1
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Appavoo SD, Heller NW, van Campenhout CT, Saunders GJ, Yudin AK. Identification of "Structural Pin" Interactions and their Significance for the Conformational Control of Macrocyclic Scaffolds. Angew Chem Int Ed Engl 2024; 63:e202402372. [PMID: 38499461 DOI: 10.1002/anie.202402372] [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: 02/01/2024] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 03/20/2024]
Abstract
While peptide macrocycles with rigidified conformations have proven to be useful in the design of chemical probes of protein targets, conformational flexibility and rapid interconversion can be equally vital for biological activity and favorable physicochemical properties. This study introduces the concept of "structural pin", which describes a hydrogen bond that is largely responsible for stabilizing the entire macrocycle backbone conformation. Structural analysis of macrocycles using nuclear magnetic resonance (NMR), molecular modelling and X-ray diffraction indicates that disruption of the structural pin can drastically influence the conformation of the entire ring, resulting in novel states with increased flexibility. This finding provides a new tool to interrogate dynamic behaviour of macrocycles. Identification of structural pins offers a useful conceptual framework to understand positions that can either be modified to give flexible structures or retained to maintain the rigidity of the scaffold.
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Affiliation(s)
- Solomon D Appavoo
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada, M5S 3H6
| | - Nicholas W Heller
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada, M5S 3H6
| | - Christian T van Campenhout
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada, M5S 3H6
| | - George J Saunders
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada, M5S 3H6
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada, M5S 3H6
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2
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Chen TH, Ando A, Shamoto O, Fuse S. Effect of Brønsted Acids on the Activation of Mixed Anhydride/Mixed Carbonic Anhydride and C-Terminal-Free N-Methylated Peptide Synthesis in a Micro-Flow Reactor. Chemistry 2024; 30:e202401402. [PMID: 38719730 DOI: 10.1002/chem.202401402] [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: 04/10/2024] [Indexed: 06/19/2024]
Abstract
Amidations employing mixed (carbonic) anhydrides have long been favoured in peptide synthesis because of their cost-effectiveness and less waste generation. Despite their long history, no study has compared the effects of additives on the activation of mixed anhydrides and carbonic anhydrides. In this study, we investigated the amidation of mixed (carbonic) anhydride in the presence of a base and/or Brønsted acids. The use of NMI⋅HCl significantly improved the conversion of the mixed carbonic anhydride, while expediting nucleophilic attacks on the desired carbonyl group. In contrast, in the case of mixed anhydrides, neither the conversion nor the desired nucleophilic attack improved significantly. We developed a C-terminus-free N-methylated peptide synthesis method using mixed carbonic anhydrides in a micro-flow reactor. Fourteen N-alkylated peptides were synthesized in moderate to high yields (55-99 %) without severe racemization (<1 %). Additionally, a significant enhancement in the amidation between mixed carbonic anhydrides and bis-TMS-protected N-methyl amino acids with the inclusion of NMI⋅HCl was observed for the first time. In addition, we observed unexpected C-terminal epimerization of the C-terminus-free N-methyl peptides.
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Affiliation(s)
- Ting-Ho Chen
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Akira Ando
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Otoka Shamoto
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Shinichiro Fuse
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
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3
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Sato H, Murase H, Ishida Y, Sugiyama H, Uekusa H, Nakagawa H, Yoshida M, Doi T. Destruxin E backbone modification effects on osteoclast Morphology: Synthesis and SAR study of N-Desmethyl and N-Methyl analogs. Bioorg Med Chem 2024; 108:117777. [PMID: 38852256 DOI: 10.1016/j.bmc.2024.117777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/26/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The design and synthesis of N-desmethyl and N-methyl destruxin E analogs have been demonstrated. The X-ray single crystal structure of destruxin E (1a) revealed a stable three-dimensional (3D) structure, including a s-cis amide bond at the MeVal-MeAla moiety and two intramolecular hydrogen bonds between NH(β-Ala) and OC(Ile) and between NH(Ile) and OC(β-Ala). N-Desmethyl analogs 2a (MeAla → Ala) and 2b (MeVal → Val) were synthesized through macrolactonization similar to our previously reported synthesis of 1a. Conversely, for the synthesis of N-methyl analogs 2c (Ile → MeIle) and 2d (β-Ala → Meβ-Ala), macrolactonization did not proceed; therefore, cyclization precursors 10c and 10d were designed to maintain the intramolecular hydrogen bonds described above during their cyclization. The macrolactamization proceeded despite the presence of a less reactive N-methylamino group at the N-terminus in both cases. Analog 2a, which exhibits multiple conformers in solutions, was inactive at 50 μM, whereas analog 2b, which exhibits a conformation similar to that of 1a in solutions, exhibited morphological changes against osteoclast-like multinuclear cells at 1.6 μM. The activity of the MeIle analog 2c, which cannot take the intramolecular hydrogen bond (Ile)NH•••OC(β-Ala) in 1a, was markedly diminished compared with that of 1a, and that of the Meβ-Ala analog 2d, which cannot take the intramolecular hydrogen bond (β-Ala)NH•••OC(Ile) in 1a, was further reduced to one-fourth of that of 2c. The overall results indicate that both the s-cis amide bond at the MeVal-MeAla moiety and two intramolecular hydrogen bonds (β-Ala)NH•••OC(Ile) and (Ile)NH•••OC(β-Ala) are important for constraining the conformation of the macrocyclic peptide backbone in destruxin E, thereby exhibiting its potent biological activity.
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Affiliation(s)
- Hiroshi Sato
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan; Mitsubishi Tanabe Pharma Corporation, 1-1-1, Marunouchi, Chiyoda-ku, Tokyo 100-8205, Japan
| | - Hayato Murase
- Department of Applied Biological Chemistry, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Yoshitaka Ishida
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Haruki Sugiyama
- Research and Education Center for Natural Sciences, Keio University, 4-1-1 Hiyoshi, Kohoku 223-8521, Japan; Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo 152-8551, Japan
| | - Hidehiro Uekusa
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo 152-8551, Japan
| | - Hiroshi Nakagawa
- Department of Applied Biological Chemistry, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Masahito Yoshida
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan; Degree Programs in Pure and Applied Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukba, Ibaraki 305-8571, Japan; Department of Chemistry, Institute of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Takayuki Doi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan.
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4
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Zhong C, Zou J, Mao W, Yang P, Zhang J, Gou S, Zhang Y, Liu H, Ni J. Structure modification of anoplin for fighting resistant bacteria. Eur J Med Chem 2024; 268:116276. [PMID: 38452726 DOI: 10.1016/j.ejmech.2024.116276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/09/2024]
Abstract
The emergence of bacterial resistance has posed a significant challenge to clinical antimicrobial treatment, rendering commonly used antibiotics ineffective. The development of novel antimicrobial agents and strategies is imperative for the treatment of resistant bacterial infections. Antimicrobial peptides (AMPs) are considered a promising class of antimicrobial agents due to their low propensity for resistance and broad-spectrum activity. Anoplin is a small linear α-helical natural antimicrobial peptide that was isolated from the venom of the solitary wasp Anplius samariensis. It exhibits rich biological activity, particularly broad-spectrum antimicrobial activity and low hemolytic activity. Over the past three decades, more than 40 research publications on anoplin have been made available online. This review focuses on the advancements of anoplin in antimicrobial research, encompassing its sources, characterization, antimicrobial activity, influencing factors and structural modifications. The aim is to provide assistances for the development of new antimicrobial agents that can combat bacterial resistance.
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Affiliation(s)
- Chao Zhong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China; Institute of Pharmaceutics, School of Pharmacy, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, PR China.
| | - Jing Zou
- Institute of Pharmaceutics, School of Pharmacy, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, PR China
| | - Wenbo Mao
- Institute of Pharmaceutics, School of Pharmacy, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, PR China
| | - Ping Yang
- Institute of Pharmaceutics, School of Pharmacy, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, PR China
| | - Jingying Zhang
- Institute of Pharmaceutics, School of Pharmacy, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, PR China
| | - Sanhu Gou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China; Institute of Pharmaceutics, School of Pharmacy, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, PR China
| | - Yun Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China; Institute of Pharmaceutics, School of Pharmacy, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, PR China
| | - Hui Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China; Institute of Pharmaceutics, School of Pharmacy, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, PR China
| | - Jingman Ni
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China; Institute of Pharmaceutics, School of Pharmacy, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, PR China.
