1
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McCartney F, Caisse P, Dumont C, Brayden DJ. Labrafac TM MC60 is an efficacious intestinal permeation enhancer for macromolecules: Comparisons with Labrasol® ALF in ex vivo and in vivo rat studies. Int J Pharm 2024; 661:124353. [PMID: 38909926 DOI: 10.1016/j.ijpharm.2024.124353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
Labrafac™ MC60 (glycerol monocaprylocaprate) is a lipid-based excipient used in oral formulations as a solubiliser. Due to the high proportions of established permeability enhancers, caprylate (C8) and caprate (C10), in Labrafac™ MC60, we hypothesised that it might behave as an intestinal permeation enhancer. We therefore evaluated this using two paracellular markers (ex vivo) and insulin (in vivo) as model molecules. Ex vivo studies were conducted in isolated muscle-stripped rat colonic mucosae mounted in Ussing chambers. Apical addition of Labrafac™ MC60 (8, 12, and 16 mg/ml) enhanced the apparent permeability coefficients (Papp) of [14C] mannitol and FITC-dextran 4 kDa (FD4) across colonic mucosae. Similar effects were observed in isolated jejunal mucosae, but at higher concentrations (40 mg/ml). The enhancing capacity of Labrafac™ MC60 was transient due to reversibility of reductions in transepithelial electrical resistance (TEER) upon wash-out and effects on fluxes were molecular weight-dependent (MW) as suggested by fluxes of a set of high MW FITC-dextrans. The permeability enhancing effects of Labrafac™ MC60 ex vivo were maintained in the presence of simulated intestinal fluids, FaSSIF and FaSSCoF, in both jejunal and colonic mucosae, respectively. Following intra-intestinal regional instillations to rats, the relative bioavailability of 50 IU/kg insulin ad-mixed with Labrafac™ MC60 was 5 % in jejunum (40 mg/ml) and 6 % in colon (8 mg/ml). When Labrafac™ MC60 was combined with PEG-60 hydrogenated castor oil (1 % v/v), this further increased the bioavailability of insulin to 8 % in jejunum. Absorption enhancement was also maintained in the presence of FaSSIF in jejunal instillations. Histology after 120 min exposure to Labrafac™ MC60 in vivo for both jejunum and colon was similar to untreated control. Labrafac™ MC60 therefore acts as a non-damaging intestinal permeation enhancer for macromolecules and can be considered as another excipient in screening programmes to develop orally administered macromolecules.
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Affiliation(s)
- Fiona McCartney
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
| | | | - Camille Dumont
- Gattefossé SAS, 36, Chemin de Genas, Saint-Priest, France
| | - David J Brayden
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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2
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Wu J, Wang Y, Cai W, Chen D, Peng X, Dong H, Li J, Liu H, Shi S, Tang S, Li Z, Sui H, Wang Y, Wu C, Zhang Y, Fu X, Yin Y. Ribosomal translation of fluorinated non-canonical amino acids for de novo biologically active fluorinated macrocyclic peptides. Chem Sci 2024:d4sc04061a. [PMID: 39129776 PMCID: PMC11310889 DOI: 10.1039/d4sc04061a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 07/25/2024] [Indexed: 08/13/2024] Open
Abstract
Fluorination has emerged as a promising strategy in medicinal chemistry to improve the pharmacological profiles of drug candidates. Similarly, incorporating fluorinated non-canonical amino acids into macrocyclic peptides expands chemical diversity and enhances their pharmacological properties, from improved metabolic stability to enhanced cell permeability and target interactions. However, only a limited number of fluorinated non-canonical amino acids, which are canonical amino acid analogs, have been incorporated into macrocyclic peptides by ribosomes for de novo construction and target-based screening of fluorinated macrocyclic peptides. In this study, we report the ribosomal translation of a series of distinct fluorinated non-canonical amino acids, including mono-to tri-fluorinated variants, as well as fluorinated l-amino acids, d-amino acids, β-amino acids, etc. This enabled the de novo discovery of fluorinated macrocyclic peptides with high affinity for EphA2, and particularly the identification of those exhibiting broad-spectrum activity against Gram-negative bacteria by targeting the BAM complex. This study not only expands the scope of ribosomally translatable fluorinated amino acids but also underscores the versatility of fluorinated macrocyclic peptides as potent therapeutic agents.
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Affiliation(s)
- Junjie Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University Qingdao 266237 China
| | - Yuchan Wang
- College of Life Sciences, Fujian Normal University Fuzhou 350117 China
| | - Wenfeng Cai
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University Qingdao 266237 China
| | - Danyan Chen
- College of Life Sciences, Fujian Normal University Fuzhou 350117 China
| | - Xiangda Peng
- Shanghai Zelixir Biotech Company Ltd Shanghai 200030 China
| | - Huilei Dong
- College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Jinjing Li
- College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Hongtan Liu
- College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Shuting Shi
- College of Life Sciences, Fujian Normal University Fuzhou 350117 China
| | - Sen Tang
- College of Life Sciences, Fujian Normal University Fuzhou 350117 China
| | - Zhifeng Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University Qingdao 266237 China
| | - Haiyan Sui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University Qingdao 266237 China
| | - Yan Wang
- College of Life Sciences, Fujian Normal University Fuzhou 350117 China
| | - Chuanliu Wu
- College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University Qingdao 266237 China
| | - Xinmiao Fu
- College of Life Sciences, Fujian Normal University Fuzhou 350117 China
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University Qingdao 266237 China
- Shandong Research Institute of Industrial Technology Jinan 250101 China
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3
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Kage M, Hayashi R, Matsuo A, Tamiya M, Kuramoto S, Ohara K, Irie M, Chiyoda A, Takano K, Ito T, Kotake T, Takeyama R, Ishikawa S, Nomura K, Furuichi N, Morita Y, Hashimoto S, Kawada H, Nishimura Y, Nii K, Sase H, Ohta A, Kojima T, Iikura H, Tanada M, Shiraishi T. Structure-activity relationships of middle-size cyclic peptides, KRAS inhibitors derived from an mRNA display. Bioorg Med Chem 2024; 110:117830. [PMID: 38981216 DOI: 10.1016/j.bmc.2024.117830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/11/2024]
Abstract
Cyclic peptides are attracting attention as therapeutic agents due to their potential for oral absorption and easy access to tough intracellular targets. LUNA18, a clinical KRAS inhibitor, was transformed-without scaffold hopping-from the initial hit by using an mRNA display library that met our criteria for drug-likeness. In drug discovery using mRNA display libraries, hit compounds always possess a site linked to an mRNA tag. Here, we describe our examination of the Structure-Activity Relationship (SAR) using X-ray structures for chemical optimization near the site linked to the mRNA tag, equivalent to the C-terminus. Structural modifications near the C-terminus demonstrated a relatively wide range of tolerance for side chains. Furthermore, we show that a single atom modification is enough to change the pharmacokinetic (PK) profile. Since there are four positions where side chain modification is permissible in terms of activity, it is possible to flexibly adjust the pharmacokinetic profile by structurally optimizing the side chain. The side chain transformation findings demonstrated here may be generally applicable to hits obtained from mRNA display libraries.
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Affiliation(s)
- Mirai Kage
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Ryuji Hayashi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan.
| | - Atsushi Matsuo
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Minoru Tamiya
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Shino Kuramoto
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Kazuhiro Ohara
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Machiko Irie
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Aya Chiyoda
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Koji Takano
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Toshiya Ito
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Tomoya Kotake
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Ryuuichi Takeyama
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Shiho Ishikawa
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Kenichi Nomura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Noriyuki Furuichi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Yuya Morita
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Satoshi Hashimoto
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hatsuo Kawada
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Yoshikazu Nishimura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Keiji Nii
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hitoshi Sase
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Atsushi Ohta
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Tetsuo Kojima
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hitoshi Iikura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Mikimasa Tanada
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan.
| | - Takuya Shiraishi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan.
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4
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You S, McIntyre G, Passioura T. The coming of age of cyclic peptide drugs: an update on discovery technologies. Expert Opin Drug Discov 2024; 19:961-973. [PMID: 38872502 DOI: 10.1080/17460441.2024.2367024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024]
Abstract
INTRODUCTION Cyclic peptides are an established class of pharmaceuticals, with the ability to bind to a broader range of protein targets than traditional small molecules while also being capable of oral availability and cell penetration. Historically, cyclic peptide drugs have been discovered almost exclusively through natural product mining approaches; however, the last two decades have seen the development of display screening approaches capable of rapidly identifying de novo (i.e. not natural product derived) cyclic peptide ligands to targets of interest. AREAS COVERED In this review, the authors describe the current clinical landscape for cyclic peptide pharmaceuticals. This article focuses on the discovery approaches that have led to the development of different classes of molecules and how the development of newer technologies, particularly phage and mRNA display, has broadened the clinical applicability of such molecules. EXPERT OPINION The field of de novo cyclic peptide drug discovery is reaching maturity, with the first drugs identified through display screening approaches reaching the market in recent years. Many more are in clinical trials; however, significant technical challenges remain. Technological improvements will be required over the coming years to facilitate the identification of membrane permeable cyclic peptides capable of oral availability and targeting intracellular proteins.
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Affiliation(s)
- Sophia You
- Insamo South, Chippendale, NSW, Australia
| | | | - Toby Passioura
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia
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5
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Eslami SM, Padhi C, Rahman IR, van der Donk WA. Expression and Subcellular Localization of Lanthipeptides in Human Cells. ACS Synth Biol 2024; 13:2128-2140. [PMID: 38925629 PMCID: PMC11264318 DOI: 10.1021/acssynbio.4c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/19/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
Cyclic peptides, such as most ribosomally synthesized and post-translationally modified peptides (RiPPs), represent a burgeoning area of interest in therapeutic and biotechnological research because of their conformational constraints and reduced susceptibility to proteolytic degradation compared to their linear counterparts. Herein, an expression system is reported that enables the production of structurally diverse lanthipeptides and derivatives in mammalian cells. Successful targeting of lanthipeptides to the nucleus, the endoplasmic reticulum, and the plasma membrane is demonstrated. In vivo expression and targeting of such peptides in mammalian cells may allow for screening of lanthipeptide-based cyclic peptide inhibitors of native, organelle-specific protein-protein interactions in mammalian systems.
