallego
- Department of Chemistry; La Jolla Laboratories; Pfizer; 10770 Science Center Drive San Diego CA 92121 USA
| | - Shouliang Yang
- Department of Chemistry; La Jolla Laboratories; Pfizer; 10770 Science Center Drive San Diego CA 92121 USA
| | - Michael R. Collins
- Department of Chemistry; La Jolla Laboratories; Pfizer; 10770 Science Center Drive San Diego CA 92121 USA
| | - Jennifer X. Qiao
- Department of Discovery Chemistry; Bristol-Myers Squibb Company; Research and Development; P.O. Box 4000 Princeton NJ 08543 USA
| | - Kap-Sun Yeung
- Department of Discovery Chemistry; Bristol-Myers Squibb Research and Development; 5 Research Parkway Wallingford CT 06492 USA
| | - David R. Langley
- Department of Discovery Chemistry; Bristol-Myers Squibb Research and Development; 5 Research Parkway Wallingford CT 06492 USA
| | - Michael A. Poss
- Department of Discovery Chemistry; Bristol-Myers Squibb Company; Research and Development; P.O. Box 4000 Princeton NJ 08543 USA
| | - Paul M. Scola
- Department of Discovery Chemistry; Bristol-Myers Squibb Research and Development; 5 Research Parkway Wallingford CT 06492 USA
| | - Tian Qin
- Scripps Research; North Torrey Pines Road La Jolla CA 92037 USA
| | - Phil S. Baran
- Scripps Research; North Torrey Pines Road La Jolla CA 92037 USA
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7
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Zhou J, Wang Y, Chen J, Xu M, Yang T, Zheng J, Zhang X, Rao Z. Rational Engineering of Bacillus cereus
Leucine Dehydrogenase Towards α-keto Acid Reduction for Improving Unnatural Amino Acid Production. Biotechnol J 2018; 14:e1800253. [DOI: 10.1002/biot.201800253] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/06/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Junping Zhou
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| | - Yaling Wang
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| | - Jiajie Chen
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| | - Junxian Zheng
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
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8
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Gomes B, Augusto MT, Felício MR, Hollmann A, Franco OL, Gonçalves S, Santos NC. Designing improved active peptides for therapeutic approaches against infectious diseases. Biotechnol Adv 2018; 36:415-429. [PMID: 29330093 DOI: 10.1016/j.biotechadv.2018.01.004] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 12/13/2017] [Accepted: 01/06/2018] [Indexed: 12/25/2022]
Abstract
Infectious diseases are one of the main causes of human morbidity and mortality. In the last few decades, pathogenic microorganisms' resistance to conventional drugs has been increasing, and it is now pinpointed as a major worldwide health concern. The need to search for new therapeutic options, as well as improved treatment outcomes, has therefore increased significantly, with biologically active peptides representing a new alternative. A substantial research effort is being dedicated towards their development, especially due to improved biocompatibility and target selectivity. However, the inherent limitations of peptide drugs are restricting their application. In this review, we summarize the current status of peptide drug development, focusing on antiviral and antimicrobial peptide activities, highlighting the design improvements needed, and those already being used, to overcome the drawbacks of the therapeutic application of biologically active peptides.
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Affiliation(s)
- Bárbara Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Marcelo T Augusto
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Mário R Felício
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Axel Hollmann
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal; Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Buenos Aires, Argentina; Laboratory of Biointerfaces and Biomimetic Systems, CITSE, National University of Santiago del Estero-CONICET, Santiago del Estero, Argentina
| | - Octávio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, DF, Brazil; S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal.
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9
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Abstract
Unusual amino acids are fundamental building blocks of modern medicinal chemistry. The combination of readily functionalized amine and carboxyl groups attached to a chiral central core along with one or two potentially diverse side chains provides a unique three-dimensional structure with a high degree of functionality. This makes them invaluable as starting materials for syntheses of complex molecules, highly diverse elements for SAR campaigns, integral components of peptidomimetic drugs, and potential drugs on their own. This Perspective highlights the diversity of unnatural amino acid structures found in hit-to-lead and lead optimization campaigns and clinical stage and approved drugs, reflecting their increasingly important role in medicinal chemistry.