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5
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Cao L, Xu Z, Shang T, Zhang C, Wu X, Wu Y, Zhai S, Zhan Z, Duan H. Multi_CycGT: A Deep Learning-Based Multimodal Model for Predicting the Membrane Permeability of Cyclic Peptides. J Med Chem 2024; 67:1888-1899. [PMID: 38270541 DOI: 10.1021/acs.jmedchem.3c01611] [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: 01/26/2024]
Abstract
Cyclic peptides are gaining attention for their strong binding affinity, low toxicity, and ability to target "undruggable" proteins; however, their therapeutic potential against intracellular targets is constrained by their limited membrane permeability, and researchers need much time and money to test this property in the laboratory. Herein, we propose an innovative multimodal model called Multi_CycGT, which combines a graph convolutional network (GCN) and a transformer to extract one- and two-dimensional features for predicting cyclic peptide permeability. The extensive benchmarking experiments show that our Multi_CycGT model can attain state-of-the-art performance, with an average accuracy of 0.8206 and an area under the curve of 0.8650, and demonstrates satisfactory generalization ability on several external data sets. To the best of our knowledge, it is the first deep learning-based attempt to predict the membrane permeability of cyclic peptides, which is beneficial in accelerating the design of cyclic peptide active drugs in medicinal chemistry and chemical biology applications.
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Affiliation(s)
- Lujing Cao
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Zhenyu Xu
- AI Department, Shanghai Highslab Therapeutics, Inc., Shanghai 201203, China
| | - Tianfeng Shang
- AI Department, Shanghai Highslab Therapeutics, Inc., Shanghai 201203, China
| | - Chengyun Zhang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- AI Department, Shanghai Highslab Therapeutics, Inc., Shanghai 201203, China
| | - Xinyi Wu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Yejian Wu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Silong Zhai
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Zhajun Zhan
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Hongliang Duan
- Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
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6
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Myšková A, Sýkora D, Kuneš J, Maletínská L. Lipidization as a tool toward peptide therapeutics. Drug Deliv 2023; 30:2284685. [PMID: 38010881 PMCID: PMC10987053 DOI: 10.1080/10717544.2023.2284685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/12/2023] [Indexed: 11/29/2023] Open
Abstract
Peptides, as potential therapeutics continue to gain importance in the search for active substances for the treatment of numerous human diseases, some of which are, to this day, incurable. As potential therapeutic drugs, peptides have many favorable chemical and pharmacological properties, starting with their great diversity, through their high affinity for binding to all sort of natural receptors, and ending with the various pathways of their breakdown, which produces nothing but amino acids that are nontoxic to the body. Despite these and other advantages, however, they also have their pitfalls. One of these disadvantages is the very low stability of natural peptides. They have a short half-life and tend to be cleared from the organism very quickly. Their instability in the gastrointestinal tract, makes it impossible to administer peptidic drugs orally. To achieve the best pharmacologic effect, it is desirable to look for ways of modifying peptides that enable the use of these substances as pharmaceuticals. There are many ways to modify peptides. Herein we summarize the approaches that are currently in use, including lipidization, PEGylation, glycosylation and others, focusing on lipidization. We describe how individual types of lipidization are achieved and describe their advantages and drawbacks. Peptide modifications are performed with the goal of reaching a longer half-life, reducing immunogenicity and improving bioavailability. In the case of neuropeptides, lipidization aids their activity in the central nervous system after the peripheral administration. At the end of our review, we summarize all lipidized peptide-based drugs that are currently on the market.
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Affiliation(s)
- Aneta Myšková
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Prague, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic, Prague, Czech Republic
| | - David Sýkora
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Jaroslav Kuneš
- Institute of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic, Prague, Czech Republic
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lenka Maletínská
- Institute of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic, Prague, Czech Republic
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7
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L'Exact M, Comeau C, Bourhis A, Boisvert O, Fröhlich U, Létourneau D, Marsault É, Lavigne P, Grandbois M, Boudreault PL. Beyond Rule-of-five: Permeability Assessment of Semipeptidic Macrocycles. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184196. [PMID: 37400050 DOI: 10.1016/j.bbamem.2023.184196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/08/2023] [Accepted: 06/26/2023] [Indexed: 07/05/2023]
Abstract
Compounds beyond the rule-of-five are generating interest as they expand the molecular toolbox for modulating targets previously considered "undruggable". Macrocyclic peptides are an efficient class of molecules for modulating protein-protein interactions. However, predicting their permeability is difficult as they differ from small molecules. Although constrained by macrocyclization, they generally retain some conformational flexibility associated with an enhanced ability to cross biological membranes. In this study, we investigated the relationship between the structure of semi-peptidic macrocycles and their membrane permeability through structural modifications. Based on a scaffold of four amino acids and a linker, we synthesized 56 macrocycles incorporating modifications in either stereochemistry, N-methylation, or lipophilicity and assessed their passive permeability using the parallel artificial membrane permeability assay (PAMPA). Our results show that some semi-peptidic macrocycles have adequate passive permeability even with properties outside the Lipinski rule of five. We found that N-methylation in position 2 and the addition of lipophilic groups to the side chain of tyrosine led to an improvement in permeability with a decrease in tPSA and 3D-PSA. This enhancement could be attributed to the shielding effect of the lipophilic group on some regions of the macrocycle, which in turn, facilitates a favorable macrocycle conformation for permeability, suggesting some degree of chameleonic behavior.
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Affiliation(s)
- Marion L'Exact
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Christian Comeau
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Alix Bourhis
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Olivier Boisvert
- Institut de Pharmacologie de Sherbrooke, Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Ulrike Fröhlich
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Danny Létourneau
- Institut de Pharmacologie de Sherbrooke, Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Éric Marsault
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierre Lavigne
- Institut de Pharmacologie de Sherbrooke, Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Michel Grandbois
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierre-Luc Boudreault
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada.
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8
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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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9
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Mizuno-Kaneko M, Hashimoto I, Miyahara K, Kochi M, Ohashi N, Tsumura K, Suzuki K, Tamura T. Molecular Design of Cyclic Peptides with Cell Membrane Permeability and Development of MDMX-p53 Inhibitor. ACS Med Chem Lett 2023; 14:1174-1178. [PMID: 37736191 PMCID: PMC10510666 DOI: 10.1021/acsmedchemlett.3c00102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 09/23/2023] Open
Abstract
Cyclic peptides have been expected to be one of the modalities of intracellular protein-protein interaction (PPI) inhibitors, but they are generally known to have low cell membrane permeability. In this study, we focused on the conformation of cyclic peptides in the cell membrane to determine the requirement for their cell membrane permeability through passive diffusion. Utilizing the requirement, we searched for structures with high affinity for MDMX via computational chemistry and acquired cyclic peptide 19 (Papp = 0.80 × 10-6 cm s-1, IC50 = 0.07 μM).
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Affiliation(s)
- Mai Mizuno-Kaneko
- Synthetic
Organic Chemistry Laboratories, FUJIFILM
Corporation, 577, Ushijima, Kaisei-machi, Ashigarakami-gun, Kanagawa 258-8577, Japan
| | - Ichihiko Hashimoto
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Kenta Miyahara
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Masahiro Kochi
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Noriyuki Ohashi
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Kyosuke Tsumura
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Koo Suzuki
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Takashi Tamura
- Synthetic
Organic Chemistry Laboratories, FUJIFILM
Corporation, 577, Ushijima, Kaisei-machi, Ashigarakami-gun, Kanagawa 258-8577, Japan
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10
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Taherali F, Chouhan N, Wang F, Lavielle S, Baran M, McCoubrey LE, Basit AW, Yadav V. Impact of Peptide Structure on Colonic Stability and Tissue Permeability. Pharmaceutics 2023; 15:1956. [PMID: 37514143 PMCID: PMC10384666 DOI: 10.3390/pharmaceutics15071956] [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: 06/16/2023] [Revised: 07/08/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Most marketed peptide drugs are administered parenterally due to their inherent gastrointestinal (GI) instability and poor permeability across the GI epithelium. Several molecular design techniques, such as cyclisation and D-amino acid (D-AA) substitution, have been proposed to improve oral peptide drug bioavailability. However, very few of these techniques have been translated to the clinic. In addition, little is known about how synthetic peptide design may improve stability and permeability in the colon, a key site for the treatment of inflammatory bowel disease and colorectal cancer. In this study, we investigated the impact of various cyclisation modifications and D-AA substitutions on the enzymatic stability and colonic tissue permeability of native oxytocin and 11 oxytocin-based peptides. Results showed that the disulfide bond cyclisation present in native oxytocin provided an improved stability in a human colon model compared to a linear oxytocin derivative. Chloroacetyl cyclisation increased native oxytocin stability in the colonic model at 1.5 h by 30.0%, whereas thioether and N-terminal acetylated cyclisations offered no additional protection at 1.5 h. The site and number of D-AA substitutions were found to be critical for stability, with three D-AAs at Tyr, Ile and Leu, improving native oxytocin stability at 1.5 h in both linear and cyclic structures by 58.2% and 79.1%, respectively. Substitution of three D-AAs into native cyclic oxytocin significantly increased peptide permeability across rat colonic tissue; this may be because D-AA substitution favourably altered the peptide's secondary structure. This study is the first to show how the strategic design of peptide therapeutics could enable their delivery to the colon via the oral route.