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Affiliation(s)
- Sara M. Eslami
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Chandrashekhar Padhi
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Imran R. Rahman
- Department
of Biochemistry, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Biochemistry, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
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6
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Krishna Sudhakar H, Yau JTK, Alcock LJ, Lau YH. Accessing diverse bicyclic peptide conformations using 1,2,3-TBMB as a linker. Org Biomol Chem 2024. [PMID: 39007293 DOI: 10.1039/d4ob00901k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Bicyclic peptides are a powerful modality for engaging challenging drug targets such as protein-protein interactions. Here, we use 1,2,3-tris(bromomethyl)benzene (1,2,3-TBMB) to access bicyclic peptides with diverse conformations that differ from conventional bicyclisation products formed with 1,3,5-TBMB. Bicyclisation at cysteine residues under aqueous buffer conditions proceeds efficiently, with broad substrate scope, compatibility with high-throughput screening, and clean conversion (>90%) for 96 of the 115 peptides tested. We envisage that the 1,2,3-TBMB linker will be applicable to a variety of peptide screening techniques in drug discovery.
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Affiliation(s)
| | - Jackie Tsz Ki Yau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia.
| | - Lisa J Alcock
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia.
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia.
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW 2006, Australia.
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7
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Pingitore V, Pancholi J, Hornsby TW, Warne J, Pryce G, McCormick LJ, Hill J, Bhosale G, Peng J, Newton LS, Towers GJ, Coles SJ, Chan AWE, Duchen MR, Szabadkai G, Baker D, Selwood DL. Delocalized quinolinium-macrocyclic peptides, an atypical chemotype for CNS penetration. SCIENCE ADVANCES 2024; 10:eado3501. [PMID: 38985859 PMCID: PMC11235165 DOI: 10.1126/sciadv.ado3501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
Macrocyclic drugs can address an increasing range of molecular targets but enabling central nervous system (CNS) access to these drugs has been viewed as an intractable problem. We designed and synthesized a series of quinolinium-modified cyclosporine derivatives targeted to the mitochondrial cyclophilin D protein. Modification of the cation to enable greater delocalization was confirmed by x-ray crystallography of the cations. Critically, greater delocalization improved brain concentrations. Assessment of the compounds in preclinical assays and for pharmacokinetics identified a molecule JP1-138 with at least 20 times the brain levels of a non-delocalized compound or those reported for cyclosporine. Levels were maintained over 24 hours together with low hERG potential. The paradigm outlined here could have widespread utility in the treatment of CNS diseases.
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Affiliation(s)
- Valeria Pingitore
- Drug Discovery, UCL Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
- Department of Biological and Health Sciences, Universidad Loyola Andalucía, Dos Hermanas, Seville 41704, Spain
| | - Jessica Pancholi
- Drug Discovery, UCL Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Thomas W Hornsby
- Drug Discovery, UCL Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Justin Warne
- Drug Discovery, UCL Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Gareth Pryce
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Laura J McCormick
- EPSRC National Crystallography Service, School of Chemistry, University of Southampton, Highfield Southampton SO17 1BJ, UK
| | - Julia Hill
- Department of Cell and Developmental Biology, UCL Consortium for Mitochondrial Research, London WC1E 6BT, UK
| | - Gauri Bhosale
- Department of Cell and Developmental Biology, UCL Consortium for Mitochondrial Research, London WC1E 6BT, UK
| | - Jing Peng
- Drug Discovery, UCL Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Lydia S Newton
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Simon J Coles
- EPSRC National Crystallography Service, School of Chemistry, University of Southampton, Highfield Southampton SO17 1BJ, UK
| | - Ah Wing Edith Chan
- Drug Discovery, UCL Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Michael R Duchen
- Department of Cell and Developmental Biology, UCL Consortium for Mitochondrial Research, London WC1E 6BT, UK
| | - Gyorgy Szabadkai
- Department of Cell and Developmental Biology, UCL Consortium for Mitochondrial Research, London WC1E 6BT, UK
- Department of Biomedical Sciences, University of Padua, Padua 35131 Italy
| | - David Baker
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - David L Selwood
- Drug Discovery, UCL Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
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8
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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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9
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Hurd CA, Bush JT, Powell AJ, Walport LJ. mRNA Display in Cell Lysates Enables Identification of Cyclic Peptides Targeting the BRD3 Extraterminal Domain. Angew Chem Int Ed Engl 2024:e202406414. [PMID: 38899853 DOI: 10.1002/anie.202406414] [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: 04/04/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 06/21/2024]
Abstract
mRNA display is a powerful technology to screen libraries of >1012 cyclic peptides against a protein target, enabling the rapid discovery of high affinity ligands. These cyclic peptides are particularly well suited to challenging protein targets that have been difficult to drug with small molecules. However, target choice can still be limited as screens are typically performed against purified proteins which often demands the use of isolated domains and precludes the use of aggregation-prone targets. Herein, we report a method to perform mRNA display selections in mammalian cell lysates without the need for prior target purification, vastly expanding the potential target scope of mRNA display. We have applied the methodology to identify low to sub-nanomolar peptide binders for two targets: a NanoLuc subunit (LgBiT) and full-length bromodomain-containing protein 3 (BRD3). Our cyclic peptides for BRD3 were found to bind to the extraterminal (ET) domain of BRD3 and the closely related BRD proteins, BRD2 and BRD4. While many chemical probes exist for the bromodomains of BRD proteins, the ET domain is relatively underexplored, making these peptides valuable additions to the BRD toolbox.
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Affiliation(s)
- Catherine A Hurd
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ
- Crick-GSK Biomedical LinkLabs, The Francis Crick Institute, London, NW1 1AT
| | - Jacob T Bush
- Crick-GSK Biomedical LinkLabs, GSK, Gunnels Wood Road, Stevenage, SG1 2NY
| | - Andrew J Powell
- Crick-GSK Biomedical LinkLabs, GSK, Gunnels Wood Road, Stevenage, SG1 2NY
| | - Louise J Walport
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT
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10
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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11
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Ouyang Y, Page CG, Bilodeau C, Hyster TK. Synergistic Photoenzymatic Catalysis Enables Synthesis of a-Tertiary Amino Acids Using Threonine Aldolases. J Am Chem Soc 2024; 146:13754-13759. [PMID: 38739748 DOI: 10.1021/jacs.4c04661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
a-Tertiary amino acids are essential components of drugs and agrochemicals, yet traditional syntheses are step-intensive and provide access to a limited range of structures with varying levels of enantioselectivity. Here, we report the α-alkylation of unprotected alanine and glycine by pyridinium salts using pyridoxal (PLP)-dependent threonine aldolases with a Rose Bengal photoredox catalyst. The strategy efficiently prepares various a-tertiary amino acids in a single chemical step as a single enantiomer. UV-vis spectroscopy studies reveal a ternary interaction between the pyridinium salt, protein, and photocatalyst, which we hypothesize is responsible for localizing radical formation to the active site. This method highlights the opportunity for combining photoredox catalysts with enzymes to reveal new catalytic functions for known enzymes.
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Affiliation(s)
- Yao Ouyang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Claire G Page
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Catherine Bilodeau
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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12
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Feng Y, Qirjollari A, Fawaz MV, Cancilla MT, Gonzalez RJ, Pearson K. Rapid and Definitive Identification of Cyclic Peptide Soft Spots by Isotope-Labeled Reductive Dimethylation and Mass Spectrometry Fragmentation. Anal Chem 2024; 96:7756-7762. [PMID: 38690743 DOI: 10.1021/acs.analchem.4c01372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Cyclic peptides are an emerging therapeutic modality over the past few decades. To identify drug candidates with sufficient proteolytic stability for oral administration, it is critical to pinpoint the amide bond hydrolysis sites, or soft spots, to better understand their metabolism and provide guidance on further structure optimization. However, the unambiguous characterization of cyclic peptide soft spots remains a significant challenge during early stage discovery studies, as amide bond hydrolysis forms a linearized isobaric sequence with the addition of a water molecule, regardless of the amide hydrolysis location. In this study, an innovative strategy was developed to enable the rapid and definitive identification of cyclic peptide soft spots by isotope-labeled reductive dimethylation and mass spectrometry fragmentation. The dimethylated immonium ion with enhanced MS signal at a distinctive m/z in MS/MS fragmentation spectra reveals the N-terminal amino acid on a linearized peptide sequence definitively and, thus, significantly simplifies the soft spot identification workflow. This approach has been evaluated to demonstrate the potential of isotope-labeled dimethylation to be a powerful analytical tool in cyclic peptide drug discovery and development.
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Affiliation(s)
- Yu Feng
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Athanasia Qirjollari
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Maria V Fawaz
- Pharmacokinetics, Dynamics, Metabolism, and Bioanalytics, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Mark T Cancilla
- Pharmacokinetics, Dynamics, Metabolism, and Bioanalytics, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Raymond J Gonzalez
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Kara Pearson
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
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13
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Sinha K, Basu I, Shah Z, Shah S, Chakrabarty S. Leveraging Bidirectional Nature of Allostery To Inhibit Protein-Protein Interactions (PPIs): A Case Study of PCSK9-LDLR Interaction. J Chem Inf Model 2024; 64:3923-3932. [PMID: 38615325 DOI: 10.1021/acs.jcim.4c00294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The protein PCSK9 (proprotein convertase subtilisin/Kexin type 9) negatively regulates the recycling of LDLR (low-density lipoprotein receptor), leading to an elevated plasma level of LDL. Inhibition of PCSK9-LDLR interaction has emerged as a promising therapeutic strategy to manage hypercholesterolemia. However, the large interaction surface area between PCSK9 and LDLR makes it challenging to identify a small molecule competitive inhibitor. An alternative strategy would be to identify distal cryptic sites as targets for allosteric inhibitors that can remotely modulate PCSK9-LDLR interaction. Using several microseconds long molecular dynamics (MD) simulations, we demonstrate that on binding with LDLR, there is a significant conformational change (population shift) in a distal loop (residues 211-222) region of PCSK9. Consistent with the bidirectional nature of allostery, we establish a clear correlation between the loop conformation and the binding affinity with LDLR. Using a thermodynamic argument, we establish that the loop conformations predominantly present in the apo state of PCSK9 would have lower LDLR binding affinity, and they would be potential targets for designing allosteric inhibitors. We elucidate the molecular origin of the allosteric coupling between this loop and the LDLR binding interface in terms of the population shift in a set of salt bridges and hydrogen bonds. Overall, our work provides a general strategy toward identifying allosteric hotspots: compare the conformational ensemble of the receptor between the apo and bound states of the protein and identify distal conformational changes, if any. The inhibitors should be designed to bind and stabilize the apo-specific conformations.
