1
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Huang G, Cierpicki T, Grembecka J. Thioamides in medicinal chemistry and as small molecule therapeutic agents. Eur J Med Chem 2024; 277:116732. [PMID: 39106658 DOI: 10.1016/j.ejmech.2024.116732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/18/2024] [Accepted: 07/30/2024] [Indexed: 08/09/2024]
Abstract
Thioamides, which are fascinating isosteres of amides, have garnered significant attention in drug discovery and medicinal chemistry programs, spanning peptides and small molecule compounds. This review provides an overview of the various applications of thioamides in small molecule therapeutic agents targeting a range of human diseases, including cancer, microbial infections (e.g., tuberculosis, bacteria, and fungi), viral infections, neurodegenerative conditions, analgesia, and others. Particular focus is given to design strategies of biologically active thioamide-containing compounds and their biological targets, such as kinases and histone methyltransferase ASH1L. Additionally, the review discusses the impact of the thioamide moiety on key properties, including potency, target interactions, physicochemical characteristics, and pharmacokinetics profiles. We hope that this work will offer valuable insights to inspire the future development of novel bioactive thioamide-containing compounds, facilitating their effective use in combating a wide array of human diseases.
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Affiliation(s)
- Guang Huang
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
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2
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Li Y, Cao T, Peng R, Zhou S, Long X, Jiang H, Zhu C. Chemoselective Thioacylation of Amines Enabled by Synergistic Defluorinative Coupling. Org Lett 2024; 26:6438-6443. [PMID: 39046793 DOI: 10.1021/acs.orglett.4c02237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
A mild and chemoselective method for the thioacylation of amines, including amino acids and peptides, using gem-difluoroalkenes and sulfide, is reported. The distinguishing of the different nucleophilic sites (S-site and diverse N-sites) by the chemoselective C-F bond functionalization of gem-difluoroalkenes enables the unique synergistic defluorinative coupling reaction. This reaction features mild conditions, is operationally simple, efficient, and gram-scalable, tolerates various functional groups, and is activator-free and without racemization. Thioamide moieties were incorporated site-specifically into bioactive compounds. The proposed mechanism is illustrated by a DFT calculation.
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Affiliation(s)
- Yuqi Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Functional Molecular Engineering of Guangdong Province, South China University of Technology, Guangzhou 510640, China
| | - Tongxiang Cao
- School of Chemistry and Chemical Engineering, Key Laboratory of Functional Molecular Engineering of Guangdong Province, South China University of Technology, Guangzhou 510640, China
| | - Rongbin Peng
- School of Chemistry and Chemical Engineering, Key Laboratory of Functional Molecular Engineering of Guangdong Province, South China University of Technology, Guangzhou 510640, China
| | - Shang Zhou
- School of Chemistry and Chemical Engineering, Key Laboratory of Functional Molecular Engineering of Guangdong Province, South China University of Technology, Guangzhou 510640, China
| | - Xujing Long
- School of Chemistry and Chemical Engineering, Key Laboratory of Functional Molecular Engineering of Guangdong Province, South China University of Technology, Guangzhou 510640, China
| | - Huanfeng Jiang
- School of Chemistry and Chemical Engineering, Key Laboratory of Functional Molecular Engineering of Guangdong Province, South China University of Technology, Guangzhou 510640, China
| | - Chuanle Zhu
- School of Chemistry and Chemical Engineering, Key Laboratory of Functional Molecular Engineering of Guangdong Province, South China University of Technology, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Technique and Equipment for Macromolecular Advanced Manufacturing, South China University of Technology, Guangzhou 510640, China
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3
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Guo HM, Wang JJ, Xiong Y, Wu X. Visible-Light-Driven Multicomponent Reactions for the Versatile Synthesis of Thioamides by Radical Thiocarbamoylation. Angew Chem Int Ed Engl 2024:e202409605. [PMID: 38975961 DOI: 10.1002/anie.202409605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/06/2024] [Accepted: 07/08/2024] [Indexed: 07/09/2024]
Abstract
Thioamides are widely used structures in pharmaceuticals and agrochemicals, as well as important synthons for the construction of sulfur-containing heterocycles. This report presents a series of visible-light-driven multicomponent reactions of amines, carbon disulfide, and olefins for the mild and versatile synthesis of linear thioamides and cyclic thiolactams. The use of inexpensive and readily available carbon disulfide as the thiocarbonyl source in a radical pathway enables the facile assembly of structurally diverse amine moieties with non-nucleophilic carbon-based reaction partners. Radical thiocarbamoylative cyclization provides a practical protocol that complements traditional approaches to thiolactams relying on deoxythionation. Mechanistic studies reveal that direct photoexcitation of in situ formed dithiocarbamate anions as well as versatile photoinduced electron transfer with diverse electron acceptors are key to the reactions.
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Affiliation(s)
- Hong-Mei Guo
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Jia-Jin Wang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Yanjiao Xiong
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Xuesong Wu
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
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4
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Liu S, Tang Y, Chen S, Li X, Liu H. Total Syntheses of Streptamidine and Klebsazolicin Using Biomimetic On-Resin Ring-Closing Amidine Formation. Angew Chem Int Ed Engl 2024:e202407952. [PMID: 38923770 DOI: 10.1002/anie.202407952] [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: 04/26/2024] [Revised: 06/16/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
Diketopiperazine (DKP) derived cyclic amidine structures widely exist in peptide natural products according to the genome mining result. The largely unknown bioactivity and mode of action are partially caused by the poor availability of the compounds via microbiological and chemical approaches. To tackle this challenge, in this work, we have developed the on-resin ring-closing amidine formation strategy to synthesize peptides containing N-terminal DKP derived cyclic amidine structure, in which the 6-exo-trig cyclization mediated by HgCl2 activation of thioamides was the key step. Leveraging from this new strategy, we finished the total syntheses of streptamidine and klebsazolicin. Meanwhile, eleven klebsazolicin analogues were synthesized for its structure-activity relationship study.
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Affiliation(s)
- Shunhe Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Yang Tang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, P. R. China
| | - Sheng Chen
- Department of Food Science and Nutrition, State Key Lab of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, P. R. China
| | - Han Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
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5
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Byerly-Duke J, O'Brien EA, Wall BJ, VanVeller B. Thioimidates provide general access to thioamide, amidine, and imidazolone peptide-bond isosteres. Methods Enzymol 2024; 698:27-55. [PMID: 38886036 DOI: 10.1016/bs.mie.2024.04.012] [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] [Indexed: 06/20/2024]
Abstract
Thioamides, amidines, and heterocycles are three classes of modifications that can act as peptide-bond isosteres to alter the peptide backbone. Thioimidate protecting groups can address many of the problematic synthetic issues surrounding installation of these groups. Historically, amidines have received little attention in peptides due to limitations in methods to access them. The first robust and general procedure for the introduction of amidines into peptide backbones exploits the utility of thioimidate protecting groups as a means to side-step reactivity that ultimately renders existing methods unsuitable for the installation of amidines along the main-chain of peptides. Further, amidines formed on-resin can be reacted to form (4H)-imidazolone heteorcycles which have recently been shown to act as cis-amide isosteres. General methods for heterocyclic installation capable of geometrically restricting peptide conformation are also under-developed. This work is significant because it describes a generally applicable and divergent approach to access unexplored peptide designs and architectures.
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Affiliation(s)
- Jacob Byerly-Duke
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Emily A O'Brien
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Brendan J Wall
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, IA, United States.
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6
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Byerly-Duke J, VanVeller B. Thioimidate Solutions to Thioamide Problems during Thionopeptide Deprotection. Org Lett 2024; 26:1452-1457. [PMID: 38341867 PMCID: PMC11031844 DOI: 10.1021/acs.orglett.4c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
Thioamides have structural and chemical similarity to peptide bonds, offering valuable insights when probing peptide backbone interactions, but are prone to side reactions during solid-phase peptide synthesis (SPPS). Thioimidates have been demonstrated to be effective protecting groups for thioamides during peptide elongation. We further demonstrate how thioimidates can assist thioamides through the most yield-crippling step of thionopeptide deprotection, allowing for the first isolation of an important benchmark α-helical peptide that had previously eluded synthesis and isolation.