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Affiliation(s)
- Farhan Taherali
- Intract Pharma Ltd., London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, UK
- Sygnature Discovery, Bio City, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Nerisha Chouhan
- Intract Pharma Ltd., London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, UK
| | - Fanjin Wang
- Intract Pharma Ltd., London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, UK
| | | | - Maryana Baran
- Orbit Discovery, Schrodinger Building, Heatley Rd, Oxford OX4 4GE, UK
| | - Laura E McCoubrey
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Abdul W Basit
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Vipul Yadav
- Intract Pharma Ltd., London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, UK
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11
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Costa L, Sousa E, Fernandes C. Cyclic Peptides in Pipeline: What Future for These Great Molecules? Pharmaceuticals (Basel) 2023; 16:996. [PMID: 37513908 PMCID: PMC10386233 DOI: 10.3390/ph16070996] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Cyclic peptides are molecules that are already used as drugs in therapies approved for various pharmacological activities, for example, as antibiotics, antifungals, anticancer, and immunosuppressants. Interest in these molecules has been growing due to the improved pharmacokinetic and pharmacodynamic properties of the cyclic structure over linear peptides and by the evolution of chemical synthesis, computational, and in vitro methods. To date, 53 cyclic peptides have been approved by different regulatory authorities, and many others are in clinical trials for a wide diversity of conditions. In this review, the potential of cyclic peptides is presented, and general aspects of their synthesis and development are discussed. Furthermore, an overview of already approved cyclic peptides is also given, and the cyclic peptides in clinical trials are summarized.
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Affiliation(s)
- Lia Costa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
| | - Emília Sousa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
| | - Carla Fernandes
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
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12
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Ramelot TA, Palmer J, Montelione GT, Bhardwaj G. Cell-permeable chameleonic peptides: Exploiting conformational dynamics in de novo cyclic peptide design. Curr Opin Struct Biol 2023; 80:102603. [PMID: 37178478 PMCID: PMC10923192 DOI: 10.1016/j.sbi.2023.102603] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/05/2023] [Indexed: 05/15/2023]
Abstract
Membrane-traversing peptides offer opportunities for targeting intracellular proteins and oral delivery. Despite progress in understanding the mechanisms underlying membrane traversal in natural cell-permeable peptides, there are still several challenges to designing membrane-traversing peptides with diverse shapes and sizes. Conformational flexibility appears to be a key determinant of membrane permeability of large macrocycles. We review recent developments in the design and validation of chameleonic cyclic peptides, which can switch between alternative conformations to enable improved permeability through cell membranes, while still maintaining reasonable solubility and exposed polar functional groups for target protein binding. Finally, we discuss the principles, strategies, and practical considerations for rational design, discovery, and validation of permeable chameleonic peptides.
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Affiliation(s)
- Theresa A Ramelot
- Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Jonathan Palmer
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA; Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
| | - Gaurav Bhardwaj
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA; Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA.
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13
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Shanker S, Sanner MF. Predicting Protein-Peptide Interactions: Benchmarking Deep Learning Techniques and a Comparison with Focused Docking. J Chem Inf Model 2023; 63:3158-3170. [PMID: 37167566 DOI: 10.1021/acs.jcim.3c00602] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The accurate prediction of protein structures achieved by deep learning (DL) methods is a significant milestone and has deeply impacted structural biology. Shortly after its release, AlphaFold2 has been evaluated for predicting protein-peptide interactions and shown to significantly outperform RoseTTAfold as well as a conventional blind docking method: PIPER-FlexPepDock. Since then, new AlphaFold2 models, trained specifically to predict multimeric assemblies, have been released and a new ab initio folding model OmegaFold has become available. Here, we assess docking success rates for these new DL folding models and compare their performance with our state-of-the-art, focused peptide-docking software AutoDock CrankPep (ADCP). The evaluation is done using the same dataset and performance metric for all methods. We show that, for a set of 99 nonredundant protein-peptide complexes, the new AlphaFold2 model outperforms other Deep Learning approaches and achieves remarkable docking success rates for peptides. While the docking success rate of ADCP is more modest when considering the top-ranking solution only, it samples correct solutions for around 62% of the complexes. Interestingly, different methods succeed on different complexes, and we describe a consensus docking approach using ADCP and AlphaFold2, which achieves a remarkable 60% for the top-ranking results and 66% for the top 5 results for this set of 99 protein-peptide complexes.
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Affiliation(s)
- Sudhanshu Shanker
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Michel F Sanner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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14
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Hosono Y, Uchida S, Shinkai M, Townsend CE, Kelly CN, Naylor MR, Lee HW, Kanamitsu K, Ishii M, Ueki R, Ueda T, Takeuchi K, Sugita M, Akiyama Y, Lokey SR, Morimoto J, Sando S. Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides. Nat Commun 2023; 14:1416. [PMID: 36932083 PMCID: PMC10023679 DOI: 10.1038/s41467-023-36978-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
Naturally occurring peptides with high membrane permeability often have ester bonds on their backbones. However, the impact of amide-to-ester substitutions on the membrane permeability of peptides has not been directly evaluated. Here we report the effect of amide-to-ester substitutions on the membrane permeability and conformational ensemble of cyclic peptides related to membrane permeation. Amide-to-ester substitutions are shown to improve the membrane permeability of dipeptides and a model cyclic hexapeptide. NMR-based conformational analysis and enhanced sampling molecular dynamics simulations suggest that the conformational transition of the cyclic hexapeptide upon membrane permeation is differently influenced by an amide-to-ester substitution and an amide N-methylation. The effect of amide-to-ester substitution on membrane permeability of other cyclic hexapeptides, cyclic octapeptides, and a cyclic nonapeptide is also investigated to examine the scope of the substitution. Appropriate utilization of amide-to-ester substitution based on our results will facilitate the development of membrane-permeable peptides.
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Affiliation(s)
- Yuki Hosono
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Satoshi Uchida
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Moe Shinkai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Colin N Kelly
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Matthew R Naylor
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Kayoko Kanamitsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mayumi Ishii
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koh Takeuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Masatake Sugita
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
- Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Yutaka Akiyama
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
- Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
| | - Scott R Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA.
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Shinsuke Sando
- Department of Chemistry and 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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15
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Li J, Yanagisawa K, Sugita M, Fujie T, Ohue M, Akiyama Y. CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides. J Chem Inf Model 2023; 63:2240-2250. [PMID: 36930969 PMCID: PMC10091415 DOI: 10.1021/acs.jcim.2c01573] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Recently, cyclic peptides have been considered breakthrough drugs because they can interact with "undruggable" targets such as intracellular protein-protein interactions. Membrane permeability is an essential indicator of oral bioavailability and intracellular targeting, and the development of membrane-permeable peptides is a bottleneck in cyclic peptide drug discovery. Although many experimental data on membrane permeability of cyclic peptides have been reported, a comprehensive database is not yet available. A comprehensive membrane permeability database is essential for developing computational methods for cyclic peptide drug design. In this study, we constructed CycPeptMPDB, the first web-accessible database of cyclic peptide membrane permeability. We collected information on a total of 7334 cyclic peptides, including the structure and experimentally measured membrane permeability, from 45 published papers and 2 patents from pharmaceutical companies. To unambiguously represent cyclic peptides larger than small molecules, we used the hierarchical editing language for macromolecules notation to generate a uniform sequence representation of peptides. In addition to data storage, CycPeptMPDB provides several supporting functions such as online data visualization, data analysis, and downloading. CycPeptMPDB is expected to be a valuable platform to support membrane permeability research on cyclic peptides. CycPeptMPDB can be freely accessed at http://cycpeptmpdb.com.
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Affiliation(s)
- Jianan Li
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Keisuke Yanagisawa
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Masatake Sugita
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Takuya Fujie
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Yutaka Akiyama
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
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16
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Pietz HL, Abbas A, Johnson ZL, Oldham ML, Suga H, Chen J. A macrocyclic peptide inhibitor traps MRP1 in a catalytically incompetent conformation. Proc Natl Acad Sci U S A 2023; 120:e2220012120. [PMID: 36893260 PMCID: PMC10089224 DOI: 10.1073/pnas.2220012120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/06/2023] [Indexed: 03/11/2023] Open
Abstract
Adenosine triphosphate-binding cassette (ABC) transporters, such as multidrug resistance protein 1 (MRP1), protect against cellular toxicity by exporting xenobiotic compounds across the plasma membrane. However, constitutive MRP1 function hinders drug delivery across the blood-brain barrier, and MRP1 overexpression in certain cancers leads to acquired multidrug resistance and chemotherapy failure. Small-molecule inhibitors have the potential to block substrate transport, but few show specificity for MRP1. Here we identify a macrocyclic peptide, named CPI1, which inhibits MRP1 with nanomolar potency but shows minimal inhibition of a related multidrug transporter P-glycoprotein. A cryoelectron microscopy (cryo-EM) structure at 3.27 Å resolution shows that CPI1 binds MRP1 at the same location as the physiological substrate leukotriene C4 (LTC4). Residues that interact with both ligands contain large, flexible sidechains that can form a variety of interactions, revealing how MRP1 recognizes multiple structurally unrelated molecules. CPI1 binding prevents the conformational changes necessary for adenosine triphosphate (ATP) hydrolysis and substrate transport, suggesting it may have potential as a therapeutic candidate.