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Affiliation(s)
- Krishnendu Sinha
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700 106, India
| | - Ipsita Basu
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700 106, India
| | - Zacharia Shah
- Hingez Therapeutics Inc., 8000 Towers Crescent Drive, STE 1331, Vienna, Virginia 22182, United States
| | - Salim Shah
- Hingez Therapeutics Inc., 8000 Towers Crescent Drive, STE 1331, Vienna, Virginia 22182, United States
| | - Suman Chakrabarty
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700 106, India
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14
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Agarwala A, Asim R, Ballantyne CM. Oral PCSK9 Inhibitors. Curr Atheroscler Rep 2024; 26:147-152. [PMID: 38536608 DOI: 10.1007/s11883-024-01199-2] [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] [Accepted: 03/13/2024] [Indexed: 05/12/2024]
Abstract
PURPOSE OF REVIEW In this review, we will discuss the data from early clinical studies of MK-0616 and summarize clinical trials of other oral proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors. RECENT FINDINGS The success of PCSK9 inhibition with monoclonal antibody injections has fueled the development of additional therapies targeting PCSK9, including oral formulations, the most advanced of which is MK-0616. MK-0616 is a novel, orally administered macrocyclic peptide that binds to PCSK9 and inhibits binding of PCSK9 to the LDL receptor, thereby decreasing plasma levels of LDL-C. Clinical trial data on the safety and efficacy of MK-0616 are promising and report LDL-C-lowering efficacy comparable to that provided by injectable PCSK9 inhibitors. Ongoing and future studies of oral PCSK9 inhibitors in development will evaluate the safety, efficacy, and effectiveness of these agents and their potential role in preventing cardiovascular disease events.
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Affiliation(s)
- Anandita Agarwala
- Center for Cardiovascular Disease Prevention, Cardiovascular Division, Baylor Scott and White Health Heart Hospital Baylor Plano, Plano, TX, USA
| | - Ramsha Asim
- College of Osteopathic Medicine, Kansas City University, Kansas City, MO, USA
| | - Christie M Ballantyne
- Section of Cardiovascular Research and Center for Cardiometabolic Disease Prevention, Department of Medicine, Baylor College of Medicine, One Baylor Plaza, MS BCM285, Houston, TX, 77030, USA.
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15
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Keyes ED, Mifflin MC, Austin MJ, Sandres J, Roberts AG. Chemical cyclization of tyrosine-containing peptides via in situ generated triazolinedione peptides. Methods Enzymol 2024; 698:89-109. [PMID: 38886041 DOI: 10.1016/bs.mie.2024.04.019] [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
Tyr-derived cyclic peptide natural products are formed by enzymatic manifolds that oxidatively cross-link embedded phenolic side chains of tyrosine (Tyr) and 4-hydroxyphenylglycine residues during their controlled production. Bioactive Tyr-derived cyclic peptides, such as the arylomycins and vancomycins, continue to motivate the development of enzymatic and chemical strategies for their de novo assembly and modification. However, chemical access to these structurally diverse natural cycles can be challenging and step intensive. Therefore, we developed an oxidative procedure to selectively convert Tyr-containing N4-substituted 1,2,4-triazolidine-3,5-dione peptides (urazole peptides) into stable Tyr-linked cyclic peptides. We show that Tyr-containing urazole peptides are simple to prepare and convert into reactive N4-substituted 1,2,4-triazoline-3,5-dione peptides by oxidation, which then undergo spontaneous cyclization under mildly basic aqueous conditions to form a cross-linkage with the phenol side chain of embedded Tyr residues. Using this approach, we have demonstrated access to over 25 Tyr-linked cyclic peptides (3- to 11-residue cycles) with good tolerance of native residue side chain functionalities. Importantly, this method is simple to perform, and product formation can be quickly confirmed by mass spectrometric and 1H NMR spectroscopic analyses.
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Affiliation(s)
- E Dalles Keyes
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Marcus C Mifflin
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Maxwell J Austin
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Jesus Sandres
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Andrew G Roberts
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States.
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16
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Pal S, Openy J, Krzyzanowski A, Noisier A, ‘t Hart P. On-Resin Photochemical Decarboxylative Arylation of Peptides. Org Lett 2024; 26:2795-2799. [PMID: 37819674 PMCID: PMC11019635 DOI: 10.1021/acs.orglett.3c03070] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Indexed: 10/13/2023]
Abstract
Here we describe the application of photochemical decarboxylative arylation as a late-stage functionalization reaction for peptides. The reaction uses redox-active esters of aspartic acid and glutamic acid on the solid phase to provide analogues of aromatic amino acids. By using aryl bromides as arylation reagents, a wide variety of amino acids can be accessed without having to synthesize them individually in solution. The reaction is compatible with proteinogenic amino acids and was used to perform a structure-activity relationship study of a PRMT5 binding peptide.
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Affiliation(s)
- Sunit Pal
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, 44227 Dortmund, Germany
| | - Joseph Openy
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, 44227 Dortmund, Germany
| | - Adrian Krzyzanowski
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, 44227 Dortmund, Germany
| | - Anaïs Noisier
- Medicinal
Chemistry, Research and Early Development Cardiovascular, Renal and
Metabolism BioPharmaceutical R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Peter ‘t Hart
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, 44227 Dortmund, Germany
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17
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Ball A, Mohammed S, Doigneaux C, Gardner RM, Easton JW, Turner S, Essex JW, Pairaudeau G, Tavassoli A. Identification and Development of Cyclic Peptide Inhibitors of Hypoxia Inducible Factors 1 and 2 That Disrupt Hypoxia-Response Signaling in Cancer Cells. J Am Chem Soc 2024; 146:8877-8886. [PMID: 38503564 PMCID: PMC10996005 DOI: 10.1021/jacs.3c10508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024]
Abstract
Hypoxia inducible factor (HIF) is a heterodimeric transcription factor composed of an oxygen-regulated α subunit and a constitutively expressed β subunit that serves as the master regulator of the cellular response to low oxygen concentrations. The HIF transcription factor senses and responds to hypoxia by significantly altering transcription and reprogramming cells to enable adaptation to a hypoxic microenvironment. Given the central role played by HIF in the survival and growth of tumors in hypoxia, inhibition of this transcription factor serves as a potential therapeutic approach for treating a variety of cancers. Here, we report the identification, optimization, and characterization of a series of cyclic peptides that disrupt the function of HIF-1 and HIF-2 transcription factors by inhibiting the interaction of both HIF-1α and HIF-2α with HIF-1β. These compounds are shown to bind to HIF-α and disrupt the protein-protein interaction between the α and β subunits of the transcription factor, resulting in disruption of hypoxia-response signaling by our lead molecule in several cancer cell lines.
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Affiliation(s)
- Andrew
T. Ball
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Soran Mohammed
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Cyrielle Doigneaux
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Reece M. Gardner
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K.
| | - James W. Easton
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Steven Turner
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Jonathan W. Essex
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Garry Pairaudeau
- Discovery
Sciences IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton
Road, Cambridge CB4 0WG, U.K.
| | - Ali Tavassoli
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K.
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18
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Fassi EMA, Citarella A, Albani M, Milano EG, Legnani L, Lammi C, Silvani A, Grazioso G. PCSK9 inhibitors: a patent review 2018-2023. Expert Opin Ther Pat 2024; 34:245-261. [PMID: 38588538 DOI: 10.1080/13543776.2024.2340569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/28/2024] [Indexed: 04/10/2024]
Abstract
INTRODUCTION Proprotein convertase subtilisin/kexin 9 (PCSK9) plays a crucial role in breaking down the hepatic low-density lipoprotein receptor (LDLR), thereby influencing the levels of circulating low-density lipoprotein cholesterol (LDL-C). Consequently, inhibiting PCSK9 through suitable ligands has been established as a validated therapeutic strategy for combating hypercholesterolemia and cardiovascular diseases. AREA COVERED Patent literature claiming novel compounds inhibiting PCSK9 disclosed from 2018 to June 2023 available in the espacenet database, which contains more than 150 million patent documents from over 100 patent-granting authorities worldwide. EXPERT OPINION The undisputable beneficial influence of PCSK9 as a pharmacological target has prompted numerous private and public institutions to patent chemical frameworks as inhibitors of PCSK9. While several compounds have advanced to clinical trials for treating hypercholesterolemia, they have not completed these trials yet. These compounds must contend in a complex market where new, costly, and advanced drugs, such as monoclonal antibodies and siRNA, are prescribed instead of inexpensive and less potent statins.
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Affiliation(s)
| | - Andrea Citarella
- Dipartimento di Chimica, Università degli Studi di Milano, Milano, Italy
| | - Marco Albani
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy
| | - Erica Ginevra Milano
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy
| | - Laura Legnani
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy
| | - Alessandra Silvani
- Dipartimento di Chimica, Università degli Studi di Milano, Milano, Italy
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy
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19
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Callahan AJ, Gandhesiri S, Travaline TL, Reja RM, Lozano Salazar L, Hanna S, Lee YC, Li K, Tokareva OS, Swiecicki JM, Loas A, Verdine GL, McGee JH, Pentelute BL. Mirror-image ligand discovery enabled by single-shot fast-flow synthesis of D-proteins. Nat Commun 2024; 15:1813. [PMID: 38418820 PMCID: PMC10901774 DOI: 10.1038/s41467-024-45634-z] [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: 06/29/2023] [Accepted: 01/26/2024] [Indexed: 03/02/2024] Open
Abstract
Widespread adoption of mirror-image biological systems presents difficulties in accessing the requisite D-protein substrates. In particular, mirror-image phage display has the potential for high-throughput generation of biologically stable macrocyclic D-peptide binders with potentially unique recognition modes but is hindered by the individualized optimization required for D-protein chemical synthesis. We demonstrate a general mirror-image phage display pipeline that utilizes automated flow peptide synthesis to prepare D-proteins in a single run. With this approach, we prepare and characterize 12 D-proteins - almost one third of all reported D-proteins to date. With access to mirror-image protein targets, we describe the successful discovery of six macrocyclic D-peptide binders: three to the oncoprotein MDM2, and three to the E3 ubiquitin ligase CHIP. Reliable production of mirror-image proteins can unlock the full potential of D-peptide drug discovery and streamline the study of mirror-image biology more broadly.
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Affiliation(s)
- Alex J Callahan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Satish Gandhesiri
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Tara L Travaline
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
| | - Rahi M Reja
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Lia Lozano Salazar
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Stephanie Hanna
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Yen-Chun Lee
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Chemistry, National Cheng Kung University, No.1, University Road, Tainan City, 701, Taiwan
| | - Kunhua Li
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
| | - Olena S Tokareva
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
| | - Jean-Marie Swiecicki
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
- Relay Therapeutics, Inc., 399 Binney Street, 2nd Floor, Cambridge, MA, 02139, USA
| | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Gregory L Verdine
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA, 02138, USA
| | - John H McGee
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA.
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02142, USA.