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Affiliation(s)
- Jacob Byerly-Duke
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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7
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Hansen TN, Olsen CA. Contemporary Applications of Thioamides and Methods for Their Synthesis. Chemistry 2024; 30:e202303770. [PMID: 38088462 DOI: 10.1002/chem.202303770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Indexed: 12/23/2023]
Abstract
Thioamides are naturally occurring isosteres of amide bonds in which the chalcogen atom of the carbonyl is changed from oxygen to sulfur. This substitution gives rise to altered nucleophilicity and hydrogen bonding properties with importance for both chemical reactivity and non-covalent interactions. As such, thioamides have been introduced into biologically active compounds to achieve improved target affinity and/or stability towards hydrolytic enzymes but have also been applied as probes of protein and peptide folding and dynamics. Recently, a series of new methods have been developed for the synthesis of thioamides as well as their utilization in peptide chemistry. Further, novel strategies for the incorporation of thioamides into proteins have been developed, enabling both structural and functional studies to be performed. In this Review, we highlight the recent developments in the preparation of thioamides and their applications for peptide modification and study of protein function.
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Affiliation(s)
- Tobias N Hansen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
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8
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Gibadullin R, Morris RK, Niu J, Sidney J, Sette A, Gellman SH. Thioamide Analogues of MHC I Antigen Peptides. J Am Chem Soc 2023; 145:25559-25569. [PMID: 37968794 PMCID: PMC10782604 DOI: 10.1021/jacs.3c05300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Short, synthetic peptides that are displayed by major histocompatibility complex I (MHC I) can stimulate CD8 T cells in vivo to destroy virus-infected or cancer cells. The development of such peptides as vaccines that provide protective immunity, however, is limited by rapid proteolytic degradation. Introduction of unnatural amino acid residues can suppress MHC I antigen proteolysis, but the modified peptides typically display lower affinity for MHC I and/or diminished ability to activate CD8 T cells relative to native antigen. Here, we report a new strategy for modifying MHC I antigens to enhance resistance to proteolysis while preserving MHC I affinity and T cell activation properties. This approach, replacing backbone amide groups with thioamides, was evaluated in two well-characterized antigens presented by HLA-A2, a common human MHC I. For each antigen, singly modified thioamide analogues retained affinity for HLA-A2 and activated T cells specific for the native antigen, as measured via interferon-γ secretion. In each system, we identified a highly potent triply substituted thioamide antigen ("thio-antigen") that displayed substantial resistance to proteolytic cleavage. Collectively, our results suggest that thio-antigens may represent a general and readily accessible source of potent vaccine candidates that resist degradation.
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Affiliation(s)
- Ruslan Gibadullin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Present address: Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Rylie K. Morris
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jiani Niu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States
- Department of Medicine, University of California, San Diego, California 92093, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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9
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Tsuji K, Ishii T, Kobayakawa T, Higashi-Kuwata N, Shinohara K, Azuma C, Miura Y, Nakano H, Wada N, Hattori SI, Bulut H, Mitsuya H, Tamamura H. Structure-Activity Relationship Studies of SARS-CoV-2 Main Protease Inhibitors Containing 4-Fluorobenzothiazole-2-carbonyl Moieties. J Med Chem 2023; 66:13516-13529. [PMID: 37756225 DOI: 10.1021/acs.jmedchem.3c00777] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
The main protease (Mpro) of SARS-CoV-2 is an attractive target for the development of drugs to treat COVID-19. Here, we report the design, synthesis, and structure-activity relationship (SAR) studies of highly potent SARS-CoV-2 Mpro inhibitors including TKB245 (5)/TKB248 (6). Since we have previously developed Mpro inhibitors (3) and (4), several hybrid molecules of these previous compounds combined with nirmatrelvir (1) were designed and synthesized. Compounds such as TKB245 (5) and TKB248 (6), containing a 4-fluorobenzothiazole moiety at the P1' site, are highly effective in the blockade of SARS-CoV-2 replication in VeroE6 cells. Replacement of the P1-P2 amide with the thioamide surrogate in TKB248 (6) improved its PK profile in mice compared to that of TKB245 (5). A new diversity-oriented synthetic route to TKB245 (5) derivatives was also developed. The results of the SAR studies suggest that TKB245 (5) and TKB248 (6) are useful lead compounds for the further development of Mpro inhibitors.
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Affiliation(s)
- Kohei Tsuji
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takahiro Ishii
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takuya Kobayakawa
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Kouki Shinohara
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Chika Azuma
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Yutaro Miura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hiroki Nakano
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Naoya Wada
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Shin-Ichiro Hattori
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Haydar Bulut
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Hiroaki Mitsuya
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
- Department of Clinical Sciences, Kumamoto University Hospital, Chuo-ku, Kumamoto 860-8556, Japan
| | - Hirokazu Tamamura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
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10
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Yu Z, Kreitler DF, Chiu YTT, Xu R, Bruchs AT, Bingman CA, Gellman SH. Harnessing Aromatic-Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification. Angew Chem Int Ed Engl 2023; 62:e202308100. [PMID: 37587780 PMCID: PMC10668598 DOI: 10.1002/anie.202308100] [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: 06/08/2023] [Revised: 07/31/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Peptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high-resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor-1, which is targeted by osteoporosis drugs. These results should motivate other structure-based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.
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Affiliation(s)
- Zhen Yu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Dale F Kreitler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Yin Ting T Chiu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Ruiwen Xu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Austin T Bruchs
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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11
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Skowron KJ, Baliga C, Johnson T, Kremiller KM, Castroverde A, Dean TT, Allen AC, Lopez-Hernandez AM, Aleksandrova EV, Klepacki D, Mankin AS, Polikanov YS, Moore TW. Structure-Activity Relationships of the Antimicrobial Peptide Natural Product Apidaecin. J Med Chem 2023; 66:11831-11842. [PMID: 37603874 PMCID: PMC10768847 DOI: 10.1021/acs.jmedchem.3c00406] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
With the growing crisis of antimicrobial resistance, it is critical to continue to seek out new sources of novel antibiotics. This need has led to renewed interest in natural product antimicrobials, specifically antimicrobial peptides. Nonlytic antimicrobial peptides are highly promising due to their unique mechanisms of action. One such peptide is apidaecin (Api), which inhibits translation termination through stabilization of the quaternary complex of the ribosome-apidaecin-tRNA-release factor. Synthetic derivatives of apidaecin have been developed, but structure-guided modifications have yet to be considered. In this work, we have focused on modifying key residues in the Api sequence that are responsible for the interactions that stabilize the quaternary complex. We present one of the first examples of a highly modified Api peptide that maintains its antimicrobial activity and interaction with the translation complex. These findings establish a starting point for further structure-guided optimization of Api peptides.
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Affiliation(s)
- Kornelia J Skowron
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Chetana Baliga
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Tatum Johnson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Kyle M Kremiller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Alexandra Castroverde
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Trevor T Dean
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - A'Lester C Allen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Ana M Lopez-Hernandez
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Elena V Aleksandrova
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Dorota Klepacki
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Alexander S Mankin
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Yury S Polikanov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, Illinois 60607, United States
- Center for Biomolecular Sciences, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Terry W Moore
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
- University of Illinois Cancer Center, University of Illinois Chicago, Chicago, Illinois 60612, United States
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12
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Kim S, Cho M, Kim TH. Novel Compounds Derived from DFPM Induce Root Growth Arrest through the Specific VICTR Alleles of Arabidopsis Accessions. Life (Basel) 2023; 13:1797. [PMID: 37763201 PMCID: PMC10532556 DOI: 10.3390/life13091797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/15/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
The small compound [5-(3,4-dichlorophenyl) furan-2-yl]-piperidine-1-ylmethanethione (DFPM) inhibits ABA responses by activating effector-triggered immune signal transduction in Arabidopsis. In addition to the known function of DFPM as an antagonist of ABA signaling, DFPM causes accession-specific root growth arrest in Arabidopsis Columbia-0 via the TIR-NLR protein VICTR (VARIATION IN COMPOUND TRIGGERED ROOT growth response) in an EDS1/PAD4/RAR1/SGT1B-dependent manner. Although DFPM could control the specific steps of various cellular responses, the functional residues for the activity of DFPM or the existence of a stronger version of DFPM modification have not been characterized thoroughly. This study analyzed twenty-two DFPM derivatives during root growth arrest, inhibition of ABA signaling, and induction of biotic signal transduction to determine critical residues that confer the specific activity of DFPM. Furthermore, this study identified two more Arabidopsis accessions that generate significant root growth arrest in response to DFPM derivatives dependent on multiple amino acid polymorphisms in the coding region of VICTR. The isolation of novel compounds, such as DFPM-5, and specific amino acid polymorphisms critical for the compound-induced responses will help determine the detailed regulatory mechanism for how DFPM regulates abiotic and biotic stress signaling interactions.