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Affiliation(s)
- Harlan L Pietz
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY 10065
| | - Ata Abbas
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Zachary Lee Johnson
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY 10065
| | - Michael L Oldham
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY 10065
- HHMI, New York, NY 10065
| | - Hiroaki Suga
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Jue Chen
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY 10065
- HHMI, New York, NY 10065
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17
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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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18
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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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19
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Katoh T, Suga H. Ribosomal incorporation of negatively charged d-α- and N-methyl-l-α-amino acids enhanced by EF-Sep. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220038. [PMID: 36633283 PMCID: PMC9835608 DOI: 10.1098/rstb.2022.0038] [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: 02/19/2022] [Accepted: 08/10/2022] [Indexed: 01/13/2023] Open
Abstract
Ribosomal incorporation of d-α-amino acids (dAA) and N-methyl-l-α-amino acids (MeAA) with negatively charged sidechains, such as d-Asp, d-Glu, MeAsp and MeGlu, into nascent peptides is far more inefficient compared to those with neutral or positively charged ones. This is because of low binding affinity of their aminoacyl-transfer RNA (tRNA) to elongation factor-thermo unstable (EF-Tu), a translation factor responsible for accommodation of aminoacyl-tRNA onto ribosome. It is well known that EF-Tu binds to two parts of aminoacyl-tRNA, the amino acid moiety and the T-stem; however, the amino acid binding pocket of EF-Tu bearing Glu and Asp causes electric repulsion against the negatively charged amino acid charged on tRNA. To circumvent this issue, here we adopted two strategies: (i) use of an EF-Tu variant, called EF-Sep, in which the Glu216 and Asp217 residues in EF-Tu are substituted with Asn216 and Gly217, respectively; and (ii) reinforcement of the T-stem affinity using an artificially developed chimeric tRNA, tRNAPro1E2, whose T-stem is derived from Escherichia coli tRNAGlu that has high affinity to EF-Tu. Consequently, we could successfully enhance the incorporation efficiencies of d-Asp, d-Glu, MeAsp and MeGlu and demonstrated for the first time, to our knowledge, ribosomal synthesis of macrocyclic peptides containing multiple d-Asp or MeAsp. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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20
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Linker S, Schellhaas C, Kamenik AS, Veldhuizen MM, Waibl F, Roth HJ, Fouché M, Rodde S, Riniker S. Lessons for Oral Bioavailability: How Conformationally Flexible Cyclic Peptides Enter and Cross Lipid Membranes. J Med Chem 2023; 66:2773-2788. [PMID: 36762908 PMCID: PMC9969412 DOI: 10.1021/acs.jmedchem.2c01837] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Indexed: 02/11/2023]
Abstract
Cyclic peptides extend the druggable target space due to their size, flexibility, and hydrogen-bonding capacity. However, these properties impact also their passive membrane permeability. As the "journey" through membranes cannot be monitored experimentally, little is known about the underlying process, which hinders rational design. Here, we use molecular simulations to uncover how cyclic peptides permeate a membrane. We show that side chains can act as "molecular anchors", establishing the first contact with the membrane and enabling insertion. Once inside, the peptides are positioned between headgroups and lipid tails─a unique polar/apolar interface. Only one of two distinct orientations at this interface allows for the formation of the permeable "closed" conformation. In the closed conformation, the peptide crosses to the lower leaflet via another "anchoring" and flipping mechanism. Our findings provide atomistic insights into the permeation process of flexible cyclic peptides and reveal design considerations for each step of the process.
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Affiliation(s)
- Stephanie
M. Linker
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Christian Schellhaas
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Anna S. Kamenik
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Mac M. Veldhuizen
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Franz Waibl
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Hans-Jörg Roth
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Marianne Fouché
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Stephane Rodde
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Sereina Riniker
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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21
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Yamane T, Ekimoto T, Ikeguchi M. Development of the force field for cyclosporine A. Biophys Physicobiol 2022; 19:e190045. [PMID: 36567735 PMCID: PMC9751258 DOI: 10.2142/biophysico.bppb-v19.0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/17/2022] [Indexed: 11/19/2022] Open
Abstract
Membrane permeability of cyclic peptides is an important factor in drug design. To investigate the membrane permeability of cyclic peptides using molecular dynamics (MD) simulations, the accurate force fields for unnatural amino acids present in the cyclic peptides are required. Therefore, we developed the CHARMM force fields of the unnatural amino acids present in cyclosporin A (CsA), a cyclic peptide used as an immune suppressor. Especially for N-methyl amino acids, which contribute to the membrane permeability of cyclic peptides, we developed a grid correction map (CMAP) of the energy surface using the φ and ψ dihedral angles in the main chain of CsA. To validate the developed force field, we performed MD simulations, including the generalized replica exchange with solute tempering method, of CsA in water and chloroform solvents. The conformations of CsA in water and chloroform sampled using the developed force field were consistent with those of the experimental results of the solution nuclear magnetic resonance spectroscopy.
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Affiliation(s)
- Tsutomu Yamane
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan,HPC- and AI-driven Drug Development Platform Division, Center for Computational Science, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan,HPC- and AI-driven Drug Development Platform Division, Center for Computational Science, RIKEN, Yokohama, Kanagawa 230-0045, Japan
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22
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Anand U, Bandyopadhyay A, Jha NK, Pérez de la Lastra JM, Dey A. Translational aspect in peptide drug discovery and development: An emerging therapeutic candidate. Biofactors 2022; 49:251-269. [PMID: 36326181 DOI: 10.1002/biof.1913] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/11/2022] [Indexed: 11/06/2022]
Abstract
In the last two decades, protein-protein interactions (PPIs) have been used as the main target for drug development. However, with larger or superficial binding sites, it has been extremely difficult to disrupt PPIs with small molecules. On the other hand, intracellular PPIs cannot be targeted by antibodies that cannot penetrate the cell membrane. Peptides that have a combination of conformational rigidity and flexibility can be used to target difficult binding interfaces with appropriate binding affinity and specificity. Since the introduction of insulin nearly a century ago, more than 80 peptide drugs have been approved to treat a variety of diseases. These include deadly diseases such as cancer and human immunodeficiency virus infection. It is also useful against diabetes, chronic pain, and osteoporosis. Today, more research is being done on these drugs as lessons learned from earlier approaches, which are still valid today, complement newer approaches such as peptide display libraries. At the same time, integrated genomics and peptide display libraries are new strategies that open new avenues for peptide drug discovery. The purpose of this review is to examine the problems in elucidating the peptide-protein recognition mechanism. This is important to develop peptide-based interventions that interfere with endogenous protein interactions. New approaches are being developed to improve the binding affinity and specificity of existing approaches and to develop peptide agents as potentially useful drugs. We also highlight the key challenges that must be overcome in peptide drug development to realize their potential and provide an overview of recent trends in peptide drug development. In addition, we take an in-depth look at early efforts in human hormone discovery, smart medicinal chemistry and design, natural peptide drugs, and breakthrough advances in molecular biology and peptide chemistry.
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Affiliation(s)
- Uttpal Anand
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, Punjab, India
- Department of Biotechnology, School of Applied and Life Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - José M Pérez de la Lastra
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología, IPNA-CSIC, Tenerife, Spain
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
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23
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Bracegirdle J, Casandra D, Rocca JR, Adams JH, Baker BJ. Highly N-Methylated Peptides from the Antarctic Sponge Inflatella coelosphaeroides Are Active against Plasmodium falciparum. JOURNAL OF NATURAL PRODUCTS 2022; 85:2454-2460. [PMID: 36178104 DOI: 10.1021/acs.jnatprod.2c00684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Malaria, caused by the parasite Plasmodium falciparum, continues to threaten much of the world's population, and there is a pressing need for expanding treatment options. Natural products have been a vital source of such drugs, and here we report seven new highly N-methylated linear peptides, friomaramide B (2) and shagamides A-F (3-8) from the marine sponge Inflatella coelosphaeroides, collected in Antarctic waters, which demonstrate activity against three strains of blood-stage P. falciparum. The planar structures of these metabolites were solved by interpreting NMR data, as well as HRESIMS/MS fragmentation patterns, while Marfey's analysis was used to establish the configurations of the amino acids. Reisolation of the previously reported compound friomaramide A (1) allowed us to revise its structure. The panel of isolated compounds allowed establishing structure/activity relationships and provided information for future structure optimization for this class of P. falciparum inhibitory metabolites.