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
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20
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Faris J, Adaligil E, Popovych N, Ono S, Takahashi M, Nguyen H, Plise E, Taechalertpaisarn J, Lee HW, Koehler MFT, Cunningham CN, Lokey RS. Membrane Permeability in a Large Macrocyclic Peptide Driven by a Saddle-Shaped Conformation. J Am Chem Soc 2024; 146:4582-4591. [PMID: 38330910 PMCID: PMC10885153 DOI: 10.1021/jacs.3c10949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/10/2024]
Abstract
The effort to modulate challenging protein targets has stimulated interest in ligands that are larger and more complex than typical small-molecule drugs. While combinatorial techniques such as mRNA display routinely produce high-affinity macrocyclic peptides against classically undruggable targets, poor membrane permeability has limited their use toward primarily extracellular targets. Understanding the passive membrane permeability of macrocyclic peptides would, in principle, improve our ability to design libraries whose leads can be more readily optimized against intracellular targets. Here, we investigate the permeabilities of over 200 macrocyclic 10-mers using the thioether cyclization motif commonly found in mRNA display macrocycle libraries. We identified the optimal lipophilicity range for achieving permeability in thioether-cyclized 10-mer cyclic peptide-peptoid hybrid scaffolds and showed that permeability could be maintained upon extensive permutation in the backbone. In one case, changing a single amino acid from d-Pro to d-NMe-Ala, representing the loss of a single methylene group in the side chain, resulted in a highly permeable scaffold in which the low-dielectric conformation shifted from the canonical cross-beta geometry of the parent compounds into a novel saddle-shaped fold in which all four backbone NH groups were sequestered from the solvent. This work provides an example by which pre-existing physicochemical knowledge of a scaffold can benefit the design of macrocyclic peptide mRNA display libraries, pointing toward an approach for biasing libraries toward permeability by design. Moreover, the compounds described herein are a further demonstration that geometrically diverse, highly permeable scaffolds exist well beyond conventional drug-like chemical space.
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Affiliation(s)
- Justin
H. Faris
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Emel Adaligil
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Nataliya Popovych
- Department
of Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, United States
| | - Satoshi Ono
- Innovative
Research Division, Mitsubishi Tanabe Pharma
Corporation, Kanagawa 227-0033, Japan
| | - Mifune Takahashi
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, South
San Francisco, California 94080, United States
| | - Huy Nguyen
- Department
of Analytical Research, Genentech, South San Francisco, California 94080, United States
| | - Emile Plise
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, South
San Francisco, California 94080, United States
| | - Jaru Taechalertpaisarn
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Hsiau-Wei Lee
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Michael F. T. Koehler
- Department
of Medicinal Chemistry, Genentech, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - R. Scott Lokey
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
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21
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Giannessi L, Lupo MG, Rossi I, Martina MG, Vilella A, Bodria M, Giuliani D, Zimetti F, Zanotti I, Potì F, Bernini F, Ferri N, Radi M. Identification of 4-amino-2-Pyridones as new potent PCSK9 inhibitors: From phenotypic hit discovery to in vivo tolerability. Eur J Med Chem 2024; 265:116063. [PMID: 38160616 DOI: 10.1016/j.ejmech.2023.116063] [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: 06/09/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
Among the strategies to overcome the underperformance of statins in cardiovascular diseases (CVDs), the development of drugs targeting the Proprotein Convertase Subtilisin-like Kexin type 9 (PCSK9) is considered one of the most promising. However, only anti-PCSK9 biological drugs have been approved to date, and orally available small-molecules for the treatment of hypercholesterolemic conditions are still missing on the market. In the present work, we describe the application of a phenotypic approach to the identification and optimization of 4-amino-2-pyridone derivatives as a new chemotype with anti-PCSK9 activity. Starting from an in-house collection of compounds, functional assays on HepG2 cells followed by a chemistry-driven hit optimization campaign, led to the potent anti-PCSK9 candidate 5c. This compound, at 5 μM, totally blocked PCSK9 secretion from HepG2 cells, significantly increased LDL receptor (LDLR) expression, and acted cooperatively with simvastatin by reducing its induction of PCSK9 expression. Finally, compound 5c also proved to be well tolerated in C57BL/6J mice at the tested concentration (40 mg/kg) with no sign of toxicity or behavior modifications.
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Affiliation(s)
- Lisa Giannessi
- Dipartimento di Scienze Degli Alimenti e Del Farmaco (DipALIFAR), Università Degli Studi di Parma, Viale Delle Scienze, 27/A, 43124, Parma, Italy
| | | | - Ilaria Rossi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 351131, Padova, Italy
| | - Maria Grazia Martina
- Dipartimento di Scienze Degli Alimenti e Del Farmaco (DipALIFAR), Università Degli Studi di Parma, Viale Delle Scienze, 27/A, 43124, Parma, Italy
| | - Antonietta Vilella
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Martina Bodria
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Daniela Giuliani
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Francesca Zimetti
- Dipartimento di Scienze Degli Alimenti e Del Farmaco (DipALIFAR), Università Degli Studi di Parma, Viale Delle Scienze, 27/A, 43124, Parma, Italy
| | - Ilaria Zanotti
- Dipartimento di Scienze Degli Alimenti e Del Farmaco (DipALIFAR), Università Degli Studi di Parma, Viale Delle Scienze, 27/A, 43124, Parma, Italy
| | - Francesco Potì
- Department of Medicine and Surgery, Unit of Neuroscience, University of Parma, 43125, Parma, Italy
| | - Franco Bernini
- Dipartimento di Scienze Degli Alimenti e Del Farmaco (DipALIFAR), Università Degli Studi di Parma, Viale Delle Scienze, 27/A, 43124, Parma, Italy
| | - Nicola Ferri
- Department of Medicine, University of Padova, 35128, Padova, Italy; Veneto Institute of Molecular Medicine, Padua, 35129, Italy.
| | - Marco Radi
- Dipartimento di Scienze Degli Alimenti e Del Farmaco (DipALIFAR), Università Degli Studi di Parma, Viale Delle Scienze, 27/A, 43124, Parma, Italy.
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22
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Abstract
Cyclic peptides are fascinating molecules abundantly found in nature and exploited as molecular format for drug development as well as other applications, ranging from research tools to food additives. Advances in peptide technologies made over many years through improved methods for synthesis and drug development have resulted in a steady stream of new drugs, with an average of around one cyclic peptide drug approved per year. Powerful technologies for screening random peptide libraries, and de novo generating ligands, have enabled the development of cyclic peptide drugs independent of naturally derived molecules and now offer virtually unlimited development opportunities. In this review, we feature therapeutically relevant cyclic peptides derived from nature and discuss the unique properties of cyclic peptides, the enormous technological advances in peptide ligand development in recent years, and current challenges and opportunities for developing cyclic peptides that address unmet medical needs.
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Affiliation(s)
- Xinjian Ji
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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23
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Bao X, Liang Y, Chang H, Cai T, Feng B, Gordon K, Zhu Y, Shi H, He Y, Xie L. Targeting proprotein convertase subtilisin/kexin type 9 (PCSK9): from bench to bedside. Signal Transduct Target Ther 2024; 9:13. [PMID: 38185721 PMCID: PMC10772138 DOI: 10.1038/s41392-023-01690-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 09/27/2023] [Accepted: 10/27/2023] [Indexed: 01/09/2024] Open
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) has evolved as a pivotal enzyme in lipid metabolism and a revolutionary therapeutic target for hypercholesterolemia and its related cardiovascular diseases (CVD). This comprehensive review delineates the intricate roles and wide-ranging implications of PCSK9, extending beyond CVD to emphasize its significance in diverse physiological and pathological states, including liver diseases, infectious diseases, autoimmune disorders, and notably, cancer. Our exploration offers insights into the interaction between PCSK9 and low-density lipoprotein receptors (LDLRs), elucidating its substantial impact on cholesterol homeostasis and cardiovascular health. It also details the evolution of PCSK9-targeted therapies, translating foundational bench discoveries into bedside applications for optimized patient care. The advent and clinical approval of innovative PCSK9 inhibitory therapies (PCSK9-iTs), including three monoclonal antibodies (Evolocumab, Alirocumab, and Tafolecimab) and one small interfering RNA (siRNA, Inclisiran), have marked a significant breakthrough in cardiovascular medicine. These therapies have demonstrated unparalleled efficacy in mitigating hypercholesterolemia, reducing cardiovascular risks, and have showcased profound value in clinical applications, offering novel therapeutic avenues and a promising future in personalized medicine for cardiovascular disorders. Furthermore, emerging research, inclusive of our findings, unveils PCSK9's potential role as a pivotal indicator for cancer prognosis and its prospective application as a transformative target for cancer treatment. This review also highlights PCSK9's aberrant expression in various cancer forms, its association with cancer prognosis, and its crucial roles in carcinogenesis and cancer immunity. In conclusion, this synthesized review integrates existing knowledge and novel insights on PCSK9, providing a holistic perspective on its transformative impact in reshaping therapeutic paradigms across various disorders. It emphasizes the clinical value and effect of PCSK9-iT, underscoring its potential in advancing the landscape of biomedical research and its capabilities in heralding new eras in personalized medicine.
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Affiliation(s)
- Xuhui Bao
- Institute of Therapeutic Cancer Vaccines, Fudan University Pudong Medical Center, Shanghai, China.
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China.
- Department of Oncology, Fudan University Pudong Medical Center, Shanghai, China.
- Center for Clinical Research, Fudan University Pudong Medical Center, Shanghai, China.
- Clinical Research Center for Cell-based Immunotherapy, Fudan University, Shanghai, China.
- Department of Pathology, Duke University Medical Center, Durham, NC, USA.
| | - Yongjun Liang
- Center for Medical Research and Innovation, Fudan University Pudong Medical Center, Shanghai, China
| | - Hanman Chang
- Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL, USA
| | - Tianji Cai
- Department of Sociology, University of Macau, Taipa, Macau, China
| | - Baijie Feng
- Department of Oncology, Fudan University Pudong Medical Center, Shanghai, China
| | - Konstantin Gordon
- Medical Institute, Peoples' Friendship University of Russia, Moscow, Russia
- A. Tsyb Medical Radiological Research Center, Obninsk, Russia
| | - Yuekun Zhu
- Department of Colorectal Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Hailian Shi
- Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Zhangjiang Hi-tech Park, Shanghai, China
| | - Yundong He
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China.
| | - Liyi Xie
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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24
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Hossain S, Kneiszl R, Larsson P. Revealing the interaction between peptide drugs and permeation enhancers in the presence of intestinal bile salts. NANOSCALE 2023; 15:19180-19195. [PMID: 37982184 DOI: 10.1039/d3nr05571j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Permeability enhancer-based formulations offer a promising approach to enhance the oral bioavailability of peptides. We used all-atom molecular dynamics simulations to investigate the interaction between two permeability enhancers (sodium caprate, and SNAC), and four different peptides (octreotide, hexarelin, degarelix, and insulin), in the presence of taurocholate, an intestinal bile salt. The permeability enhancers exhibited distinct effects on peptide release based on their properties, promoting hydrophobic peptide release while inhibiting water-soluble peptide release. Lowering peptide concentrations in the simulations reduced peptide-peptide interactions but increased their interactions with the enhancers and taurocholates. Introducing peptides randomly with enhancer and taurocholate molecules yielded dynamic molecular aggregation, and reduced peptide-peptide interactions and hydrogen bond formation compared to peptide-only systems. The simulations provided insights into molecular-level interactions, highlighting the specific contacts between peptide residues responsible for aggregation, and the interactions between peptide residues and permeability enhancers/taurocholates that are crucial within the mixed colloids. Therefore, our results can provide insights into how modifications of these critical contacts can be made to alter drug release profiles from peptide-only or mixed peptide-PE-taurocholate aggregates. To further probe the molecular nature of permeability enhancers and peptide interactions, we also analyzed insulin secondary structures using Fourier transform infrared spectroscopy. The presence of SNAC led to an increase in β-sheet formation in insulin. In contrast, both in the absence and presence of caprate, α-helices, and random structures dominated. These molecular-level insights can guide the design of improved permeability enhancer-based dosage forms, allowing for precise control of peptide release profiles near the intended absorption site.