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Affiliation(s)
- Seojung Kim
- Department of Bio-Health Convergence, Duksung Women’s University, Seoul 01369, Republic of Korea
| | - Miri Cho
- Department of Bio-Health Convergence, Duksung Women’s University, Seoul 01369, Republic of Korea
| | - Tae-Houn Kim
- Department of Bio-Health Convergence, Duksung Women’s University, Seoul 01369, Republic of Korea
- Department of Biotechnology, Duksung Women’s University, Seoul 01369, Republic of Korea
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13
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Wang X, Xu S, Tang Y, Lear MJ, He W, Li J. Nitroalkanes as thioacyl equivalents to access thioamides and thiopeptides. Nat Commun 2023; 14:4626. [PMID: 37532721 PMCID: PMC10397191 DOI: 10.1038/s41467-023-40334-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/20/2023] [Indexed: 08/04/2023] Open
Abstract
Thioamides are an important, but a largely underexplored class of amide bioisostere in peptides. Replacement of oxoamide units with thioamides in peptide therapeutics is a valuable tactic to improve biological activity and resistance to enzymatic hydrolysis. This tactic, however, has been hampered by insufficient methods to introduce thioamide bonds into peptide or protein backbones in a site-specific and stereo-retentive fashion. In this work, we developed an efficient and mild thioacylation method to react nitroalkanes with amines directly in the presence of elemental sulfur and sodium sulfide to form a diverse range of thioamides in high yields. Notably, this convenient method can be employed for the controlled thioamide coupling of multifunctionalized peptides without epimerization of stereocenters, including the late stage thioacylation of advanced compounds of biological and medicinal interest. Experimental interrogation of postulated mechanisms currently supports the intermediacy of thioacyl species.
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Affiliation(s)
- Xiaonan Wang
- School of Chemistry, and Xi'an Key Laboratory of Sustainable Energy Materials Chemistry, Xi'an Jiaotong University, 710049, Xi'an, China
| | - Silong Xu
- School of Chemistry, and Xi'an Key Laboratory of Sustainable Energy Materials Chemistry, Xi'an Jiaotong University, 710049, Xi'an, China
| | - Yuhai Tang
- School of Chemistry, and Xi'an Key Laboratory of Sustainable Energy Materials Chemistry, Xi'an Jiaotong University, 710049, Xi'an, China
| | - Martin J Lear
- School of Chemistry, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK
| | - Wangxiao He
- The First Affiliated Hospital of Xi'an Jiao Tong University, 710061, Xi'an, China
| | - Jing Li
- School of Chemistry, and Xi'an Key Laboratory of Sustainable Energy Materials Chemistry, Xi'an Jiaotong University, 710049, Xi'an, China.
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14
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Liao Y, Zhang S, Jiang X. Construction of Thioamide Peptides from Chiral Amino Acids. Angew Chem Int Ed Engl 2023; 62:e202303625. [PMID: 37118109 DOI: 10.1002/anie.202303625] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/21/2023] [Accepted: 04/28/2023] [Indexed: 04/30/2023]
Abstract
Thioamide peptides were synthesized in a straightforward one-pot process via the linkage of diverse natural amino acids in the presence of thiolphosphonate and trichlorosilane, wherein carbonyl groups were replaced with thiono compounds with minimal racemization. Experimental and computational mechanistic studies demonstrated that the trichlorosilane enables the activation of carboxylic acids via intense interactions with the Si-O bond, followed by coupling of the carboxylic acids with thiolphosphonate to obtain the key intermediate S-acyl dithiophosphate. Silyl-activated quadrangular metathesis transition states afforded the thioamide peptides. The potential applications of these thioamide peptides were further highlighted via late-stage linkages of diverse natural products and pharmaceutical drugs and the thioamide moiety.
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Affiliation(s)
- Yanyan Liao
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, Institute of Eco-Chongming, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, P. R. China
| | - Shunmin Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, Institute of Eco-Chongming, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, P. R. China
| | - Xuefeng Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, Institute of Eco-Chongming, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, P. R. China
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, P. R. China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, P. R. China
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15
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Liao Y, Wang M, Jiang X. Sulfur-containing peptides: Synthesis and application in the discovery of potential drug candidates. Curr Opin Chem Biol 2023; 75:102336. [PMID: 37269675 DOI: 10.1016/j.cbpa.2023.102336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/29/2023] [Accepted: 05/05/2023] [Indexed: 06/05/2023]
Abstract
Peptides act as biological mediators and play a key role of various physiological activities. Sulfur-containing peptides are widely used in natural products and drug molecules due to their unique biological activity and chemical reactivity of sulfur. Disulfides, thioethers, and thioamides are the most common motifs of sulfur-containing peptides, and they have been extensively studied and developed for synthetic methodology as well as pharmaceutical applications. This review focuses on the illustration of these three motifs in natural products and drugs, as well as the recent advancements in the synthesis of the corresponding core scaffolds.
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Affiliation(s)
- Yanyan Liao
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Ming Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
| | - Xuefeng Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China; State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Elemento-Organic Chemistry, Nankai University, China.
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16
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Langer MK, Rahman A, Dey H, Anderssen T, Blencke HM, Haug T, Stensvåg K, Strøm MB, Bayer A. Investigation of tetrasubstituted heterocycles reveals hydantoins as a promising scaffold for development of novel antimicrobials with membranolytic properties. Eur J Med Chem 2023; 249:115147. [PMID: 36739750 DOI: 10.1016/j.ejmech.2023.115147] [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: 11/13/2022] [Revised: 12/19/2022] [Accepted: 01/21/2023] [Indexed: 01/26/2023]
Abstract
Mimics of antimicrobial peptides (AMPs) have been proposed as a promising class of antimicrobial agents. We report the analysis of five tetrasubstituted, cationic, amphipathic heterocycles as potential AMP mimics. The analysis showed that the heterocyclic scaffold had a strong influence on the haemolytic activity of the compounds, and the hydantoin scaffold was identified as a promising template for drug lead development. Subsequently, a total of 20 hydantoin derivatives were studied for their antimicrobial potency and haemolytic activity. We found 19 of these derivatives to have very low haemolytic toxicity and identified three lead structures, 2dA, 6cG, and 6dG with very promising broad-spectrum antimicrobial activity. Lead structure 6dG displayed minimum inhibitory concentration (MIC) values as low as 1 μg/mL against Gram-positive bacteria and 4-16 μg/mL against Gram-negative bacteria. Initial mode of action (MoA) studies performed on the amine derivative 6cG, utilizing a luciferase-based biosensor assay, suggested a strong membrane disrupting effect on the outer and inner membrane of Escherichia coli. Our findings show that the physical properties and structural arrangement induced by the heterocyclic scaffolds are important factors in the design of AMP mimics.
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Affiliation(s)
- Manuel K Langer
- Department of Chemistry, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Ataur Rahman
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Hymonti Dey
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Trude Anderssen
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Hans-Matti Blencke
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Tor Haug
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Klara Stensvåg
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Morten B Strøm
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway.
| | - Annette Bayer
- Department of Chemistry, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway.
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17
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Cunliffe G, Lim YT, Chae W, Jung S. Alternative Pharmacological Strategies for the Treatment of Alzheimer's Disease: Focus on Neuromodulator Function. Biomedicines 2022; 10:3064. [PMID: 36551821 PMCID: PMC9776382 DOI: 10.3390/biomedicines10123064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder, comprising 70% of dementia diagnoses worldwide and affecting 1 in 9 people over the age of 65. However, the majority of its treatments, which predominantly target the cholinergic system, remain insufficient at reversing pathology and act simply to slow the inevitable progression of the disease. The most recent neurotransmitter-targeting drug for AD was approved in 2003, strongly suggesting that targeting neurotransmitter systems alone is unlikely to be sufficient, and that research into alternate treatment avenues is urgently required. Neuromodulators are substances released by neurons which influence neurotransmitter release and signal transmission across synapses. Neuromodulators including neuropeptides, hormones, neurotrophins, ATP and metal ions display altered function in AD, which underlies aberrant neuronal activity and pathology. However, research into how the manipulation of neuromodulators may be useful in the treatment of AD is relatively understudied. Combining neuromodulator targeting with more novel methods of drug delivery, such as the use of multi-targeted directed ligands, combinatorial drugs and encapsulated nanoparticle delivery systems, may help to overcome limitations of conventional treatments. These include difficulty crossing the blood-brain-barrier and the exertion of effects on a single target only. This review aims to highlight the ways in which neuromodulator functions are altered in AD and investigate how future therapies targeting such substances, which act upstream to classical neurotransmitter systems, may be of potential therapeutic benefit in the sustained search for more effective treatments.