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Affiliation(s)
- Joe Bracegirdle
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620, United States
| | - Debora Casandra
- Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
| | - James R Rocca
- AMRIS, McKnight Brain Institute, University of Florida, P.O. Box 100015, Gainesville, Florida 32610, United States
| | - John H Adams
- Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
| | - Bill J Baker
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620, United States
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24
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Kusumoto Y, Hayashi K, Sato S, Yamada T, Kozono I, Nakata Z, Asada N, Mitsuki S, Watanabe A, Wakasa-Morimoto C, Uemura K, Arita S, Miki S, Mizutare T, Mikamiyama H. Highly Potent and Oral Macrocyclic Peptides as a HIV-1 Protease Inhibitor: mRNA Display-Derived Hit-to-Lead Optimization. ACS Med Chem Lett 2022; 13:1634-1641. [PMID: 36262395 PMCID: PMC9575168 DOI: 10.1021/acsmedchemlett.2c00310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
Human immunodeficiency virus type-1 (HIV-1) protease is essential for viral propagation, and its inhibitors are key anti-HIV-1 drug candidates. In this study, we discovered a novel HIV-1 protease inhibitor (compound 16) with potent antiviral activity and oral bioavailability using a structure-based drug design approach via X-ray crystal structure analysis and improved metabolic stability, starting from hit macrocyclic peptides identified by mRNA display against HIV-1 protease. We found that the improvement of the proteolytic stability of macrocyclic peptides by introducing a methyl group to the α-position of amino acid is crucial to exhibit strong antiviral activity. In addition, macrocyclic peptides, which have moderate metabolic stability and solubility in solutions containing taurocholic acid, exhibited desirable plasma total clearance and oral bioavailability. These approaches may contribute to the successful discovery and development of orally bioavailable peptide drugs.
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Affiliation(s)
- Yoshifumi Kusumoto
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Kyohei Hayashi
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Soichiro Sato
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Toru Yamada
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Iori Kozono
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Zenzaburo Nakata
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Naoya Asada
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Shungo Mitsuki
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Ayahisa Watanabe
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Chiaki Wakasa-Morimoto
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Kentaro Uemura
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Shuhei Arita
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Shinobu Miki
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Tohru Mizutare
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Hidenori Mikamiyama
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
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25
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Zhang Z, Chen X, Li XS, Wang CT, Niu ZJ, Zhang BS, Liu XY, Liang YM. Ortho C–H Hydroxyalkylation or Methylation of Aryl Iodides by Ethers and TMSI via a Catellani Strategy. Org Lett 2022; 24:6897-6902. [DOI: 10.1021/acs.orglett.2c02425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhe Zhang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Xi Chen
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Xue-Song Li
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Cui-Tian Wang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Zhi-Jie Niu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Bo-Sheng Zhang
- College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, China
| | - Xue-Yuan Liu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Yong-Min Liang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China
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26
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van Neer RHP, Dranchak PK, Liu L, Aitha M, Queme B, Kimura H, Katoh T, Battaile KP, Lovell S, Inglese J, Suga H. Serum-Stable and Selective Backbone-N-Methylated Cyclic Peptides That Inhibit Prokaryotic Glycolytic Mutases. ACS Chem Biol 2022; 17:2284-2295. [PMID: 35904259 PMCID: PMC9900472 DOI: 10.1021/acschembio.2c00403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
N-Methylated amino acids (N-MeAAs) are privileged residues of naturally occurring peptides critical to bioactivity. However, de novo discovery from ribosome display is limited by poor incorporation of N-methylated amino acids into the nascent peptide chain attributed to a poor EF-Tu affinity for the N-methyl-aminoacyl-tRNA. By reconfiguring the tRNA's T-stem region to compensate and tune the EF-Tu affinity, we conducted Random nonstandard Peptides Integrated Discovery (RaPID) display of a macrocyclic peptide (MCP) library containing six different N-MeAAs. We have here devised a "pool-and-split" enrichment strategy using the RaPID display and identified N-methylated MCPs against three species of prokaryotic metal-ion-dependent phosphoglycerate mutases. The enriched MCPs reached 57% N-methylation with up to three consecutively incorporated N-MeAAs, rivaling natural products. Potent nanomolar inhibitors ranging in ortholog selectivity, strongly mediated by N-methylation, were identified. Co-crystal structures reveal an architecturally related Ce-2 Ipglycermide active-site metal-ion-coordinating Cys lariat MCP, functionally dependent on two cis N-MeAAs with broadened iPGM species selectivity over the original nematode-selective MCPs. Furthermore, the isolation of a novel metal-ion-independent Staphylococcus aureus iPGM inhibitor utilizing a phosphoglycerate mimetic mechanism illustrates the diversity of possible chemotypes encoded by the N-MeAA MCP library.
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Affiliation(s)
- R H P van Neer
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - P K Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - L Liu
- Protein Structure and X-ray Crystallography Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66045, United States
| | - M Aitha
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - B Queme
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - H Kimura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - T Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - K P Battaile
- New York Structural Biology Center, NSLS-II, Upton, New York 11973, United States
| | - S Lovell
- Protein Structure and X-ray Crystallography Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66045, United States
| | - J Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - H Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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27
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Sarkar S, Gu W, Schmidt EW. Applying Promiscuous RiPP Enzymes to Peptide Backbone N-Methylation Chemistry. ACS Chem Biol 2022; 17:2165-2178. [PMID: 35819062 PMCID: PMC9526446 DOI: 10.1021/acschembio.2c00293] [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] [Indexed: 11/29/2022]
Abstract
The methylation of peptide backbone amides is a hallmark of bioactive natural products, and it also greatly modifies the pharmacology of synthetic peptides. Usually, bioactive N-methylated peptides are cyclic. However, there is very limited knowledge about how post-translational enzymes can be applied to the synthesis of designed N-methylated peptides or peptide libraries. Here, driven by the established ability of some RiPP enzymes to process diverse substrates, we sought to define catalysts for the in vivo and in vitro macrocyclization of backbone-methylated peptides. We developed efficient methods in which short, synthetic N-methylated peptides could be modified using side chain and mainchain macrocyclases, PsnB and PCY1 from plesiocin and orbitide biosynthetic pathways, respectively. Most significantly, a strategy for PsnB cyclase was designed enabling simple in vitro methods compatible with solid-phase peptide synthesis. We show that cyanobactin N-terminal protease PatA is a broadly useful catalyst that is also compatible with N-methylation chemistry, but that cyanobactin macrocyclase PatG is strongly biased against N-methylated substrates. Finally, we sought to marry these macrocyclase tools with an enzyme that N-methylates its core peptide: OphMA from the omphalotin pathway. However, instead, we reveal some limitations of OphMA and demonstrate that it unexpectedly and extensively modified the enzyme itself in vivo. Together, these results demonstrate proof-of-concept for enzymatic synthesis of N-methylated peptide macrocycles.
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Affiliation(s)
| | | | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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28
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Saunders GJ, Yudin AK. Property‐Driven Development of Passively Permeable Macrocyclic Scaffolds Using Heterocycles**. Angew Chem Int Ed Engl 2022; 61:e202206866. [DOI: 10.1002/anie.202206866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Indexed: 12/18/2022]
Affiliation(s)
- George J. Saunders
- Davenport Research Laboratories University of Toronto 80 St. George St Toronto Ontario, M5S 3H6 Canada
| | - Andrei K. Yudin
- Davenport Research Laboratories University of Toronto 80 St. George St Toronto Ontario, M5S 3H6 Canada
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29
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Ohsawa K, Fukaya S, Doi T. Total Synthesis and Structural Determination of Cyclodepsipeptide Decatransin. Org Lett 2022; 24:5552-5556. [PMID: 35867629 DOI: 10.1021/acs.orglett.2c02085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure determination of the 30-membered cyclodepsipeptide decatransin was demonstrated on the basis of total synthesis. Both (R)- and (S)-2-hydroxy-5-methylhexanoic acid derivatives were prepared via the Evans asymmetric alkylation. N-Alkyl-enriched peptide fragments were synthesized by the Cbz strategy in the solution phase without formation of diketopiperazine and epimerization. The synthesis of putative candidates was achieved by convergent peptide coupling of three peptide fragments, followed by macrocyclization under the Mitsunobu conditions.
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Affiliation(s)
- Kosuke Ohsawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Sakiko Fukaya
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Takayuki Doi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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30
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Rzepiela AA, Viarengo-Baker LA, Tatarskii V, Kombarov R, Whitty A. Conformational Effects on the Passive Membrane Permeability of Synthetic Macrocycles. J Med Chem 2022; 65:10300-10317. [PMID: 35861996 DOI: 10.1021/acs.jmedchem.1c02090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Macrocyclic compounds (MCs) can have complex conformational properties that affect pharmacologically important behaviors such as membrane permeability. We measured the passive permeability of 3600 diverse nonpeptidic MCs and used machine learning to analyze the results. Incorporating selected properties based on the three-dimensional (3D) conformation gave models that predicted permeability with Q2 = 0.81. A biased spatial distribution of polar versus nonpolar regions was particularly important for good permeability, consistent with a mechanism in which the initial insertion of nonpolar portions of a MC helps facilitate the subsequent membrane entry of more polar parts. We also examined effects on permeability of 800 substructural elements by comparing matched molecular pairs. Some substitutions were invariably beneficial or invariably deleterious to permeability, while the influence of others was highly contextual. Overall, the work provides insights into how the permeability of MCs is influenced by their 3D conformational properties and suggests design hypotheses for achieving macrocycles with high membrane permeability.