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Affiliation(s)
| | - Rosita Kneiszl
- Department of Pharmacy, Uppsala University, Uppsala 751 23, Sweden
- Department of Pharmacy and The Swedish Drug Delivery Center (SweDeliver), Uppsala University, Uppsala 751 23, Sweden.
| | - Per Larsson
- Department of Pharmacy, Uppsala University, Uppsala 751 23, Sweden
- Department of Pharmacy and The Swedish Drug Delivery Center (SweDeliver), Uppsala University, Uppsala 751 23, Sweden.
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25
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Lee JH, Shores KL, Breithaupt JJ, Lee CS, Fodera DM, Kwon JB, Ettyreddy AR, Myers KM, Evison BJ, Suchowerska AK, Gersbach CA, Leong KW, Truskey GA. PCSK9 activation promotes early atherosclerosis in a vascular microphysiological system. APL Bioeng 2023; 7:046103. [PMID: 37854060 PMCID: PMC10581720 DOI: 10.1063/5.0167440] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023] Open
Abstract
Atherosclerosis is a primary precursor of cardiovascular disease (CVD), the leading cause of death worldwide. While proprotein convertase subtilisin/kexin 9 (PCSK9) contributes to CVD by degrading low-density lipoprotein receptors (LDLR) and altering lipid metabolism, PCSK9 also influences vascular inflammation, further promoting atherosclerosis. Here, we utilized a vascular microphysiological system to test the effect of PCSK9 activation or repression on the initiation of atherosclerosis and to screen the efficacy of a small molecule PCSK9 inhibitor. We have generated PCSK9 over-expressed (P+) or repressed (P-) human induced pluripotent stem cells (iPSCs) and further differentiated them to smooth muscle cells (viSMCs) or endothelial cells (viECs). Tissue-engineered blood vessels (TEBVs) made from P+ viSMCs and viECs resulted in increased monocyte adhesion compared to the wild type (WT) or P- equivalents when treated with enzyme-modified LDL (eLDL) and TNF-α. We also found significant viEC dysfunction, such as increased secretion of VCAM-1, TNF-α, and IL-6, in P+ viECs treated with eLDL and TNF-α. A small molecule compound, NYX-1492, that was originally designed to block PCSK9 binding with the LDLR was tested in TEBVs to determine its effect on lowering PCSK9-induced inflammation. The compound reduced monocyte adhesion in P+ TEBVs with evidence of lowering secretion of VCAM-1 and TNF-α. These results suggest that PCSK9 inhibition may decrease vascular inflammation in addition to lowering plasma LDL levels, enhancing its anti-atherosclerotic effects, particularly in patients with elevated chronic inflammation.
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Affiliation(s)
- Jounghyun H. Lee
- Department of Biomedical Engineering, Columbia University, New York, New York 10032, USA
| | - Kevin L. Shores
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Jason J. Breithaupt
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Caleb S. Lee
- Department of Biomedical Engineering, Columbia University, New York, New York 10032, USA
| | - Daniella M. Fodera
- Department of Biomedical Engineering, Columbia University, New York, New York 10032, USA
| | | | | | - Kristin M. Myers
- Department of Mechanical Engineering, Columbia University, New York, New York 10032, USA
| | | | | | | | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, New York 10032, USA
| | - George A. Truskey
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
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26
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Yu L, Barros SA, Sun C, Somani S. Cyclic Peptide Linker Design and Optimization by Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:6863-6876. [PMID: 37903231 DOI: 10.1021/acs.jcim.3c01359] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Cyclic peptides are an emerging therapeutic modality that can target protein-protein interaction sites with high affinity and selectivity. A common medicinal chemistry strategy for the optimization of peptide hits is conformational stabilization through macrocyclization. We present a method based on explicit solvent enhanced sampling molecular dynamics simulations for estimating the impact of varying linker lengths and chemistry on the conformational stability of a peptide. The method is demonstrated on three cyclic peptide series that bind to proteins PCSK9, trypsin, and MDM2 adopting loop, β-sheet, and helical secondary structures. In general, the simulations show greater solution stability of the receptor-bound conformation for the higher-affinity peptides, consistent with the idea that preorganizing a ligand for binding can enhance binding affinity. The impact of the force field and sampling is discussed for one series that does not follow this trend. We have successfully applied this method to internal discovery programs to design peptides with increased potency and chemical stability.
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Affiliation(s)
- Lei Yu
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Stephanie A Barros
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Chengzao Sun
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Sandeep Somani
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
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27
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Eslami SM, Rahman IR, van der Donk WA. Expression of Lanthipeptides in Human Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563208. [PMID: 37961259 PMCID: PMC10634679 DOI: 10.1101/2023.10.19.563208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cyclic peptides represent a burgeoning area of interest in therapeutic and biotechnological research. In opposition to their linear counterparts, cyclic peptides, such as certain ribosomally synthesized and post-translationally modified peptides (RiPPs), are more conformationally constrained and less susceptible to proteolytic degradation. The lanthipeptide RiPP cytolysin L forms a covalently enforced helical structure that may be used to disrupt helical interactions at protein-protein interfaces. Herein, an expression system is reported to produce lanthipeptides and structurally diverse cytolysin L derivatives in mammalian cells. Successful targeting of lanthipeptides to the nucleus is demonstrated. In vivo expression and targeting of such peptides in mammalian cells may allow for screening of lanthipeptide inhibitors of native protein-protein interactions.
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Affiliation(s)
- Sara M. Eslami
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Imran R. Rahman
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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28
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Yan JX, Wu Q, Maity M, Braun DR, Alas I, Wang X, Yin X, Zhu Y, Bell BA, Rajski SR, Ge Y, Richardson DD, Zhong W, Bugni TS. Rapid Unambiguous Structure Elucidation of Streptnatamide A, a New Cyclic Peptide Isolated from A Marine-derived Streptomyces sp. Chemistry 2023; 29:e202301813. [PMID: 37452377 PMCID: PMC10592287 DOI: 10.1002/chem.202301813] [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: 06/15/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/18/2023]
Abstract
Cyclic peptides have been excellent source of drug leads. With the advances in discovery platforms, the pharmaceutical industry has a growing interest in cyclic peptides and has pushed several into clinical trials. However, structural complexity of cyclic peptides brings extreme challenges for structure elucidation efforts. Isotopic fine structure analysis, Nuclear magnetic resonance (NMR), and detailed tandem mass spectrometry rapidly provided peptide sequence for streptnatamide A, a cyclic peptide isolated from a marine-derived Streptomyces sp. Marfey's analysis determined the stereochemistry of all amino acids, enabling the unambiguous structure determination of this compound. A non-ribosomal peptide synthetase biosynthetic gene cluster (stp) was tentatively identified and annotated for streptnatamide A based on the in silico analysis of whole genome sequencing data. These analytical tools will be powerful tools to overcome the challenges for cyclic peptide structure elucidation and accelerate the development of bioactive cyclic peptides.
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Affiliation(s)
- Jia-Xuan Yan
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Qihao Wu
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
- Current address: Department of Chemistry, Institute of Biomolecular Design & Discovery, Yale University, 06516, West Haven, CT, USA
| | - Mitasree Maity
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Doug R Braun
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Imraan Alas
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Xiao Wang
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
| | - Xing Yin
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
| | - Bailey A Bell
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Scott R Rajski
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, 53706, Madison, WI, USA
| | | | - Wendy Zhong
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
| | - Tim S Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
- Lachman Institute for Pharmaceutical Development, University of Wisconsin-Madison, 600 Highland Ave, 53792, Madison, WI, USA
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29
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Liu M, Morewood R, Yoshisada R, Pascha MN, Hopstaken AJP, Tarcoveanu E, Poole DA, de Haan CAM, Nitsche C, Jongkees SAK. Selective thiazoline peptide cyclisation compatible with mRNA display and efficient synthesis. Chem Sci 2023; 14:10561-10569. [PMID: 37799990 PMCID: PMC10548512 DOI: 10.1039/d3sc03117a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/06/2023] [Indexed: 10/07/2023] Open
Abstract
Peptide display technologies are a powerful method for discovery of new bioactive sequences, but linear sequences are often very unstable in a biological setting. Macrocyclisation of such peptides is beneficial for target affinity, selectivity, stability, and cell permeability. However, macrocyclisation of a linear hit is unreliable and requires extensive structural knowledge. Genetically encoding macrocyclisation during the discovery process is a better approach, and so there is a need for diverse cyclisation options that can be deployed in the context of peptide display techniques such as mRNA display. In this work we show that meta-cyanopyridylalanine (mCNP) can be ribosomally incorporated into peptides, forming a macrocycle in a spontaneous and selective reaction with an N-terminal cysteine generated from bypassing the initiation codon in translation. This reactive amino acid can also be easily incorporated into peptides during standard Fmoc solid phase peptide synthesis, which can otherwise be a bottleneck in transferring from peptide discovery to peptide testing and application. We demonstrate the potential of this new method by discovery of macrocyclic peptides targeting influenza haemagglutinin, and molecular dynamics simulation indicates the mCNP cross-link stabilises a beta sheet structure in a representative of the most abundant cluster of active hits. Cyclisation by mCNP is also shown to be compatible with thioether macrocyclisation at a second cysteine to form bicycles of different architectures, provided that cysteine placement reinforces selectivity, with this bicyclisation happening spontaneously and in a controlled manner during peptide translation. Our new approach generates macrocycles with a more rigid cross-link and with better control of regiochemistry when additional cysteines are present, opening these up for further exploitation in chemical modification of in vitro translated peptides, and so is a valuable addition to the peptide discovery toolbox.