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Affiliation(s)
- Grace Cunliffe
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Yi Tang Lim
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore
- Faculty of Science, National University of Singapore, Singapore 117546, Singapore
| | - Woori Chae
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Seongnam-si 13120, Republic of Korea
| | - Sangyong Jung
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
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18
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Tsuji K, Ishii T, Kobayakawa T, Higashi-Kuwata N, Azuma C, Nakayama M, Onishi T, Nakano H, Wada N, Hori M, Shinohara K, Miura Y, Kawada T, Hayashi H, Hattori SI, Bulut H, Das D, Takamune N, Kishimoto N, Saruwatari J, Okamura T, Nakano K, Misumi S, Mitsuya H, Tamamura H. Potent and biostable inhibitors of the main protease of SARS-CoV-2. iScience 2022; 25:105365. [PMID: 36338434 PMCID: PMC9623849 DOI: 10.1016/j.isci.2022.105365] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/24/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022] Open
Abstract
Potent and biostable inhibitors of the main protease (Mpro) of SARS-CoV-2 were designed and synthesized based on an active hit compound 5h (2). Our strategy was based not only on the introduction of fluorine atoms into the inhibitor molecule for an increase of binding affinity for the pocket of Mpro and cell membrane permeability but also on the replacement of the digestible amide bond by a surrogate structure to increase the biostability of the compounds. Compound 3 is highly potent and blocks SARS-CoV-2 infection in vitro without a viral breakthrough. The derivatives, which contain a thioamide surrogate in the P2-P1 amide bond of these compounds (2 and 3), showed remarkably preferable pharmacokinetics in mice compared with the corresponding parent compounds. These data show that compounds 3 and its biostable derivative 4 are potential drugs for treating COVID-19 and that replacement of the digestible amide bond by its thioamide surrogate structure is an effective method.
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Affiliation(s)
- Kohei Tsuji
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takahiro Ishii
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takuya Kobayakawa
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Chika Azuma
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Miyuki Nakayama
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takato Onishi
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hiroki Nakano
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Naoya Wada
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Miki Hori
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Kouki Shinohara
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Yutaro Miura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takuma Kawada
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hironori Hayashi
- Department of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University, Aoba-ku, Sendai 980-8572, Japan
| | - Shin-ichiro Hattori
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Haydar Bulut
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Debananda Das
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nobutoki Takamune
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Chuo-ku, Kumamoto 862-0973, Japan
| | - Naoki Kishimoto
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Chuo-ku, Kumamoto 862-0973, Japan
| | - Junji Saruwatari
- Division of Pharmacology and Therapeutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, Chuo-ku, Kumamoto 862-0973, Japan
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Kenta Nakano
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Shogo Misumi
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Chuo-ku, Kumamoto 862-0973, Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Clinical Sciences, Kumamoto University Hospital, Chuo-ku, Kumamoto 860-8556, Japan
| | - Hirokazu Tamamura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
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19
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Wang P, Hill TA, Mitchell J, Fitzsimmons RL, Xu W, Loh Z, Suen JY, Lim J, Iyer A, Fairlie DP. Modifying a Hydroxyl Patch in Glucagon-like Peptide 1 Produces Biased Agonists with Unique Signaling Profiles. J Med Chem 2022; 65:11759-11775. [PMID: 35984914 DOI: 10.1021/acs.jmedchem.2c00653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glucagon-like peptide-1 (GLP-1) lowers blood glucose by inducing insulin but also has other poorly understood properties. Here, we show that hydroxy amino acids (Thr11, Ser14, Ser17, Ser18) in GLP-1(7-36) act in concert to direct cell signaling. Mutating any single residue to alanine removes one hydroxyl group, thereby reducing receptor affinity and cAMP 10-fold, with Ala11 or Ala14 also reducing β-arrestin-2 10-fold, while Ala17 or Ala18 also increases ERK1/2 phosphorylation 5-fold. Multiple alanine mutations more profoundly bias signaling, differentially silencing or restoring one or more signaling properties. Mutating three serines silences only ERK1/2, the first example of such bias. Mutating all four residues silences β-arrestin-2, ERK1/2, and Ca2+ maintains the ligand and receptor at the membrane but still potently stimulates cAMP and insulin secretion in cells and mice. These novel findings indicate that hydrogen bonding cooperatively controls cell signaling and highlight an important regulatory hydroxyl patch in hormones that activate class B G protein-coupled receptors.
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Affiliation(s)
- Peiqi Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane Queensland 4072, Australia
| | - Timothy A Hill
- Institute for Molecular Bioscience, The University of Queensland, Brisbane Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane Queensland 4072, Australia
| | - Justin Mitchell
- Institute for Molecular Bioscience, The University of Queensland, Brisbane Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane Queensland 4072, Australia
| | - Rebecca L Fitzsimmons
- Institute for Molecular Bioscience, The University of Queensland, Brisbane Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane Queensland 4072, Australia.,Centre for Inflammation and Disease Research, The University of Queensland, Brisbane Queensland 4072, Australia
| | - Weijun Xu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane Queensland 4072, Australia
| | - Zhixuan Loh
- Institute for Molecular Bioscience, The University of Queensland, Brisbane Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane Queensland 4072, Australia.,Centre for Inflammation and Disease Research, The University of Queensland, Brisbane Queensland 4072, Australia
| | - Jacky Y Suen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane Queensland 4072, Australia
| | - Junxian Lim
- Institute for Molecular Bioscience, The University of Queensland, Brisbane Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane Queensland 4072, Australia.,Centre for Inflammation and Disease Research, The University of Queensland, Brisbane Queensland 4072, Australia
| | - Abishek Iyer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane Queensland 4072, Australia.,Centre for Inflammation and Disease Research, The University of Queensland, Brisbane Queensland 4072, Australia
| | - David P Fairlie
- Institute for Molecular Bioscience, The University of Queensland, Brisbane Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane Queensland 4072, Australia.,Centre for Inflammation and Disease Research, The University of Queensland, Brisbane Queensland 4072, Australia
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20
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Zhang WJ, Wang C, Wang K, Zhang P, Hu SX. The stability and chemical bonding of a series tridentate ligand-actinyl complexes: [AnO2(L)2]2+ (An: U and Am). J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Levine PM, Craven TW, Li X, Balana AT, Bird GH, Godes M, Salveson PJ, Erickson PW, Lamb M, Ahlrichs M, Murphy M, Ogohara C, Said MY, Walensky LD, Pratt MR, Baker D. Generation of Potent and Stable GLP-1 Analogues Via "Serine Ligation". ACS Chem Biol 2022; 17:804-809. [PMID: 35319882 PMCID: PMC9173702 DOI: 10.1021/acschembio.2c00075] [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
Peptide and protein bioconjugation technologies have revolutionized our ability to site-specifically or chemoselectively install a variety of functional groups for applications in chemical biology and medicine, including the enhancement of bioavailability. Here, we introduce a site-specific bioconjugation strategy inspired by chemical ligation at serine that relies on a noncanonical amino acid containing a 1-amino-2-hydroxy functional group and a salicylaldehyde ester. More specifically, we harness this technology to generate analogues of glucagon-like peptide-1 that resemble Semaglutide, a long-lasting blockbuster drug currently used in the clinic to regulate glucose levels in the blood. We identify peptides that are more potent than unmodified peptide and equipotent to Semaglutide in a cell-based activation assay, improve the stability in human serum, and increase glucose disposal efficiency in vivo. This approach demonstrates the potential of "serine ligation" for various applications in chemical biology, with a particular focus on generating stabilized peptide therapeutics.
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Affiliation(s)
- Paul M. Levine
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Timothy W. Craven
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Xinting Li
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | | | | | | | - Patrick J. Salveson
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Patrick W. Erickson
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Mila Lamb
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Maggie Ahlrichs
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Michael Murphy
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Cassandra Ogohara
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Meerit Y. Said
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | | | | | - David Baker
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
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22
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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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23
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Li G, Xing Y, Zhao H, Zhang J, Hong X, Szostak M. Chemoselective Transamidation of Thioamides by Transition-Metal-Free N-C(S) Transacylation. Angew Chem Int Ed Engl 2022; 61:e202200144. [PMID: 35122374 PMCID: PMC8983593 DOI: 10.1002/anie.202200144] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Indexed: 01/13/2023]
Abstract
Thioamides represent highly valuable isosteric in the strictest sense "single-atom substitution" analogues of amides that have found broad applications in chemistry and biology. A long-standing challenge is the direct transamidation of thioamides, a process which would convert one thioamide bond (R-C(S)-NR1 R2 ) into another (R-C(S)-NR3 N4 ). Herein, we report the first general method for the direct transamidation of thioamides by highly chemoselective N-C(S) transacylation. The method relies on site-selective N-tert-butoxycarbonyl activation of 2° and 1° thioamides, resulting in ground-state-destabilization of thioamides, thus enabling to rationally manipulate nucleophilic addition to the thioamide bond. This method showcases a remarkably broad scope including late-stage functionalization (>100 examples). We further present extensive DFT studies that provide insight into the chemoselectivity and provide guidelines for the development of transamidation methods of the thioamide bond.