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Affiliation(s)
- Anna A Rzepiela
- Pyxis Discovery, Delftechpark 26, 2628XH Delft, The Netherlands
| | - Lauren A Viarengo-Baker
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Victor Tatarskii
- Asinex Corporation, 101 N Chestnut St # 104, Winston-Salem, North Carolina 27101,United States
| | - Roman Kombarov
- Asinex Corporation, 101 N Chestnut St # 104, Winston-Salem, North Carolina 27101,United States
| | - Adrian Whitty
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Center for Molecular Discovery, Boston University, 24 Cummington Mall, Boston, Massachusetts 02215, United States
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31
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Klepach A, Tran H, Ahmad Mohammed F, ElSayed ME. Characterization and impact of peptide physicochemical properties on oral and subcutaneous delivery. Adv Drug Deliv Rev 2022; 186:114322. [PMID: 35526665 DOI: 10.1016/j.addr.2022.114322] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/21/2022] [Accepted: 05/02/2022] [Indexed: 11/25/2022]
Abstract
Peptides, an emerging modality within the biopharmaceutical industry, are often delivered subcutaneously with evolving prospects on oral delivery. Barrier biology within the subcutis or gastrointestinal tract is a significant challenge in limiting absorption or otherwise disrupting peptide disposition. Aspects of peptide pharmacokinetic performance and ADME can be mitigated with careful molecular design that tailors for properties such as effective size, hydrophobicity, net charge, proteolytic stability, and albumin binding. In this review, we endeavor to highlight effective techniques in qualifying physicochemical properties of peptides and discuss advancements of in vitro models of subcutaneous and oral delivery. Additionally, we will delineate empirical findings around the relationship of these physicochemical properties and in vivo (animal or human) impact. We conclude that robust peptide characterization methods and in vitro techniques with demonstrated correlations to in vivo data are key routines to incorporate in the drug discovery and development to improve the probability of technical and commercial success of peptide therapeutics.
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32
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Saunders GJ, Yudin AK. Property‐Driven Development of Passively Permeable Macrocyclic Scaffolds using Heterocycles. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- George J. Saunders
- University of Toronto - St George Campus: University of Toronto Chemistry 80 St George St M5S3H6 Toronto CANADA
| | - Andrei K. Yudin
- University of Toronto Department of Chemistry 80 St. George Street M5S 3H6 Toronto CANADA
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33
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Abstract
Peptides have traditionally been perceived as poor drug candidates due to unfavorable characteristics mainly regarding their pharmacokinetic behavior, including plasma stability, membrane permeability and circulation half-life. Nonetheless, in recent years, general strategies to tackle those shortcomings have been established, and peptides are subsequently gaining increasing interest as drugs due to their unique ability to combine the advantages of antibodies and small molecules. Macrocyclic peptides are a special focus of drug development efforts due to their ability to address so called ‘undruggable’ targets characterized by large and flat protein surfaces lacking binding pockets. Here, the main strategies developed to date for adapting peptides for clinical use are summarized, which may soon help usher in an age highly shaped by peptide-based therapeutics. Nonetheless, limited membrane permeability is still to overcome before peptide therapeutics will be broadly accepted.
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34
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Thurston R, Zantop V, Park KS, Maid H, Seitz A, Heinrich MR. pH-Dependent Conformational Switching of Amide Bonds─from Full trans to Full cis and Vice Versa. Org Lett 2022; 24:3488-3492. [PMID: 35544347 DOI: 10.1021/acs.orglett.2c00938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Strategies enabling the pH-dependent conformational switching of amide bonds from trans to cis, and vice versa, are yet limited in the sense that, in a suitable pH range, one rotamer may be stabilized to a large extent while the complementary pH range only leads to a mixture of isomers. By exploiting the effects of steric demand and the interaction of the amide carbonyl with a positive charge, we herein present the first examples for reversible pH-dependent switching from full trans to full cis.
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Affiliation(s)
- Ryan Thurston
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Viviane Zantop
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Kristen Sodam Park
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Harald Maid
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Organic Chemistry II, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Anke Seitz
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Markus R Heinrich
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
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35
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Faugeras V, Duclos O, Bazile D, Thiam AR. Impact of Cyclization and Methylation on Peptide Penetration through Droplet Interface Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:5682-5691. [PMID: 35452243 DOI: 10.1021/acs.langmuir.2c00269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cell-penetrating peptides enter cells via diverse mechanisms, such as endocytosis, active transport, or direct translocation. For the design of orally delivered cell-penetrating peptides, it is crucial to know the contribution of these different mechanisms. In particular, the ability of a peptide to translocate through a lipid bilayer remains a key parameter for the delivery of cargos. However, existing approaches used to assess translocation often provide discrepant results probably because they have different sensitivities to the distinct translocation mechanisms. Here, we focus on the passive permeation of a range of hydrophobic cyclic peptides inspired by somatostatin, a somatotropin release-inhibiting factor. Using droplet interface bilayers (DIB), we assess the passive membrane permeability of these peptides and study the impact of the peptide cyclization and backbone methylation on translocation rates. Cyclization systematically improved the permeability of the tested peptides while methylation did not. By studying the interaction of the peptides with the DIB interfaces, we found membrane insertion and peptide intrinsic diffusion to be two independent factors of permeability. Compared to the industrial gold standard Caco-2 and parallel artificial membrane permeability assay (PAMPA) models, DIBs provide intermediate membrane permeability values, closer to Caco-2. Even for conditions where Caco-2 and PAMPA are discrepant, the DIB approach also gives results closer to Caco-2. Thereupon, DIBs represent a robust alternative to the PAMPA approach for predicting the permeability of peptides, even if the latter present extremely small structural differences.
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Affiliation(s)
- Vincent Faugeras
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris Cité, F-75005 Paris, France
- Pharmaceutics Development Platform, Sanofi R&D, 94250 Gentilly, France
| | - Olivier Duclos
- Integrated Drug Discovery Platform, Sanofi R&D, 91380 Chilly-Mazarin, France
| | - Didier Bazile
- Pharmaceutics Development Platform, Sanofi R&D, 94250 Gentilly, France
| | - Abdou Rachid Thiam
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris Cité, F-75005 Paris, France
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36
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Lai Z, Yuan X, Chen H, Zhu Y, Dong N, Shan A. Strategies employed in the design of antimicrobial peptides with enhanced proteolytic stability. Biotechnol Adv 2022; 59:107962. [PMID: 35452776 DOI: 10.1016/j.biotechadv.2022.107962] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/14/2022] [Accepted: 04/13/2022] [Indexed: 12/12/2022]
Abstract
Due to the alarming developing rate of multidrug-resistant bacterial pathogens, the development and modification of antimicrobial peptides (AMPs) are unprecedentedly active. Despite the fact that considerable efforts have been expended on the discovery and design strategies of AMPs, the clinical translation of peptide antibiotics remains inadequate. A large number of articles and reviews credited the limited success of AMPs to their poor stability in the biological environment, particularly their poor proteolytic stability. In the past forty years, various design strategies have been used to improve the proteolytic stability of AMPs, such as sequence modification, cyclization, peptidomimetics, and nanotechnology. Herein, we focus our discussion on the progress made in improving the proteolytic stability of AMPs and the principle, successes, and limitations of various anti-proteolytic design strategies. It is of prospective significance to extend current insights into the degradation-related inactivation of AMPs and also alleviate/overcome the problem.
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Affiliation(s)
- Zhenheng Lai
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Xiaojie Yuan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Hongyu Chen
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Yunhui Zhu
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Na Dong
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China.
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37
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Kremsmayr T, Aljnabi A, Blanco-Canosa JB, Tran HNT, Emidio NB, Muttenthaler M. On the Utility of Chemical Strategies to Improve Peptide Gut Stability. J Med Chem 2022; 65:6191-6206. [PMID: 35420805 PMCID: PMC9059125 DOI: 10.1021/acs.jmedchem.2c00094] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Inherent susceptibility
of peptides to enzymatic degradation in
the gastrointestinal tract is a key bottleneck in oral peptide drug
development. Here, we present a systematic analysis of (i) the gut
stability of disulfide-rich peptide scaffolds, orally administered
peptide therapeutics, and well-known neuropeptides and (ii) medicinal
chemistry strategies to improve peptide gut stability. Among a broad
range of studied peptides, cyclotides were the only scaffold class
to resist gastrointestinal degradation, even when grafted with non-native
sequences. Backbone cyclization, a frequently applied strategy, failed
to improve stability in intestinal fluid, but several site-specific
alterations proved efficient. This work furthermore highlights the
importance of standardized gut stability test conditions and suggests
defined protocols to facilitate cross-study comparison. Together,
our results provide a comparative overview and framework for the chemical
engineering of gut-stable peptides, which should be valuable for the
development of orally administered peptide therapeutics and molecular
probes targeting receptors within the gastrointestinal tract.