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Affiliation(s)
- Minglong Liu
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Richard Morewood
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - Ryoji Yoshisada
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Mirte N Pascha
- Section Virology, Division Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University Yalelaan 1 3584 CL Utrecht The Netherlands
| | - Antonius J P Hopstaken
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Eliza Tarcoveanu
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - David A Poole
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Cornelis A M de Haan
- Section Virology, Division Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University Yalelaan 1 3584 CL Utrecht The Netherlands
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - Seino A K Jongkees
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
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30
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Raschi E, Casula M, Cicero AFG, Corsini A, Borghi C, Catapano A. Beyond statins: New pharmacological targets to decrease LDL-cholesterol and cardiovascular events. Pharmacol Ther 2023; 250:108507. [PMID: 37567512 DOI: 10.1016/j.pharmthera.2023.108507] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
The pharmacological treatment of dyslipidemia, a major modifiable risk factor for developing atherosclerotic cardiovascular disease (ASCVD), remains a debated and controversial issue, not only in terms of the most appropriate therapeutic range for lipid levels, but also with regard to the optimal strategy and sequence approach (stepwise vs upstream therapy). Current treatment guidelines for the management of dyslipidemia focus on the intensity of low-density lipoprotein cholesterol (LDL-C) reduction, stratified according to risk for developing ASCVD. Beyond statins and ezetimibe, different medications targeting LDL-C have been recently approved by regulatory agencies with potential innovative mechanisms of action, including proprotein convertase subtilisin/kexin type 9 modulators (monoclonal antibodies such as evolocumab and alirocumab; small interfering RNA molecules such as inclisiran), ATP-citrate lyase inhibitors (bempedoic acid), angiopoietin-like 3 inhibitors (evinacumab), and microsomal triglyceride transfer protein inhibitors (lomitapide). An understanding of their pharmacological aspects, benefit-risk profile, including impact on hard cardiovascular endpoints beyond LDL-C reduction, and potential advantages from the patient perspective (e.g., adherence) - the focus of this evidence-based review - is crucial for practitioners across medical specialties to minimize therapeutic inertia and support clinical practice.
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Affiliation(s)
- Emanuel Raschi
- Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy.
| | - Manuela Casula
- Epidemiology and Preventive Pharmacology Service (SEFAP), Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy; IRCCS MultiMedica, Sesto S. Giovanni, Milan, Italy
| | - Arrigo F G Cicero
- Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy; IRCCS AOU S. Orsola-Malpighi, Bologna, Italy
| | - Alberto Corsini
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Claudio Borghi
- Department of Medical and Surgical Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy; IRCCS AOU S. Orsola-Malpighi, Bologna, Italy
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31
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Koziolek M, Augustijns P, Berger C, Cristofoletti R, Dahlgren D, Keemink J, Matsson P, McCartney F, Metzger M, Mezler M, Niessen J, Polli JE, Vertzoni M, Weitschies W, Dressman J. Challenges in Permeability Assessment for Oral Drug Product Development. Pharmaceutics 2023; 15:2397. [PMID: 37896157 PMCID: PMC10609725 DOI: 10.3390/pharmaceutics15102397] [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: 07/10/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Drug permeation across the intestinal epithelium is a prerequisite for successful oral drug delivery. The increased interest in oral administration of peptides, as well as poorly soluble and poorly permeable compounds such as drugs for targeted protein degradation, have made permeability a key parameter in oral drug product development. This review describes the various in vitro, in silico and in vivo methodologies that are applied to determine drug permeability in the human gastrointestinal tract and identifies how they are applied in the different stages of drug development. The various methods used to predict, estimate or measure permeability values, ranging from in silico and in vitro methods all the way to studies in animals and humans, are discussed with regard to their advantages, limitations and applications. A special focus is put on novel techniques such as computational approaches, gut-on-chip models and human tissue-based models, where significant progress has been made in the last few years. In addition, the impact of permeability estimations on PK predictions in PBPK modeling, the degree to which excipients can affect drug permeability in clinical studies and the requirements for colonic drug absorption are addressed.
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Affiliation(s)
- Mirko Koziolek
- NCE Drug Product Development, Development Sciences, AbbVie Deutschland GmbH & Co. KG, 67061 Ludwigshafen, Germany
| | - Patrick Augustijns
- Drug Delivery and Disposition, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Constantin Berger
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, 97070 Würzburg, Germany;
| | - Rodrigo Cristofoletti
- Department of Pharmaceutics, University of Florida, 6550 Sanger Road, Orlando, FL 32827, USA
| | - David Dahlgren
- Department of Pharmaceutical Biosciences, Uppsala University, 75124 Uppsala, Sweden (J.N.)
| | - Janneke Keemink
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland;
| | - Pär Matsson
- Department of Pharmacology and SciLifeLab Gothenburg, University of Gothenburg, 40530 Gothenburg, Sweden;
| | - Fiona McCartney
- School of Veterinary Medicine, University College Dublin, D04 V1W8 Dublin, Ireland;
| | - Marco Metzger
- Translational Center for Regenerative Therapies (TLZ-RT) Würzburg, Branch of the Fraunhofer Institute for Silicate Research (ISC), 97082 Würzburg, Germany
| | - Mario Mezler
- Quantitative, Translational & ADME Sciences, AbbVie Deutschland GmbH & Co. KG, 67061 Ludwigshafen, Germany;
| | - Janis Niessen
- Department of Pharmaceutical Biosciences, Uppsala University, 75124 Uppsala, Sweden (J.N.)
| | - James E. Polli
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD 21021, USA;
| | - Maria Vertzoni
- Department of Pharmacy, National and Kapodistrian University of Athens, 157 84 Zografou, Greece;
| | - Werner Weitschies
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
| | - Jennifer Dressman
- Fraunhofer Institute of Translational Medicine and Pharmacology, 60596 Frankfurt, Germany
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32
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Hummelgaard S, Vilstrup JP, Gustafsen C, Glerup S, Weyer K. Targeting PCSK9 to tackle cardiovascular disease. Pharmacol Ther 2023; 249:108480. [PMID: 37331523 DOI: 10.1016/j.pharmthera.2023.108480] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 06/20/2023]
Abstract
Lowering blood cholesterol levels efficiently reduces the risk of developing atherosclerotic cardiovascular disease (ASCVD), including coronary artery disease (CAD), which is the main cause of death worldwide. CAD is caused by plaque formation, comprising cholesterol deposits in the coronary arteries. Proprotein convertase subtilisin kexin/type 9 (PCSK9) was discovered in the early 2000s and later identified as a key regulator of cholesterol metabolism. PCSK9 induces lysosomal degradation of the low-density lipoprotein (LDL) receptor in the liver, which is responsible for clearing LDL-cholesterol (LDL-C) from the circulation. Accordingly, gain-of-function PCSK9 mutations are causative of familial hypercholesterolemia, a severe condition with extremely high plasma cholesterol levels and increased ASCVD risk, whereas loss-of-function PCSK9 mutations are associated with very low LDL-C levels and protection against CAD. Since the discovery of PCSK9, extensive investigations in developing PCSK9 targeting therapies have been performed. The combined delineation of clear biology, genetic risk variants, and PCSK9 crystal structures have been major drivers in developing antagonistic molecules. Today, two antibody-based PCSK9 inhibitors have successfully progressed to clinical application and shown to be effective in reducing cholesterol levels and mitigating the risk of ASCVD events, including myocardial infarction, stroke, and death, without any major adverse effects. A third siRNA-based inhibitor has been FDA-approved but awaits cardiovascular outcome data. In this review, we outline the PCSK9 biology, focusing on the structure and nonsynonymous mutations reported in the PCSK9 gene and elaborate on PCSK9-lowering strategies under development. Finally, we discuss future perspectives with PCSK9 inhibition in other severe disorders beyond cardiovascular disease.
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Affiliation(s)
| | | | | | - Simon Glerup
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Draupnir Bio, INCUBA Skejby, Aarhus, Denmark
| | - Kathrin Weyer
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
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33
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Cavett V, Chan AI, Cunningham CN, Paegel BM. Hydrogel-Encapsulated Beads Enable Proximity-Driven Encoded Library Synthesis and Screening. ACS CENTRAL SCIENCE 2023; 9:1603-1610. [PMID: 37637732 PMCID: PMC10451030 DOI: 10.1021/acscentsci.3c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Indexed: 08/29/2023]
Abstract
Encoded combinatorial library technologies have dramatically expanded the chemical space for screening but are usually only analyzed by affinity selection binding. It would be highly advantageous to reformat selection outputs to "one-bead-one-compound" solid-phase libraries, unlocking activity-based and cellular screening capabilities. Here, we describe hydrogel-encapsulated magnetic beads that enable such a transformation. Bulk emulsion polymerization of polyacrylamide hydrogel shells around magnetic microbeads yielded uniform particles (7 ± 2 μm diameter) that are compatible with diverse in-gel functionalization (amine, alkyne, oligonucleotides) and transformations associated with DNA-encoded library synthesis (acylation, enzymatic DNA ligation). In a case study of reformatting mRNA display libraries, transcription from DNA-templated magnetic beads encapsulated in gel particles colocalized both RNA synthesis via hybridization with copolymerized complementary DNA and translation via puromycin labeling. Two control epitope templates (V5, HA) were successfully enriched (50- and 99-fold, respectively) from an NNK5 library bead screen via FACS. Proximity-driven library synthesis in concert with magnetic sample manipulation provides a plausible means for reformatting encoded combinatorial libraries at scale.
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Affiliation(s)
- Valerie Cavett
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Alix I Chan
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Departments
of Chemistry & Biomedical Engineering, University of California, Irvine, California 92697, United States
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34
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Miles SA, Nillama JA, Hunter L. Tinker, Tailor, Soldier, Spy: The Diverse Roles That Fluorine Can Play within Amino Acid Side Chains. Molecules 2023; 28:6192. [PMID: 37687021 PMCID: PMC10489206 DOI: 10.3390/molecules28176192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Side chain-fluorinated amino acids are useful tools in medicinal chemistry and protein science. In this review, we outline some general strategies for incorporating fluorine atom(s) into amino acid side chains and for elaborating such building blocks into more complex fluorinated peptides and proteins. We then describe the diverse benefits that fluorine can offer when located within amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.