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Affiliation(s)
- Guangchen Li
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ 07102, USA
| | - Yangyang Xing
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
| | - Hui Zhao
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Jin Zhang
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Xin Hong
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China.,Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Beijing National Laboratory for Molecular Sciences, Zhongguancun North First Street NO. 2, Beijing, 100190, PR China
| | - Michal Szostak
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ 07102, USA
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24
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Wang C, Han C, Yang J, Zhang Z, Zhao Y, Zhao J. Ynamide-Mediated Thioamide and Primary Thioamide Syntheses. J Org Chem 2022; 87:5617-5629. [PMID: 35394769 DOI: 10.1021/acs.joc.1c03076] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Environmentally friendly ynamide-mediated thioamidation of monothiocarboxylic acids with amines or ammonium hydroxide for the syntheses of thioamides and primary thioamides is described. Simple and mild reaction conditions enable the reaction to tolerate a wide variety of functional groups such as hydroxyl group, ester, tertiary amine, ketone, and amide moieties. Readily available NaSH served as the sulfur source, avoiding the use of toxic, expensive, and malodorous organic sulfur reagents and making this strategy environmentally friendly and practical. Importantly, the stereochemical integrity of α-chiral monothiocarboxylic acids was maintained during the activation step and subsequent aminolysis process, thus offering a racemization-free strategy for peptide C-terminal modification. Furthermore, a number of thioamide-modified drugs were prepared in good yields by using this protocol and the synthesized primary thioamides were transformed into backbone thiazolyl modified peptides.
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Affiliation(s)
- Changliu Wang
- College of Chemistry and Chemical Engineering & National Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China
| | - Chunyu Han
- Key Laboratory of Molecular Target & Clinical Pharmacology and the NMPA & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, Guangdong, P. R. China
| | - Jinhua Yang
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, P. R. China
| | - Zhenjia Zhang
- National Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China
| | - Yongli Zhao
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China
| | - Junfeng Zhao
- College of Chemistry and Chemical Engineering & National Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China.,Key Laboratory of Molecular Target & Clinical Pharmacology and the NMPA & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, Guangdong, P. R. China
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25
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Li G, Xing Y, Zhao H, Zhang J, Hong X, Szostak M. Chemoselective Transamidation of Thioamides by Transition‐Metal‐Free N–C(S) Transacylation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Guangchen Li
- Rutgers University: Rutgers The State University of New Jersey Chemistry UNITED STATES
| | | | - Hui Zhao
- Shaanxi University of Science and Technology Xi\'an Campus: Shaanxi University of Science and Technology Chemistry CHINA
| | - Jin Zhang
- Shaanxi University of Science and Technology Chemistry CHINA
| | - Xin Hong
- Zhejiang University Department of Chemistry CHINA
| | - Michal Szostak
- Rutgers University Department of Chemistry 73 Warren St. 07102 Newark UNITED STATES
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26
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Yeo XY, Cunliffe G, Ho RC, Lee SS, Jung S. Potentials of Neuropeptides as Therapeutic Agents for Neurological Diseases. Biomedicines 2022; 10:343. [PMID: 35203552 PMCID: PMC8961788 DOI: 10.3390/biomedicines10020343] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Despite recent leaps in modern medicine, progress in the treatment of neurological diseases remains slow. The near impermeable blood-brain barrier (BBB) that prevents the entry of therapeutics into the brain, and the complexity of neurological processes, limits the specificity of potential therapeutics. Moreover, a lack of etiological understanding and the irreversible nature of neurological conditions have resulted in low tolerability and high failure rates towards existing small molecule-based treatments. Neuropeptides, which are small proteinaceous molecules produced by the body, either in the nervous system or the peripheral organs, modulate neurological function. Although peptide-based therapeutics originated from the treatment of metabolic diseases in the 1920s, the adoption and development of peptide drugs for neurological conditions are relatively recent. In this review, we examine the natural roles of neuropeptides in the modulation of neurological function and the development of neurological disorders. Furthermore, we highlight the potential of these proteinaceous molecules in filling gaps in current therapeutics.
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Affiliation(s)
- Xin Yi Yeo
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore; (X.Y.Y.); (G.C.)
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
| | - Grace Cunliffe
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore; (X.Y.Y.); (G.C.)
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Roger C. Ho
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
- Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore
| | - Su Seong Lee
- NanoBio Lab, Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore
| | - Sangyong Jung
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore; (X.Y.Y.); (G.C.)
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
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27
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Monteith JJ, Scotchburn K, Mills LR, Rousseaux SAL. Ni-Catalyzed Synthesis of Thiocarboxylic Acid Derivatives. Org Lett 2022; 24:619-624. [PMID: 34978834 DOI: 10.1021/acs.orglett.1c04074] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A Ni-catalyzed cross-coupling of readily accessible O-alkyl xanthate esters or thiocarbonyl imidazolides and organozinc reagents for the synthesis of thiocarboxylic acid derivatives has been developed. This method benefits from a fast reaction time, mild reaction conditions, and ease of starting material synthesis. The use of transition-metal catalysis to access a diverse range of thiocarbonyl-containing compounds provides a useful complementary approach when compared with previously established methodologies.
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Affiliation(s)
- John J Monteith
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Katerina Scotchburn
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - L Reginald Mills
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Sophie A L Rousseaux
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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28
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Lu C, Li X, Chang S, Zhang Y, Xing D, Wang S, Lin Y, Jiang H, Huang L. Thioamide synthesis via copper-catalyzed C–H activation of 1,2,3-thiadiazoles enabled by slow release and capture of thioketenes. Org Chem Front 2022. [DOI: 10.1039/d2qo00152g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A copper-catalyzed coupling of 1,2,3-thiadiazoles with various amines under base-free conditions was developed as a robust protocol for the synthesis of thioamide derivatives via C–H activation/Cu coordination strategy.
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Affiliation(s)
- Changhui Lu
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Xiaohong Li
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Shunqin Chang
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Yuqi Zhang
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Donghui Xing
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Shuo Wang
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Yueping Lin
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Huanfeng Jiang
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Liangbin Huang
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
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29
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Singh A, Saini S, Singh N, Kaur N, Jang DO. Cellulose-reinforced poly(ethylene- co-vinyl acetate)-supported Ag nanoparticles with excellent catalytic properties: synthesis of thioamides using the Willgerodt–Kindler reaction. RSC Adv 2022; 12:6659-6667. [PMID: 35424616 PMCID: PMC8982104 DOI: 10.1039/d1ra09225a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/18/2022] [Indexed: 12/12/2022] Open
Abstract
Cellulose, a bio-derived polymer, is widely used in food packaging, dye removal, coatings, and solid-supported catalysis. Heterogeneous catalysts play a critical role in environmental remediation. In this context, the demand for green and cost-effective catalysts has rapidly increased. In this study, cellulose was extracted from rice straw, and a highly active solid-supported catalytic model was developed. First, cellulose was conjugated with poly(ethylene-co-vinyl acetate) (PEVA), and then Ag nanoparticles (AgNPs) were inserted into the cellulose–PEVA composite. The process involved the reduction of AgNPs in the presence of sodium borohydride. The fabricated hybrid catalyst was characterized using Fourier-transform infrared spectroscopy, scanning electron microscopy, energy dispersive X-ray, and powder X-ray diffraction. Thereafter, the obtained hybrid was used as a catalyst for the Willgerodt–Kindler reaction of aromatic aldehydes, amines, and S8 to synthesize thioamides with excellent yields. The developed catalytic system exhibited high stability and recyclability. Moreover, the mechanical properties of the hybrid catalyst were evaluated using tensile strength and impact tests. RGB analysis of digital images was also performed to investigate the primary components of the catalyst. The AgNPs@cellulose–PEVA hybrid catalyst presented excellent catalytic efficacy for the Willgerodt–Kindler reaction, facilitating the selective formation of C
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Affiliation(s)
- Anoop Singh
- Department of Chemistry, Indian Institute of Technology Ropar, Punjab 140001, India
| | - Sanjeev Saini
- Department of Chemistry, Indian Institute of Technology Ropar, Punjab 140001, India
| | - Narinder Singh
- Department of Chemistry, Indian Institute of Technology Ropar, Punjab 140001, India
| | - Navneet Kaur
- Department of Chemistry, Panjab University, Chandigarh, 160014, India
| | - Doo Ok Jang
- Department of Chemistry, Yonsei University, Wonju 26493, Korea
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30
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Lampkin BJ, VanVeller B. Hydrogen Bond and Geometry Effects of Thioamide Backbone Modifications. J Org Chem 2021; 86:18287-18291. [PMID: 34851645 DOI: 10.1021/acs.joc.1c02373] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Thioamide substitution of backbone peptide bonds can probe interactions along the main chain of proteins. Despite theoretical predictions of the enhanced hydrogen bonding propensities of thioamides, previous studies often do not consider the geometric constraints imposed by folded peptide secondary structure. This work addresses drawbacks in previous studies that ignored the geometry dependence and local dielectric properties of thioamide hydrogen bonding and identifies cases where thioamides may be either stronger or weaker hydrogen-bonding partners than amides.