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Affiliation(s)
- Thomas Kremsmayr
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, Vienna 1090, Austria
| | - Aws Aljnabi
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, Vienna 1090, Austria
| | - Juan B Blanco-Canosa
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, Barcelona 08034, Spain
| | - Hue N T Tran
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Nayara Braga Emidio
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Markus Muttenthaler
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, Vienna 1090, Austria.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
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38
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Taechalertpaisarn J, Ono S, Okada O, Johnstone TC, Scott Lokey R. A New Amino Acid for Improving Permeability and Solubility in Macrocyclic Peptides through Side Chain-to-Backbone Hydrogen Bonding. J Med Chem 2022; 65:5072-5084. [PMID: 35275623 PMCID: PMC10681114 DOI: 10.1021/acs.jmedchem.2c00010] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite the notoriously poor membrane permeability of peptides, many cyclic peptide natural products show high passive membrane permeability and potently inhibit a variety of "undruggable" intracellular targets. A major impediment to the design of cyclic peptides with good permeability is the high desolvation energy associated with the peptide backbone amide NH groups. While several strategies have been proposed to mitigate this deleterious effect, only few studies have used polar side chains to sequester backbone NH groups. We investigated the ability of N,N-pyrrolidinylglutamine (Pye), whose side chain contains a powerful hydrogen-bond-accepting C═O amide group but no hydrogen-bond donors, to sequester exposed backbone NH groups in a series of cyclic hexapeptide diastereomers. Analyses revealed that specific Leu-to-Pye substitutions conferred dramatic improvements in aqueous solubility and permeability in a scaffold- and position-dependent manner. Therefore, this approach offers a complementary tool for improving membrane permeability and solubility in cyclic peptides.
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Affiliation(s)
- Jaru Taechalertpaisarn
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Satoshi Ono
- Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshidacho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Okimasa Okada
- Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshidacho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Timothy C. Johnstone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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39
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Zhang H, Chen S. Cyclic peptide drugs approved in the last two decades (2001-2021). RSC Chem Biol 2022; 3:18-31. [PMID: 35128405 PMCID: PMC8729179 DOI: 10.1039/d1cb00154j] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/05/2021] [Indexed: 01/01/2023] Open
Abstract
In contrast to the major families of small molecules and antibodies, cyclic peptides, as a family of synthesizable macromolecules, have distinct biochemical and therapeutic properties for pharmaceutical applications. Cyclic peptide-based drugs have increasingly been developed in the past two decades, confirming the common perception that cyclic peptides have high binding affinities and low metabolic toxicity as antibodies, good stability and ease of manufacture as small molecules. Natural peptides were the major source of cyclic peptide drugs in the last century, and cyclic peptides derived from novel screening and cyclization strategies are the new source. In this review, we will discuss and summarize 18 cyclic peptides approved for clinical use in the past two decades to provide a better understanding of cyclic peptide development and to inspire new perspectives. The purpose of the present review is to promote efforts to resolve the challenges in the development of cyclic peptide drugs that are more effective.
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Affiliation(s)
- Huiya Zhang
- Biotech Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
| | - Shiyu Chen
- Biotech Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
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40
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Wu C, Hoang HN, Hill TA, Lim J, Kok WM, Akondi K, Liu L, Fairlie DP. Helical structure in cyclic peptides: effect of N-methyl amides versus esters. Chem Commun (Camb) 2022; 58:12475-12478. [DOI: 10.1039/d2cc05092g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclic peptides with esters but not N-methyl amides are the smallest known alpha helices in water and can enter cells.
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Affiliation(s)
- Chongyang Wu
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Huy N. Hoang
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Timothy A. Hill
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Junxian Lim
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - W. Mei Kok
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Kalyani Akondi
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Ligong Liu
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - David P. Fairlie
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
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41
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Klein VG, Bond AG, Craigon C, Lokey RS, Ciulli A. Amide-to-Ester Substitution as a Strategy for Optimizing PROTAC Permeability and Cellular Activity. J Med Chem 2021; 64:18082-18101. [PMID: 34881891 PMCID: PMC8713283 DOI: 10.1021/acs.jmedchem.1c01496] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Criteria for predicting the druglike properties of "beyond Rule of 5" Proteolysis Targeting Chimeras (PROTAC) degraders are underdeveloped. PROTAC components are often combined via amide couplings due to their reliability. Amides, however, can give rise to poor absorption, distribution, metabolism, and excretion (ADME) properties. We hypothesized that a bioisosteric amide-to-ester substitution could lead to improvements in both physicochemical properties and bioactivity. Using model compounds, bearing either amides or esters, we identify parameters for optimal lipophilicity and permeability. We applied these learnings to design a set of novel amide-to-ester-substituted, VHL-based BET degraders with the goal to increase permeability. Our ester PROTACs retained intracellular stability, were overall more potent degraders than their amide counterparts, and showed an earlier onset of the hook effect. These enhancements were driven by greater cell permeability rather than improvements in ternary complex formation. This largely unexplored amide-to-ester substitution provides a simple strategy to enhance PROTAC permeability and bioactivity and may prove beneficial to other beyond Ro5 molecules.
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Affiliation(s)
- Victoria G Klein
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Adam G Bond
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - Conner Craigon
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
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42
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Hosono Y, Morimoto J, Sando S. A comprehensive study on the effect of backbone stereochemistry of a cyclic hexapeptide on membrane permeability and microsomal stability. Org Biomol Chem 2021; 19:10326-10331. [PMID: 34821247 DOI: 10.1039/d1ob02090k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Backbone stereochemistry of cyclic peptides has been reported to have a great influence on microsomal stability and membrane permeability, two important factors that determine oral bioavailability. Here, we comprehensively investigated the correlation between the backbone stereochemistry of cyclic hexapeptide stereoisomers and their stability in liver microsomes, as well as passive membrane permeability.
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Affiliation(s)
- Yuki Hosono
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Shinsuke Sando
- Department of Chemistry and 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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43
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Ono T, Aikawa K, Okazoe T, Morimoto J, Sando S. Methyl to trifluoromethyl substitution as a strategy to increase the membrane permeability of short peptides. Org Biomol Chem 2021; 19:9386-9389. [PMID: 34676842 DOI: 10.1039/d1ob01565f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Here, we investigated the effect of CH3 to CF3 substitution on the membrane permeability of peptides. We synthesized a series of peptides with CF3 groups and corresponding nonfluorinated peptides and measured the membrane permeability of the peptides. As a result, we demonstrated that CH3 to CF3 substitution is useful for increasing the membrane permeability of di-/tri-peptides.
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Affiliation(s)
- Takahiro Ono
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Kohsuke Aikawa
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Takashi Okazoe
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan. .,Material Integration Laboratories, Yokohama Technical Center, AGC Inc., Yokohama 230-0045, Japan
| | - Jumpei Morimoto
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Shinsuke Sando
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan. .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
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44
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Steverlynck J, Sitdikov R, Rueping M. The Deuterated "Magic Methyl" Group: A Guide to Site-Selective Trideuteromethyl Incorporation and Labeling by Using CD 3 Reagents. Chemistry 2021; 27:11751-11772. [PMID: 34076925 PMCID: PMC8457246 DOI: 10.1002/chem.202101179] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Indexed: 12/12/2022]
Abstract
In the field of medicinal chemistry, the precise installation of a trideuteromethyl group is gaining ever-increasing attention. Site-selective incorporation of the deuterated "magic methyl" group can provide profound pharmacological benefits and can be considered an important tool for drug optimization and development. This review provides a structured overview, according to trideuteromethylation reagent, of currently established methods for site-selective trideuteromethylation of carbon atoms. In addition to CD3 , the selective introduction of CD2 H and CDH2 groups is also considered. For all methods, the corresponding mechanism and scope are discussed whenever reported. As such, this review can be a starting point for synthetic chemists to further advance trideuteromethylation methodologies. At the same time, this review aims to be a guide for medicinal chemists, offering them the available C-CD3 formation strategies for the preparation of new or modified drugs.
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Affiliation(s)
- Joost Steverlynck
- Kaust Catalysis Center (KCC)King Abdullah University Science and Technology (KAUST)Thuwal23955-6900Saudi Arabia
| | - Ruzal Sitdikov
- Kaust Catalysis Center (KCC)King Abdullah University Science and Technology (KAUST)Thuwal23955-6900Saudi Arabia
| | - Magnus Rueping
- Kaust Catalysis Center (KCC)King Abdullah University Science and Technology (KAUST)Thuwal23955-6900Saudi Arabia
- Institute for Experimental Molecular ImagingRWTH Aachen UniversityForckenbeckstrasse 5552074Aachen
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45
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Liu F, Ye ZP, Hu YZ, Gao J, Zheng L, Chen K, Xiang HY, Chen XQ, Yang H. N, N, N', N'-Tetramethylethylenediamine-Enabled Photoredox-Catalyzed C-H Methylation of N-Heteroarenes. J Org Chem 2021; 86:11905-11914. [PMID: 34344150 DOI: 10.1021/acs.joc.1c01325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Aiming at the valuable methylation process, readily available and inexpensive N,N,N',N'-tetramethylethylenediamine (TMEDA) was first identified as a new methyl source in photoredox-catalyzed transformation in this work. By virtue of this simple methylating reagent, a facile and practical protocol for the direct C-H methylation of N-heteroarenes was developed, featuring mild reaction conditions, broad substrate scope, and scalability. Mechanistic studies disclosed that a sequential photoredox, base-assisted proton shift, fragmentation, and tautomerization process was essentially involved.