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Affiliation(s)
| | | | - Luke Hunter
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia
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35
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Iskandar SE, Chiou LF, Leisner TM, Shell DJ, Norris-Drouin JL, Vaziri C, Pearce KH, Bowers AA. Identification of Covalent Cyclic Peptide Inhibitors in mRNA Display. J Am Chem Soc 2023; 145:15065-15070. [PMID: 37395736 PMCID: PMC11246720 DOI: 10.1021/jacs.3c04833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Peptides have historically been underutilized for covalent inhibitor discovery, despite their unique abilities to interact with protein surfaces and interfaces. This is in part due to a lack of methods for screening and identifying covalent peptide ligands. Here, we report a method to identify covalent cyclic peptide inhibitors in mRNA display. We combine co- and post-translational library diversification strategies to create cyclic libraries with reactive dehydroalanines (Dhas), which we employ in selections against two model targets. The most potent hits exhibit low nanomolar inhibitory activities and disrupt known protein-protein interactions with their selected targets. Overall, we establish Dhas as electrophiles for covalent inhibition and showcase how separate library diversification methods can work synergistically to dispose mRNA display to novel applications like covalent inhibitor discovery.
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Affiliation(s)
- Sabrina E Iskandar
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Lilly F Chiou
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Tina M Leisner
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Devan J Shell
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Jacqueline L Norris-Drouin
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Cyrus Vaziri
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Curriculum in Toxicology, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H Pearce
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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36
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Tanada M, Tamiya M, Matsuo A, Chiyoda A, Takano K, Ito T, Irie M, Kotake T, Takeyama R, Kawada H, Hayashi R, Ishikawa S, Nomura K, Furuichi N, Morita Y, Kage M, Hashimoto S, Nii K, Sase H, Ohara K, Ohta A, Kuramoto S, Nishimura Y, Iikura H, Shiraishi T. Development of Orally Bioavailable Peptides Targeting an Intracellular Protein: From a Hit to a Clinical KRAS Inhibitor. J Am Chem Soc 2023. [PMID: 37463267 DOI: 10.1021/jacs.3c03886] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Cyclic peptides as a therapeutic modality are attracting a lot of attention due to their potential for oral absorption and accessibility to intracellular tough targets. Here, starting with a drug-like hit discovered using an mRNA display library, we describe a chemical optimization that led to the orally available clinical compound known as LUNA18, an 11-mer cyclic peptide inhibitor for the intracellular tough target RAS. The key findings are as follows: (i) two peptide side chains were identified that each increase RAS affinity over 10-fold; (ii) physico-chemical properties (PCP) including Clog P can be adjusted by side-chain modification to increase membrane permeability; (iii) restriction of cyclic peptide conformation works effectively to adjust PCP and improve bio-activity; (iv) cellular efficacy was observed in peptides with a permeability of around 0.4 × 10-6 cm/s or more in a Caco-2 permeability assay; and (v) while keeping the cyclic peptide's main-chain conformation, we found one example where the RAS protein structure was changed dramatically through induced-fit to our peptide side chain. This study demonstrates how the chemical optimization of bio-active peptides can be achieved without scaffold hopping, much like the processes for small molecule drug discovery that are guided by Lipinski's rule of five. Our approach provides a versatile new strategy for generating peptide drugs starting from drug-like hits.
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Affiliation(s)
- Mikimasa Tanada
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Minoru Tamiya
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Atsushi Matsuo
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Aya Chiyoda
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Koji Takano
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Toshiya Ito
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Machiko Irie
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Tomoya Kotake
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Ryuuichi Takeyama
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hatsuo Kawada
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Ryuji Hayashi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Shiho Ishikawa
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Kenichi Nomura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Noriyuki Furuichi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Yuya Morita
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Mirai Kage
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Satoshi Hashimoto
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Keiji Nii
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hitoshi Sase
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Kazuhiro Ohara
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Atsushi Ohta
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Shino Kuramoto
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Yoshikazu Nishimura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hitoshi Iikura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Takuya Shiraishi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
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37
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Kuethe JT, Lee J, Thaisrivongs D, Yasuda N, Pollack SR, Leone J, DaSilva J, Biba M, Tsay FR, Regalado EL, Qi J, Li H, Poggetto GD, Cohen R. Synthesis of a Complex and Highly Potent PCSK9 Inhibitor. Org Lett 2023; 25:5001-5005. [PMID: 37382389 DOI: 10.1021/acs.orglett.3c01635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
The solution-based gram-scale synthesis of complex and highly potent proprotein convertase subtilisin-like/kexin type 9 (PCSK9) inhibitor 1 is presented. Construction of Northern fragment 2, followed by stepwise installation of Eastern 3, Southern 4, and Western 5 fragments, provided macrocyclic precursor 19. This intermediate was cross-linked via an intramolecular azide-alkyne click reaction, which preceded macrolactamization to afford the core framework of compound 1. Finally, coupling with poly(ethylene glycol) side-chain-based 6 gave the PCSK9 inhibitor 1.
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Affiliation(s)
- Jeffrey T Kuethe
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Joshua Lee
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - David Thaisrivongs
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Nobuyoshi Yasuda
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Scott R Pollack
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Joseph Leone
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jimmy DaSilva
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Mirlinda Biba
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Fuh-Rong Tsay
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Erik L Regalado
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ji Qi
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Hongming Li
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Guilherme Dal Poggetto
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ryan Cohen
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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38
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Landmesser U, Makhmudova U. New Chapter in the PCSK9 Book: Oral Inhibition of PCSK9 Binding to the LDL Receptor With a Macrocyclic Peptide. Circulation 2023; 148:159-161. [PMID: 37428833 DOI: 10.1161/circulationaha.123.065407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Affiliation(s)
- Ulf Landmesser
- Department of Cardiology, Angiology, and Intensive Medicine, Deutsches Herzzentrum der Charité, Berlin, Germany (U.L., U.M.)
- Friede Springer Cardiovascular Prevention Center at Charité, Berlin, Germany (U.L., U.M.)
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (U.L.)
- Berlin Institute of Health, Germany (U.L.)
| | - Umidakhon Makhmudova
- Department of Cardiology, Angiology, and Intensive Medicine, Deutsches Herzzentrum der Charité, Berlin, Germany (U.L., U.M.)
- Friede Springer Cardiovascular Prevention Center at Charité, Berlin, Germany (U.L., U.M.)
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39
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Burnett JR, Hooper AJ. MK-0616: an oral PCSK9 inhibitor for hypercholesterolemia treatment. Expert Opin Investig Drugs 2023; 32:873-878. [PMID: 37815341 DOI: 10.1080/13543784.2023.2267972] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/04/2023] [Indexed: 10/11/2023]
Abstract
INTRODUCTION Atherosclerotic cardiovascular disease (ASCVD) is a leading cause of morbidity and mortality worldwide. Lowering LDL-cholesterol, by lifestyle modification or therapeutically, reduces the risk of ASCVD. Proprotein convertase subtilisin/kexin type 9 (PCSK9), a protein which binds to the LDL-receptor and induces degradation, is a clinically validated target to lower LDL-cholesterol. Injectable PCSK9 inhibitor therapies have demonstrated substantial reductions in LDL-cholesterol with associated decreased risk of ASCVD events. AREAS COVERED MK-0616 is an orally bioavailable, renally excreted, macrocyclic peptide inhibitor of PCSK9. The article provides an understanding of the chemistry and development, pharmacokinetic and pharmacodynamic characteristics of MK-0616 and insight into its clinical efficacy and safety. In clinical trials, MK-0616 produced dose-dependent reductions in LDL-cholesterol, non-HDL-cholesterol, and apolipoprotein (apo) B levels. Furthermore, MK-0616 modestly lowered lipoprotein (a) [Lp(a)]. EXPERT OPINION MK-0616 is a potent, oral macrocyclic peptide inhibitor of PCSK9 that is not only able to reduce LDL-cholesterol, non-HDL-cholesterol, and apoB, but can also lower Lp(a). Safety and tolerability studies reported to date are promising. MK-0616 may offer advantages over injectable anti-PCSK9 therapies in terms of ease of dosing, patient preference and cost. The results from phase III trials of MK-0616 on cardiovascular outcomes are awaited with interest.
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Affiliation(s)
- John R Burnett
- Department of Clinical Biochemistry, PathWest Laboratory Medicine, Perth, Western Australia
- Royal Perth Hospital & Fiona Stanley Hospital Network, Perth, Western Australia
| | - Amanda J Hooper
- Department of Clinical Biochemistry, PathWest Laboratory Medicine, Perth, Western Australia
- School of Medicine, University of Western Australia, Perth, Western Australia
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40
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Ahamad S, Bhat SA. Correction to "Recent Update on the Development of PCSK9 Inhibitors for Hypercholesterolemia Treatment". J Med Chem 2023. [PMID: 37377333 DOI: 10.1021/acs.jmedchem.3c01112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
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41
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Aspnes GE, Coffey SB, Darout E, Dechert-Schmitt AM, Dullea RG, Kamlet AS, Limberakis C, Londregan AT, McClure KF, Menhaji-Klotz E, Piotrowski DW, Polivkova J, Raymer B, Ruggeri RB, Salatto CT, Tu M, Wei L, Xiao J. Small molecule inhibitors of PCSK9. SAR investigations of head and amine groups. Bioorg Med Chem Lett 2023:129394. [PMID: 37379958 DOI: 10.1016/j.bmcl.2023.129394] [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: 03/16/2023] [Revised: 06/02/2023] [Accepted: 06/24/2023] [Indexed: 06/30/2023]
Abstract
Our previous work on the optimization of a new class of small molecule PCSK9 mRNA translation inhibitors focused on empirical optimization of the amide tail region of the lead PF-06446846 (1). This work resulted in compound 3 that showed an improved safety profile. We hypothesized that this improvement was related to diminished binding of 3 to non-translating ribosomes and an apparent improvement in transcript selectivity. Herein, we describe our efforts to further optimize this series of inhibitors through modulation of the heterocyclic head group and the amine fragment. Some of the effort was guided by an emerging cryo electron microscopy structure of the binding mode of 1 in the ribosome. These efforts led to the identification of 15 that was deemed suitable for evaluation in a humanized PCSK9 mouse model and a rat toxicology study. Compound 15 demonstrated a dose dependent reduction of plasma PCSK9 levels. The rat toxicological profile was not improved over that of 1, which precluded 15 from further consideration as a clinical candidate.