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Affiliation(s)
- Bryan J Lampkin
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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31
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Phan HAT, Giannakoulias SG, Barrett TM, Liu C, Petersson EJ. Rational design of thioamide peptides as selective inhibitors of cysteine protease cathepsin L. Chem Sci 2021; 12:10825-10835. [PMID: 35355937 PMCID: PMC8901119 DOI: 10.1039/d1sc00785h] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/30/2021] [Indexed: 12/24/2022] Open
Abstract
Aberrant levels of cathepsin L (Cts L), a ubiquitously expressed endosomal cysteine protease, have been implicated in many diseases such as cancer and diabetes. Significantly, Cts L has been identified as a potential target for the treatment of COVID-19 due to its recently unveiled critical role in SARS-CoV-2 entry into the host cells. However, there are currently no clinically approved specific inhibitors of Cts L, as it is often challenging to obtain specificity against the many highly homologous cathepsin family cysteine proteases. Peptide-based agents are often promising protease inhibitors as they offer high selectivity and potency, but unfortunately are subject to degradation in vivo. Thioamide substitution, a single-atom O-to-S modification in the peptide backbone, has been shown to improve the proteolytic stability of peptides addressing this issue. Utilizing this approach, we demonstrate herein that good peptidyl substrates can be converted into sub-micromolar inhibitors of Cts L by a single thioamide substitution in the peptide backbone. We have designed and scanned several thioamide stabilized peptide scaffolds, in which one peptide, RS 1A, was stabilized against proteolysis by all five cathepsins (Cts L, Cts V, Cts K, Cts S, and Cts B) while inhibiting Cts L with >25-fold specificity against the other cathepsins. We further showed that this stabilized RS 1A peptide could inhibit Cts L in human liver carcinoma lysates (IC50 = 19 μM). Our study demonstrates that one can rationally design a stabilized, specific peptidyl protease inhibitor by strategic placement of a thioamide and reaffirms the place of this single-atom modification in the toolbox of peptide-based rational drug design.
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Affiliation(s)
- Hoang Anh T Phan
- Department of Chemistry, University of Pennsylvania Philadelphia Pennsylvania 19104 USA
| | - Sam G Giannakoulias
- Department of Chemistry, University of Pennsylvania Philadelphia Pennsylvania 19104 USA
| | - Taylor M Barrett
- Department of Chemistry, University of Pennsylvania Philadelphia Pennsylvania 19104 USA
| | - Chunxiao Liu
- Department of Chemistry, University of Pennsylvania Philadelphia Pennsylvania 19104 USA
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture Beijing 102206 P. R. China
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania Philadelphia Pennsylvania 19104 USA
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32
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Suzuki A, Takagi K, Sato K, Wada T. Synthesis of thioamides from thiocarboxylic acids using phosphonium-type condensing reagents. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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33
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Khatri B, Raj N, Chatterjee J. Opportunities and challenges in the synthesis of thioamidated peptides. Methods Enzymol 2021; 656:27-57. [PMID: 34325789 DOI: 10.1016/bs.mie.2021.04.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Chemical modifications of peptides hold great promise for modulating their pharmacological properties. In the last few decades amide to thioamide substitution has been widely explored to modulate the conformation, non-covalent interactions, and proteolytic stability of peptides. Despite widespread utilization, there are some potential limitations including epimerization and degradation under basic and acidic conditions, respectively. In this chapter, we present the synthetic method to build thio-precursors, their site-specific incorporation onto a growing peptide chain, and troubleshooting during the elongation of thioamidated peptides. This highly efficient, rapid, and robust method can be used for positional scanning of the thioamide bond.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Nishant Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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34
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Fiore KE, Phan HAT, Robkis DM, Walters CR, Petersson EJ. Incorporating thioamides into proteins by native chemical ligation. Methods Enzymol 2021; 656:295-339. [PMID: 34325791 PMCID: PMC8617429 DOI: 10.1016/bs.mie.2021.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The thioamide is a versatile replacement of the peptide backbone with altered hydrogen bonding and conformational preferences, as well the ability participate in energy and electron transfer processes. Semi-synthetic incorporation of a thioamide into a protein can be used to study protein folding or protein/protein interactions using these properties. Semi-synthesis also provides the opportunity to study the role of thioamides in natural proteins. Here we outline the semi-synthesis of a model protein, the B1 domain of protein G (GB1) with a thioamide at the N-terminus or the C-terminus. The thioamide is synthetically incorporated into a fragment by solid-phase peptide synthesis, whereas the remainder of the protein is recombinantly expressed. Then, the two fragments are joined by native chemical ligation. The explicit protocol for GB1 synthesis is accompanied by examples of applications with GB1 and other proteins in structural biology and protein misfolding studies.
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Affiliation(s)
- Kristen E Fiore
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - Hoang Anh T Phan
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - D Miklos Robkis
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, United States
| | - Christopher R Walters
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States.
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35
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Eyles TH, Vior NM, Lacret R, Truman AW. Understanding thioamitide biosynthesis using pathway engineering and untargeted metabolomics. Chem Sci 2021; 12:7138-7150. [PMID: 34123341 PMCID: PMC8153245 DOI: 10.1039/d0sc06835g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/19/2021] [Indexed: 11/21/2022] Open
Abstract
Thiostreptamide S4 is a thioamitide, a family of promising antitumour ribosomally synthesised and post-translationally modified peptides (RiPPs). The thioamitides are one of the most structurally complex RiPP families, yet very few thioamitide biosynthetic steps have been elucidated, even though the biosynthetic gene clusters (BGCs) of multiple thioamitides have been identified. We hypothesised that engineering the thiostreptamide S4 BGC in a heterologous host could provide insights into its biosynthesis when coupled with untargeted metabolomics and targeted mutations of the precursor peptide. Modified BGCs were constructed, and in-depth metabolomics enabled a detailed understanding of the biosynthetic pathway to thiostreptamide S4, including the identification of a protein critical for amino acid dehydration that has homology to HopA1, an effector protein used by a plant pathogen to aid infection. We use this biosynthetic understanding to bioinformatically identify diverse RiPP-like BGCs, paving the way for future RiPP discovery and engineering.
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Affiliation(s)
- Tom H Eyles
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Natalia M Vior
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Rodney Lacret
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
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36
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Jena S, Tulsiyan KD, Kar RK, Kisan HK, Biswal HS. Doubling Förster Resonance Energy Transfer Efficiency in Proteins with Extrinsic Thioamide Probes: Implications for Thiomodified Nucleobases. Chemistry 2021; 27:4373-4383. [PMID: 33210381 DOI: 10.1002/chem.202004627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Indexed: 12/29/2022]
Abstract
Designing a potential protein-ligand pair is pivotal, not only to track the protein structure dynamics, but also to assist in an atomistic understanding of drug delivery. Herein, the potential of a small model thioamide probe being used to study albumin proteins is reported. By monitoring the Förster resonance energy transfer (FRET) dynamics with the help of fluorescence spectroscopic techniques, a twofold enhancement in the FRET efficiency of 2-thiopyridone (2TPY), relative to that of its amide analogue, is observed. Molecular dynamics simulations depict the relative position of the free energy minimum to be quite stable in the case of 2TPY through noncovalent interactions with sulfur, which help to enhance the FRET efficiency. Finally, its application is shown by pairing thiouracils with protein. It is found that the site-selective sulfur atom substitution approach and noncovalent interactions with sulfur can substantially enhance the FRET efficiency, which could be a potential avenue to explore in the design of FRET probes to study the structure and dynamics of biomolecules.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Hemanta K Kisan
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.,Department of Chemistry, Utkal University, 751004, Bhubaneswar, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
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37
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Robkis DM, Hoang EM, Po P, Deutsch CJ, Petersson EJ. Side-chain thioamides as fluorescence quenching probes. Biopolymers 2021; 112:e23384. [PMID: 32740927 PMCID: PMC7744324 DOI: 10.1002/bip.23384] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 12/11/2022]
Abstract
Thioamides, single atom oxygen-to-sulfur substitutions of canonical amide bonds, can be valuable probes for protein folding and protease studies. Here, we investigate the fluorescence quenching properties of thioamides incorporated into the side-chains of amino acids. We synthesize and incorporate Fmoc-protected, solid-phase peptide synthesis building blocks for introducing Nε -thioacetyl-lysine and γ-thioasparagine. Using rigid model peptides, we demonstrate the distance-dependent fluorescence quenching of these thioamides. Furthermore, we describe attempts to incorporate of Nε -thioacetyl-lysine into proteins expressed in Escherichia coli using amber codon suppression.