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Affiliation(s)
- Fang Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Zhi-Peng Ye
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Yuan-Zhuo Hu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Jie Gao
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Lan Zheng
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Kai Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China.,Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Hao-Yue Xiang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Xiao-Qing Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China.,Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, P. R. China
| | - Hua Yang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China.,Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, P. R. China
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46
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Sanner MF, Dieguez L, Forli S, Lis E. Improving Docking Power for Short Peptides Using Random Forest. J Chem Inf Model 2021; 61:3074-3090. [PMID: 34124893 PMCID: PMC8543977 DOI: 10.1021/acs.jcim.1c00573] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In recent years, therapeutic peptides have gained a lot interest as demonstrated by the 60 peptides approved as drugs in major markets and 150+ peptides currently in clinical trials. However, while small molecule docking is routinely used in rational drug design efforts, docking peptides has proven challenging partly because docking scoring functions, developed and calibrated for small molecules, perform poorly for these molecules. Here, we present random forest classifiers trained to discriminate correctly docked peptides. We show that, for a testing set of 47 protein-peptide complexes, structurally dissimilar from the training set and previously used to benchmark AutoDock Vina's ability to dock short peptides, these random forest classifiers improve docking power from ∼25% for AutoDock scoring functions to an average of ∼70%. These results pave the way for peptide-docking success rates comparable to those of small molecule docking. To develop these classifiers, we compiled the ProptPep37_2021 data set, a curated, high-quality set of 322 crystallographic protein-peptides complexes annotated with structural similarity information. The data set also provides a collection of high-quality putative poses with a range of deviations from the crystallographic pose, providing correct and incorrect poses (i.e., decoys) of the peptide for each entry. The ProptPep37_2021 data set as well as the classifiers presented here are freely available.
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Affiliation(s)
- Michel F. Sanner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 93037, USA
| | - Leonard Dieguez
- Koliber Biosciences Inc., 12265 World Trade Drive, Suite G, San Diego, CA 92128, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 93037, USA
| | - Ewa Lis
- Koliber Biosciences Inc., 12265 World Trade Drive, Suite G, San Diego, CA 92128, USA
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47
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Lee D, Lee S, Choi J, Song YK, Kim MJ, Shin DS, Bae MA, Kim YC, Park CJ, Lee KR, Choi JH, Seo J. Interplay among Conformation, Intramolecular Hydrogen Bonds, and Chameleonicity in the Membrane Permeability and Cyclophilin A Binding of Macrocyclic Peptide Cyclosporin O Derivatives. J Med Chem 2021; 64:8272-8286. [PMID: 34096287 DOI: 10.1021/acs.jmedchem.1c00211] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A macrocyclic peptide scaffold with well-established structure-property relationship is desirable for tackling undruggable targets. Here, we adopted a natural macrocycle, cyclosporin O (CsO) and its derivatives (CP1-3), and evaluated the impact of conformation on membrane permeability, cyclophilin A (CypA) binding, and the pharmacokinetic (PK) profile. In nonpolar media, CsO showed a similar conformation to cyclosporin A (CsA), a well-known chameleonic macrocycle, but less chameleonic behavior in a polar environment. The weak chameleonicity of CsO resulted in decreased membrane permeability; however, the more rigid conformation of CsO was not detrimental to its PK profile. CsO exhibited a higher plasma concentration than CsA, which resulted from minimal CypA binding and lower accumulation in red blood cells and moderate oral bioavailability (F = 12%). Our study aids understanding of CsO, a macrocyclic peptide that is less explored than CsA but with greater potential for diversity generation and rational design.
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Affiliation(s)
- Dongjae Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Sungjin Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jieun Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Yoo-Kyung Song
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Min Ju Kim
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Dae-Seop Shin
- Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Myung Ae Bae
- Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Yong-Chul Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Kyeong-Ryoon Lee
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jiwon Seo
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
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Adaligil E, Song A, Hallenbeck KK, Cunningham CN, Fairbrother WJ. Ribosomal Synthesis of Macrocyclic Peptides with β 2- and β 2,3-Homo-Amino Acids for the Development of Natural Product-Like Combinatorial Libraries. ACS Chem Biol 2021; 16:1011-1018. [PMID: 34008946 DOI: 10.1021/acschembio.1c00062] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The development of large, natural-product-like, combinatorial macrocyclic peptide libraries is essential in the quest to develop therapeutics for "undruggable" cellular targets. Herein we report the ribosomal synthesis of macrocyclic peptides containing one or more β2-homo-amino acids (β2haa) to enable their incorporation into mRNA display-based selection libraries. We confirmed the compatibility of 14 β2-homo-amino acids, (S)- and (R)-stereochemistry, for single incorporation into a macrocyclic peptide with low to high translation efficiency. Interestingly, N-methylation of the backbone amide of β2haa prevented the incorporation of this amino acid subclass by the ribosome. Additionally, we designed and incorporated several α,β-disubstituted β2,3-homo-amino acids (β2,3haa) with different R-groups on the α- and β-carbons of the same amino acid. Incorporation of these β2,3haa enables increased diversity in a single position of a macrocyclic peptide without significantly increasing the overall molecular weight, which is an important consideration for passive cell permeability. We also successfully incorporated multiple (S)-β2hAla into a single macrocycle with other non-proteinogenic amino acids, confirming that this class of β-amino acid is suitable for development of large scale macrocyclic peptide libraries.
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Affiliation(s)
- Emel Adaligil
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Aimin Song
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Kenneth K. Hallenbeck
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Wayne J. Fairbrother
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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Wang W, Khojasteh SC, Su D. Biosynthetic Strategies for Macrocyclic Peptides. Molecules 2021; 26:3338. [PMID: 34206124 PMCID: PMC8199541 DOI: 10.3390/molecules26113338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/28/2022] Open
Abstract
Macrocyclic peptides are predominantly peptide structures bearing one or more rings and spanning multiple amino acid residues. Macrocyclization has become a common approach for improving the pharmacological properties and bioactivity of peptides. A variety of ribosomal-derived and non-ribosomal synthesized cyclization approaches have been established. The biosynthesis of backbone macrocyclic peptides using seven new emerging methodologies will be discussed with regard to the features and strengths of each platform rather than medicinal chemistry tools. The mRNA display variant, known as the random nonstandard peptide integrated discovery (RaPID) platform, utilizes flexible in vitro translation (FIT) to access macrocyclic peptides containing nonproteinogenic amino acids (NAAs). As a new discovery approach, the ribosomally synthesized and post-translationally modified peptides (RiPPs) method involves the combination of ribosomal synthesis and the phage screening platform together with macrocyclization chemistries to generate libraries of macrocyclic peptides. Meanwhile, the split-intein circular ligation of peptides and proteins (SICLOPPS) approach relies on the in vivo production of macrocyclic peptides. In vitro and in vivo peptide library screening is discussed as an advanced strategy for cyclic peptide selection. Specifically, biosynthetic bicyclic peptides are highlighted as versatile and attractive modalities. Bicyclic peptides represent another type of promising therapeutics that allow for building blocks with a heterotrimeric conjugate to address intractable challenges and enable multimer complexes via linkers. Additionally, we discuss the cell-free chemoenzymatic synthesis of macrocyclic peptides with a non-ribosomal catalase known as the non-ribosomal synthetase (NRPS) and chemo-enzymatic approach, with recombinant thioesterase (TE) domains. Novel insights into the use of peptide library tools, activity-based two-hybrid screening, structure diversification, inclusion of NAAs, combinatorial libraries, expanding the toolbox for macrocyclic peptides, bicyclic peptides, chemoenzymatic strategies, and future perspectives are presented. This review highlights the broad spectrum of strategy classes, novel platforms, structure diversity, chemical space, and functionalities of macrocyclic peptides enabled by emerging biosynthetic platforms to achieve bioactivity and for therapeutic purposes.
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Affiliation(s)
| | | | - Dian Su
- Drug Metabolism and Disposition, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA; (W.W.); (S.C.K.)
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Improvement on Permeability of Cyclic Peptide/Peptidomimetic: Backbone N-Methylation as A Useful Tool. Mar Drugs 2021; 19:md19060311. [PMID: 34072121 PMCID: PMC8229464 DOI: 10.3390/md19060311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
Peptides have a three-dimensional configuration that can adopt particular conformations for binding to proteins, which are well suited to interact with larger contact surface areas on target proteins. However, low cell permeability is a major challenge in the development of peptide-related drugs. In recent years, backbone N-methylation has been a useful tool for manipulating the permeability of cyclic peptides/peptidomimetics. Backbone N-methylation permits the adjustment of molecule’s conformational space. Several pathways are involved in the drug absorption pathway; the relative importance of each N-methylation to total permeation is likely to differ with intrinsic properties of cyclic peptide/peptidomimetic. Recent studies on the permeability of cyclic peptides/peptidomimetics using the backbone N-methylation strategy and synthetic methodologies will be presented in this review.
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