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Affiliation(s)
- Mark A T Blaskovich
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland Australia 4072
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10
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A new GLP-1 analogue with prolonged glucose-lowering activity in vivo via backbone-based modification at the N-terminus. Bioorg Med Chem 2016; 24:1163-70. [PMID: 26895657 DOI: 10.1016/j.bmc.2016.01.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/18/2016] [Indexed: 12/25/2022]
Abstract
Glucagon-like peptide-1 (GLP-1) is an endogenous insulinotropic hormone with wonderful glucose-lowering activity. However, its clinical use in type II diabetes is limited due to its rapid degradation at the N-terminus by dipeptidyl peptidase IV (DPP-IV). Among the N-terminal modifications of GLP-1, backbone-based modification was rarely reported. Herein, we employed two backbone-based strategies to modify the N-terminus of tGLP-1. Firstly, the amide N-methylated analogues 2-6 were designed and synthesized to make a full screening of the N-terminal amide bonds, and the loss of GLP-1 receptor (GLP-1R) activation indicated the importance of amide H-bonds. Secondly, with retaining the N-terminal amide H-bonds, the β-peptide replacement strategy was used and analogues 7-13 were synthesized. By two rounds of screening, analogue 10 was identified. Analogue 10 greatly improved the DPP-IV resistance with maintaining good GLP-1R activation in vitro, and showed approximately a 4-fold prolonged blood glucose-lowering activity in vivo in comparison with tGLP-1. This modification strategy will benefit the development of GLP-1-based anti-diabetic drugs.
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11
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Rational, computer-enabled peptide drug design: principles, methods, applications and future directions. Future Med Chem 2015; 7:2173-93. [PMID: 26510691 DOI: 10.4155/fmc.15.142] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Peptides provide promising templates for developing drugs to occupy a middle space between small molecules and antibodies and for targeting 'undruggable' intracellular protein-protein interactions. Importantly, rational or in cerebro design, especially when coupled with validated in silico tools, can be used to efficiently explore chemical space and identify islands of 'drug-like' peptides to satisfy diverse drug discovery program objectives. Here, we consider the underlying principles of and recent advances in rational, computer-enabled peptide drug design. In particular, we consider the impact of basic physicochemical properties, potency and ADME/Tox opportunities and challenges, and recently developed computational tools for enabling rational peptide drug design. Key principles and practices are spotlighted by recent case studies. We close with a hypothetical future case study.
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12
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China H, Okada Y, Dohi T. The Multiple Reactions in the Monochlorodimedone Assay: Discovery of Unique Dehalolactonizations under Mild Conditions. ASIAN J ORG CHEM 2015. [DOI: 10.1002/ajoc.201500210] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Hideyasu China
- Department of Applied Chemistry; College of Life Sciences; Ritsumeikan University; 1-1-1 Nojihigashi Kusatsu Shiga 525-8577 Japan
| | - Yutaka Okada
- Department of Applied Chemistry; College of Life Sciences; Ritsumeikan University; 1-1-1 Nojihigashi Kusatsu Shiga 525-8577 Japan
| | - Toshifumi Dohi
- Department of Pharmaceutical Sciences; College of Pharmaceutical Sciences; Ritsumeikan University; Japan
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13
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Bayden AS, Gomez EF, Audie J, Chakravorty DK, Diller DJ. A combined cheminformatic and bioinformatic approach to address the proteolytic stability challenge in peptide-based drug discovery. Biopolymers 2015; 104:775-89. [PMID: 26270398 DOI: 10.1002/bip.22711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/22/2015] [Accepted: 08/09/2015] [Indexed: 11/10/2022]
Abstract
We have created models to predict cleavage sites for several human proteases including caspase-1, caspase-3, caspase-6, caspase-7, cathepsin B, cathepsin D, cathepsin G, cathepsin K, cathepsin L, elastase-2, granzyme A, granzyme B, matrix metallopeptidase-2 (MMP2), MMP7, MMP9, thrombin, and trypsin-1. Rather than representing the sequence pattern around the potential cleavage site through a series of flags with each flag representing one of the 20 standard amino acids, we first represent each amino acid by its calculated properties. For these calculated properties, we use validated cheminformatic descriptors, such as molecular weight, logP, and polar surface area, of the individual amino acids. Finally, the cleavage site-specific descriptors are calculated through various combinations of the individual amino acid descriptors for the residues surrounding the cleavage site. Some of these combinations do not take into account the location of the residue, as long as it is in a prescribed neighborhood of the potential cleavage site, whereas others are sensitive to the precise order of the residues in the sequence. The key advantage of this approach is that it allows one to perform meaningful calculations with nonstandard amino acids for which little or no data exists. Finally, using both docking and molecular dynamics simulations, we examine the potential for and limitations of protease crystal structures to impact the design of proteolytically stable peptides.
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Affiliation(s)
| | - Edwin F Gomez
- Department of Chemistry, University of New Orleans, New Orleans, LA
| | - Joseph Audie
- CMDBioscience Inc., 5 Science Park, New Haven, CT
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14
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Ojo OO, Srinivasan DK, Owolabi BO, Flatt PR, Abdel-Wahab YH. Beneficial effects of tigerinin-1R on glucose homeostasis and beta cell function in mice with diet-induced obesity-diabetes. Biochimie 2015; 109:18-26. [DOI: 10.1016/j.biochi.2014.11.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 11/28/2014] [Indexed: 11/29/2022]
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