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Affiliation(s)
- D Miklos Robkis
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eileen M Hoang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pengse Po
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carol J Deutsch
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - E James Petersson
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Boaro A, Ageitos L, Torres M, Bartoloni FH, de la Fuente-Nunez C. Light-Emitting Probes for Labeling Peptides. CELL REPORTS. PHYSICAL SCIENCE 2020; 1:100257. [PMID: 34396352 PMCID: PMC8360326 DOI: 10.1016/j.xcrp.2020.100257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Peptides are versatile biopolymers composed of 2-100 amino acid residues that present a wide range of biological functions and constitute potential therapies for numerous diseases, partly due to their ability to penetrate cell membranes. However, their mechanisms of action have not been fully elucidated due to the lack of appropriate tools. Existing light-emitting probes are limited by their cytotoxicity and large size, which can alter peptide structure and function. Here, we describe the available fluorescent, bioluminescent, and chemiluminescent probes for labeling peptides, with a focus on minimalistic options.
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Affiliation(s)
- Andreia Boaro
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados, 5001, Santo André, São Paulo 09210-580, Brazil
| | - Lucía Ageitos
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
- Centro de Investigacións Científicas Avanzadas (CICA) e Departamento de Química, Facultade de Ciencias, Universidade da Coruña, Calle de la Maestranza, 9, A Coruña 15071, Spain
| | - Marcelo Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
| | - Fernando Heering Bartoloni
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados, 5001, Santo André, São Paulo 09210-580, Brazil
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
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Yang P, Wang X, Ma Y, Sun Y, Zhang L, Yue J, Fu K, Zhou JS, Tang B. Nickel-catalyzed C-alkylation of thioamide, amides and esters by primary alcohols through a hydrogen autotransfer strategy. Chem Commun (Camb) 2020; 56:14083-14086. [PMID: 33107876 DOI: 10.1039/d0cc06468h] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A simple catalyst of Ni(OAc)2 and P(t-Bu)3 enables selective C-alkylation of thioacetamides and primary acetamides with alcohols for the first time. Monoalkylation of thioamides, amides and t-butyl esters occurs in excellent yields (>95%). Mechanistic studies reveal that the reaction proceeds via a hydrogen autotransfer pathway.
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Affiliation(s)
- Peng Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
| | - Xiuhua Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
| | - Yu Ma
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
| | - Yaxin Sun
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
| | - Li Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
| | - Jieyu Yue
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
| | - Kaiyue Fu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
| | - Jianrong Steve Zhou
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Room F312, 2199 Lishui Road, Nanshan District, Shenzhen 518055, China.
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
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40
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Giannakoulias S, Shringari SR, Liu C, Phan HAT, Barrett TM, Ferrie JJ, Petersson EJ. Rosetta Machine Learning Models Accurately Classify Positional Effects of Thioamides on Proteolysis. J Phys Chem B 2020; 124:8032-8041. [PMID: 32869996 DOI: 10.1021/acs.jpcb.0c05981] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Thioamide substitutions of the peptide backbone have been shown to stabilize therapeutic and imaging peptides toward proteolysis. In order to rationally design thioamide modifications, we have developed a novel Rosetta custom score function to classify thioamide positional effects on proteolysis in substrates of serine and cysteine proteases. Peptides of interest were docked into proteases using the FlexPepDock application in Rosetta. Docked complexes were modified to contain thioamides parametrized through the creation of custom atom types in Rosetta based on ab intio simulations. Thioamide complexes were simulated, and the resultant structural complexes provided features for machine learning classification as the decomposed values of the Rosetta score function. An ensemble, majority voting model was developed to be a robust predictor of previously unpublished thioamide proteolysis holdout data. Theoretical control simulations with pseudo-atoms that modulate only one physical characteristic of the thioamide show differential effects on prediction accuracy by the optimized voting classification model. These pseudo-atom model simulations, as well as statistical analyses of the full thioamide simulations, implicate steric effects on peptide binding as being primarily responsible for thioamide positional effects on proteolytic resistance.
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Affiliation(s)
- Sam Giannakoulias
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Sumant R Shringari
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chunxiao Liu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Hoang Anh T Phan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Taylor M Barrett
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - John J Ferrie
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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41
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Rečnik LM, Kandioller W, Mindt TL. 1,4-Disubstituted 1,2,3-Triazoles as Amide Bond Surrogates for the Stabilisation of Linear Peptides with Biological Activity. Molecules 2020; 25:E3576. [PMID: 32781656 PMCID: PMC7465391 DOI: 10.3390/molecules25163576] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/20/2022] Open
Abstract
Peptides represent an important class of biologically active molecules with high potential for the development of diagnostic and therapeutic agents due to their structural diversity, favourable pharmacokinetic properties, and synthetic availability. However, the widespread use of peptides and conjugates thereof in clinical applications can be hampered by their low stability in vivo due to rapid degradation by endogenous proteases. A promising approach to circumvent this potential limitation includes the substitution of metabolically labile amide bonds in the peptide backbone by stable isosteric amide bond mimetics. In this review, we focus on the incorporation of 1,4-disubstituted 1,2,3-triazoles as amide bond surrogates in linear peptides with the aim to increase their stability without impacting their biological function(s). We highlight the properties of this heterocycle as a trans-amide bond surrogate and summarise approaches for the synthesis of triazole-containing peptidomimetics via the Cu(I)-catalysed azide-alkyne cycloaddition (CuAAC). The impacts of the incorporation of triazoles in the backbone of diverse peptides on their biological properties such as, e.g., blood serum stability and affinity as well as selectivity towards their respective molecular target(s) are discussed.
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Affiliation(s)
- Lisa-Maria Rečnik
- Ludwig Boltzmann Institute Applied Diagnostics, General Hospital Vienna, 1090 Vienna, Austria;
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria;
- Department of Biomedical Imaging and Image Guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Wolfgang Kandioller
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria;
| | - Thomas L. Mindt
- Ludwig Boltzmann Institute Applied Diagnostics, General Hospital Vienna, 1090 Vienna, Austria;
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria;
- Department of Biomedical Imaging and Image Guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, 1090 Vienna, Austria
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Saito M, Murakami S, Nanjo T, Kobayashi Y, Takemoto Y. Mild and Chemoselective Thioacylation of Amines Enabled by the Nucleophilic Activation of Elemental Sulfur. J Am Chem Soc 2020; 142:8130-8135. [DOI: 10.1021/jacs.0c03256] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Masato Saito
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sho Murakami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takeshi Nanjo
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yusuke Kobayashi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshiji Takemoto
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
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43
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Shah SS, Casanova N, Antuono G, Sabatino D. Polyamide Backbone Modified Cell Targeting and Penetrating Peptides in Cancer Detection and Treatment. Front Chem 2020; 8:218. [PMID: 32296681 PMCID: PMC7136562 DOI: 10.3389/fchem.2020.00218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 03/09/2020] [Indexed: 12/15/2022] Open
Abstract
Cell penetrating and targeting peptides (CPPs and CTPs) encompass an important class of biochemically active peptides owning the capabilities of targeting and translocating within selected cell types. As such, they have been widely used in the delivery of imaging and therapeutic agents for the diagnosis and treatment of various diseases, especially in cancer. Despite their potential utility, first generation CTPs and CPPs based on the native peptide sequences are limited by poor biological and pharmacological properties, thereby restricting their efficacy. Therefore, medicinal chemistry approaches have been designed and developed to construct related peptidomimetics. Of specific interest herein, are the design applications which modify the polyamide backbone of lead CTPs and CPPs. These modifications aim to improve the biochemical characteristics of the native peptide sequence in order to enhance its diagnostic and therapeutic capabilities. This review will focus on a selected set of cell penetrating and targeting peptides and their related peptidomimetics whose polyamide backbone has been modified in order to improve their applications in cancer detection and treatment.
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Affiliation(s)
- Sunil S Shah
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, United States
| | - Nelson Casanova
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, United States
| | - Gina Antuono
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, United States
| | - David Sabatino
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, United States
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Lucey M, Pickford P, Bitsi S, Minnion J, Ungewiss J, Schoeneberg K, Rutter GA, Bloom SR, Tomas A, Jones B. Disconnect between signalling potency and in vivo efficacy of pharmacokinetically optimised biased glucagon-like peptide-1 receptor agonists. Mol Metab 2020; 37:100991. [PMID: 32278079 PMCID: PMC7262448 DOI: 10.1016/j.molmet.2020.100991] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/23/2020] [Accepted: 04/01/2020] [Indexed: 01/14/2023] Open
Abstract
Objective The objective of this study was to determine how pharmacokinetically advantageous acylation impacts on glucagon-like peptide-1 receptor (GLP-1R) signal bias, trafficking, anti-hyperglycaemic efficacy, and appetite suppression. Methods In vitro signalling responses were measured using biochemical and biosensor assays. GLP-1R trafficking was determined by confocal microscopy and diffusion-enhanced resonance energy transfer. Pharmacokinetics, glucoregulatory effects, and appetite suppression were measured in acute, sub-chronic, and chronic settings in mice. Results A C-terminally acylated ligand, [F1,G40,K41.C16 diacid]exendin-4, was identified that showed undetectable β-arrestin recruitment and GLP-1R internalisation. Depending on the cellular system used, this molecule was up to 1000-fold less potent than the comparator [D3,G40,K41.C16 diacid]exendin-4 for cyclic AMP signalling, yet was considerably more effective in vivo, particularly for glucose regulation. Conclusions C-terminal acylation of biased GLP-1R agonists increases their degree of signal bias in favour of cAMP production and improves their therapeutic potential. Programming of GLP-1R agonists for selective signalling. Signal bias allows “low efficacy” agonists to be highly effective in vivo. GLP-1R endocytosis does not affect pharmacokinetics.
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Affiliation(s)
- Maria Lucey
- Section of Investigative Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Philip Pickford
- Section of Investigative Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Stavroula Bitsi
- Section of Cell Biology and Functional Genomics, Imperial College London, London W12 0NN, United Kingdom
| | - James Minnion
- Section of Investigative Medicine, Imperial College London, London W12 0NN, United Kingdom
| | | | | | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Imperial College London, London W12 0NN, United Kingdom
| | - Stephen R Bloom
- Section of Investigative Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Alejandra Tomas
- Section of Cell Biology and Functional Genomics, Imperial College London, London W12 0NN, United Kingdom.
| | - Ben Jones
- Section of Investigative Medicine, Imperial College London, London W12 0NN, United Kingdom.
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45
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Khatri B, Bhat P, Chatterjee J. Convenient synthesis of thioamidated peptides and proteins. J Pept Sci 2020; 26:e3248. [PMID: 32202029 DOI: 10.1002/psc.3248] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 12/13/2022]
Abstract
The unique physicochemical properties of a thioamide bond, which is an ideal isostere of an amide bond, have not been fully exploited because of the tedious synthesis of thionated amino acid building blocks. Here, we report a purification-free and highly efficient synthesis of thiobenzotriazolides of Fmoc-protected and orthogonally protected 20 naturally occurring amino acids including asparagine, glutamine, and histidine. The near-quantitative conversion to the respective thioamidated peptides on solid support demonstrates the robustness of the synthetic route. Furthermore, the unaltered incorporation efficiency of thiobenzotriazolides from their stock solution till 48 h suggests their compatibility toward automated peptide synthesis. Finally, utilizing an optimized cocktail of 2% DBU + 5% piperazine for fast Fmoc-deprotection, we report the synthesis of a thioamidated Pin1 WW domain and thioamidated GB1 directly on solid support.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Prabhat Bhat
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
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Barrett TM, Chen XS, Liu C, Giannakoulias S, Phan HAT, Wang J, Keenan EK, Karpowicz RJ, Petersson EJ. Studies of Thioamide Effects on Serine Protease Activity Enable Two-Site Stabilization of Cancer Imaging Peptides. ACS Chem Biol 2020; 15:774-779. [PMID: 32141733 DOI: 10.1021/acschembio.9b01036] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Thioamide substitutions in peptides can be used as fluorescence quenchers in protease sensors and as stabilizing modifications of hormone analogs. To guide these applications in the context of serine proteases, we here examine the cleavage of several model substrates, scanning a thioamide between the P3 and P3' positions, and identify perturbing positions for thioamide substitution. While all serine proteases tested were affected by P1 thioamidation, certain proteases were also significantly affected by other thioamide positions. We demonstrate how these findings can be applied by harnessing the combined P3/P1 effect of a single thioamide on kallikrein proteolysis to protect two key positions in a neuropeptide Y-based imaging probe, increasing its serum half-life to >24 h while maintaining potency for binding to Y1 receptor expressing cells. Such stabilized peptide probes could find application in imaging cell populations in animal models or even in clinical applications such as fluorescence-guided surgery.
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Affiliation(s)
- Taylor M. Barrett
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Xing S. Chen
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chunxiao Liu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Applied Chemistry, China Agricultural University, Yuanmingyuan West Road 2, Beijing 100193, China
| | - Sam Giannakoulias
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Hoang Anh T. Phan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jieliang Wang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - E. Keith Keenan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Richard J. Karpowicz
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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47
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Davenport AP, Scully CCG, de Graaf C, Brown AJH, Maguire JJ. Advances in therapeutic peptides targeting G protein-coupled receptors. Nat Rev Drug Discov 2020; 19:389-413. [PMID: 32494050 DOI: 10.1038/s41573-020-0062-z] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2020] [Indexed: 02/06/2023]
Abstract
Dysregulation of peptide-activated pathways causes a range of diseases, fostering the discovery and clinical development of peptide drugs. Many endogenous peptides activate G protein-coupled receptors (GPCRs) - nearly 50 GPCR peptide drugs have been approved to date, most of them for metabolic disease or oncology, and more than 10 potentially first-in-class peptide therapeutics are in the pipeline. The majority of existing peptide therapeutics are agonists, which reflects the currently dominant strategy of modifying the endogenous peptide sequence of ligands for peptide-binding GPCRs. Increasingly, novel strategies are being employed to develop both agonists and antagonists, to both introduce chemical novelty and improve drug-like properties. Pharmacodynamic improvements are evolving to allow biasing ligands to activate specific downstream signalling pathways, in order to optimize efficacy and reduce side effects. In pharmacokinetics, modifications that increase plasma half-life have been revolutionary. Here, we discuss the current status of the peptide drugs targeting GPCRs, with a focus on evolving strategies to improve pharmacokinetic and pharmacodynamic properties.
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Affiliation(s)
- Anthony P Davenport
- Experimental Medicine and Immunotherapeutics, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK.
| | | | | | | | - Janet J Maguire
- Experimental Medicine and Immunotherapeutics, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
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48
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Li J, Ren X, Li G, Liang H, Zhao Y, Wang Z, Li H, Yuan B. Mixed bases mediated synthesis of thioamides in water. J Sulphur Chem 2020. [DOI: 10.1080/17415993.2020.1722818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Jiao Li
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Xuanhe Ren
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Ganzhong Li
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Helong Liang
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yajie Zhao
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Zhiwu Wang
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Heng Li
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Bingxin Yuan
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
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49
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Maini R, Kimura H, Takatsuji R, Katoh T, Goto Y, Suga H. Ribosomal Formation of Thioamide Bonds in Polypeptide Synthesis. J Am Chem Soc 2019; 141:20004-20008. [DOI: 10.1021/jacs.9b11097] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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50
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Zhan Z, Luo N, Ma H, He J, Lu G, Cui X, Huang G. Self‐Coupling Reaction of Benzylamine to Form Thioamides and Amides by Elemental Sulfur. ChemistrySelect 2019. [DOI: 10.1002/slct.201903512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Zhenzhen Zhan
- State Key Laboratory of Applied Organic Chemistry Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province Department of Chemistry Lanzhou University Lanzhou P. R. China
| | - Nan Luo
- State Key Laboratory of Applied Organic Chemistry Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province Department of Chemistry Lanzhou University Lanzhou P. R. China
| | - Haojie Ma
- College of Chemistry and Chemical EngineeringShaanxi Key laboratory of Chemical Reaction Engineering Yan'an University, Yan'an Shaanxi Province 716000 P. R. China
| | - Jianping He
- State Key Laboratory of Applied Organic Chemistry Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province Department of Chemistry Lanzhou University Lanzhou P. R. China
| | - Guoqiang Lu
- State Key Laboratory of Applied Organic Chemistry Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province Department of Chemistry Lanzhou University Lanzhou P. R. China
| | - Xinfeng Cui
- State Key Laboratory of Applied Organic Chemistry Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province Department of Chemistry Lanzhou University Lanzhou P. R. China
| | - Guosheng Huang
- State Key Laboratory of Applied Organic Chemistry Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province Department of Chemistry Lanzhou University Lanzhou P. R. China
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