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Affiliation(s)
- Gary E Aspnes
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Steven B Coffey
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Etzer Darout
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | | | - Robert G Dullea
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Adam S Kamlet
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Chris Limberakis
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Allyn T Londregan
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Kim F McClure
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Elnaz Menhaji-Klotz
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - David W Piotrowski
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA.
| | - Jana Polivkova
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Brian Raymer
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Roger B Ruggeri
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | | | - Meihua Tu
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Liuqing Wei
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Jun Xiao
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
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42
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Lammi C, Fassi EMA, Manenti M, Brambilla M, Conti M, Li J, Roda G, Camera M, Silvani A, Grazioso G. Computational Design, Synthesis, and Biological Evaluation of Diimidazole Analogues Endowed with Dual PCSK9/HMG-CoAR-Inhibiting Activity. J Med Chem 2023. [PMID: 37261954 DOI: 10.1021/acs.jmedchem.3c00279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Proprotein convertase subtilisin/kexin 9 (PCSK9) is responsible for the degradation of the hepatic low-density lipoprotein receptor (LDLR), which regulates circulating cholesterol levels. Consequently, the PCSK9 inhibition is a valuable therapeutic approach for the treatment of hypercholesterolemia and cardiovascular diseases. In our studies, we discovered Rim13, a polyimidazole derivative reducing the protein-protein interaction between PCSK9 and LDLR with an IC50 of 1.6 μM. The computational design led to the optimization of the shape of the PCSK9/ligand complementarity, enabling the discovery of potent diimidazole derivatives. In fact, carrying out biological assays to fully characterize the cholesterol-lowering activity of the new analogues and using both biochemical and cellular techniques, compound Dim16 displayed improved PCSK9 inhibitory activity (IC50 0.9 nM). Interestingly, similar to other lupin-derived peptides and their synthetic analogues, some compounds in this series showed dual hypocholesterolemic activity since some of them complementarily inhibited the 3-hydroxy-3-methylglutaryl coenzyme A reductase.
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Affiliation(s)
- Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Enrico M A Fassi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Marco Manenti
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 10, 20133 Milan, Italy
| | - Marta Brambilla
- Centro Cardiologico Monzino IRCCS, via Parea 4, 20138 Milan, Italy
| | - Maria Conti
- Centro Cardiologico Monzino IRCCS, via Parea 4, 20138 Milan, Italy
| | - Jianqiang Li
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Gabriella Roda
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Marina Camera
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
- Centro Cardiologico Monzino IRCCS, via Parea 4, 20138 Milan, Italy
| | - Alessandra Silvani
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 10, 20133 Milan, Italy
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
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Fleming MC, Bowler MM, Park R, Popov KI, Bowers AA. Tyrosinase-Catalyzed Peptide Macrocyclization for mRNA Display. J Am Chem Soc 2023; 145:10445-10450. [PMID: 37155687 PMCID: PMC11091840 DOI: 10.1021/jacs.2c12629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
mRNA display of macrocyclic peptides has proven itself to be a powerful technique to discover high-affinity ligands for a protein target. However, only a limited number of cyclization chemistries are known to be compatible with mRNA display. Tyrosinase is a copper-dependent oxidase that oxidizes tyrosine phenol to an electrophilic o-quinone, which is readily attacked by cysteine thiol. Here we show that peptides containing tyrosine and cysteine are rapidly cyclized upon tyrosinase treatment. Characterization of the cyclization reveals it to be widely applicable to multiple macrocycle sizes and scaffolds. We combine tyrosinase-mediated cyclization with mRNA display to discover new macrocyclic ligands targeting melanoma-associated antigen A4 (MAGE-A4). These macrocycles potently inhibit the MAGE-A4 binding axis with nanomolar IC50 values. Importantly, macrocyclic ligands show clear advantage over noncyclized analogues with ∼40-fold or greater decrease in IC50 values.
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Affiliation(s)
- Matthew C. Fleming
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 301 Pharmacy Lane, Chapel Hill, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Matthew M. Bowler
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 301 Pharmacy Lane, Chapel Hill, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Rodney Park
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Konstantin I. Popov
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 301 Pharmacy Lane, Chapel Hill, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 301 Pharmacy Lane, Chapel Hill, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Zivkovic S, Maric G, Cvetinovic N, Lepojevic-Stefanovic D, Bozic Cvijan B. Anti-Inflammatory Effects of Lipid-Lowering Drugs and Supplements-A Narrative Review. Nutrients 2023; 15:nu15061517. [PMID: 36986246 PMCID: PMC10053759 DOI: 10.3390/nu15061517] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Cardiovascular diseases (CVD) are the leading cause of death worldwide. Since the establishment of the "lipid hypothesis", according to which, cholesterol level is directly correlated to the risk of CVD, many different lipid-lowering agents have been introduced in clinical practice. A majority of these drugs, in addition to their lipid-lowering properties, may also exhibit some anti-inflammatory and immunomodulatory activities. This hypothesis was based on the observation that a decrease in lipid levels occurs along with a decrease in inflammation. Insufficient reduction in the inflammation during treatment with lipid-lowering drugs could be one of the explanations for treatment failure and recurrent CVD events. Thus, the aim of this narrative review was to evaluate the anti-inflammatory properties of currently available lipid-lowering medications including statins, ezetimibe, bile acid sequestrants (BAS), proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors, fibrates, omega-3 fatty acids, and niacin, as well as dietary supplements and novel drugs used in modern times.
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Affiliation(s)
- Stefan Zivkovic
- Department of Cardiovascular Disease, Zvezdara University Medical Center, 11000 Belgrade, Serbia
| | - Gorica Maric
- Faculty of Medicine, Institute of Epidemiology, University of Belgrade, Dr. Subotica 8, 11000 Belgrade, Serbia
| | - Natasa Cvetinovic
- Department of Cardiovascular Disease, University Medical Center "Dr Dragisa Misovic-Dedinje", 11000 Belgrade, Serbia
| | | | - Bojana Bozic Cvijan
- Department of Pharmacology, Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
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Alannan M, Seidah NG, Merched AJ. PCSK9 in Liver Cancers at the Crossroads between Lipid Metabolism and Immunity. Cells 2022; 11:cells11244132. [PMID: 36552895 PMCID: PMC9777286 DOI: 10.3390/cells11244132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Metabolic rewiring and defective immune responses are considered to be the main driving forces sustaining cell growth and oncogenesis in many cancers. The atypical enzyme, proprotein convertase subtilisin/kexin type 9 (PCSK9), is produced by the liver in large amounts and plays a major role in lipid metabolism via the control of the low density lipoprotein receptor (LDLR) and other cell surface receptors. In this context, many clinical studies have clearly demonstrated the high efficacy of PCSK9 inhibitors in treating hyperlipidemia and cardiovascular diseases. Recent data implicated PCSK9 in the degradation of major histocompatibility complex I (MHC-I) receptors and the immune system as well as in other physiological activities. This review highlights the complex crosstalk between PCSK9, lipid metabolism and immunosuppression and underlines the latest advances in understanding the involvement of this convertase in other critical functions. We present a comprehensive assessment of the different strategies targeting PCSK9 and show how these approaches could be extended to future therapeutic options to treat cancers with a main focus on the liver.
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Affiliation(s)
- Malak Alannan
- Bordeaux Institute of Oncology (BRIC), INSERM U1312, University of Bordeaux, F-33000 Bordeaux, France
| | - Nabil G. Seidah
- Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute, IRCM, University of Montreal, Montreal, QC H2W 1R7, Canada
| | - Aksam J. Merched
- Bordeaux Institute of Oncology (BRIC), INSERM U1312, University of Bordeaux, F-33000 Bordeaux, France
- Correspondence:
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Liang K, Dai JY. Progress of potential drugs targeted in lipid metabolism research. Front Pharmacol 2022; 13:1067652. [PMID: 36588702 PMCID: PMC9800514 DOI: 10.3389/fphar.2022.1067652] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Lipids are a class of complex hydrophobic molecules derived from fatty acids that not only form the structural basis of biological membranes but also regulate metabolism and maintain energy balance. The role of lipids in obesity and other metabolic diseases has recently received much attention, making lipid metabolism one of the attractive research areas. Several metabolic diseases are linked to lipid metabolism, including diabetes, obesity, and atherosclerosis. Additionally, lipid metabolism contributes to the rapid growth of cancer cells as abnormal lipid synthesis or uptake enhances the growth of cancer cells. This review introduces the potential drug targets in lipid metabolism and summarizes the important potential drug targets with recent research progress on the corresponding small molecule inhibitor drugs. The significance of this review is to provide a reference for the clinical treatment of metabolic diseases related to lipid metabolism and the treatment of tumors, hoping to deepen the understanding of lipid metabolism and health.
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Affiliation(s)
- Kai Liang
- School of Life Science, Peking University, Beijing, China,*Correspondence: Kai Liang, ; Jian-Ye Dai,
| | - Jian-Ye Dai
- School of Pharmacy, Lanzhou University, Lanzhou, China,Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou, China,*Correspondence: Kai Liang, ; Jian-Ye Dai,
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Ahamad S, Bhat SA. Recent Update on the Development of PCSK9 Inhibitors for Hypercholesterolemia Treatment. J Med Chem 2022; 65:15513-15539. [PMID: 36446632 DOI: 10.1021/acs.jmedchem.2c01290] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The proprotein convertase subtilisin/kexin-type 9 (PCSK9) binds to low-density lipoprotein receptors (LDLR), thereby trafficking them to lysosomes upon endocytosis and enhancing intracellular degradation to prevent their recycling. As a result, the levels of circulating LDL cholesterol (LDL-C) increase, which is a prominent risk factor for developing atherosclerotic cardiovascular diseases (ASCVD). Thus, PCSK9 has become a promising therapeutic target that offers a fertile testing ground for new drug modalities to regulate plasma LDL-C levels to prevent ASCVD. In this review, we have discussed the role of PCSK9 in lipid metabolism and briefly summarized the current clinical status of modalities targeting PCSK9. In particular, a detailed overview of peptide-based PCSK9 inhibitors is presented, which emphasizes their structural features and design, therapeutic effects on patients, and preclinical cardiovascular disease (CVD) models, along with PCSK9 modulation mechanisms. As a promising alternative to monoclonal antibodies (mAbs) for managing LDL-C, anti-PCSK9 peptides are emerging as a prospective next generation therapy.
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Affiliation(s)
- Shakir Ahamad
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Shahnawaz A Bhat
- Department of Zoology, Aligarh Muslim University, Aligarh 202002, India
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Alfonzo E, Das A, Arnold FH. New Additions to the Arsenal of Biocatalysts for Noncanonical Amino Acid Synthesis. CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY 2022; 38:100701. [PMID: 36561208 PMCID: PMC9770695 DOI: 10.1016/j.cogsc.2022.100701] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Noncanonical amino acids (ncAAs) merge the conformational behavior and native interactions of proteinogenic amino acids with nonnative chemical motifs and have proven invaluable in developing modern therapeutics. This blending of native and nonnative characteristics has resulted in essential drugs like nirmatrelvir, which comprises three ncAAs and is used to treat COVID-19. Enzymes are appearing prominently in recent syntheses of ncAAs, where they demonstrate impressive control over the stereocenters and functional groups found therein. Here we review recent efforts to expand the biocatalyst arsenal for synthesizing ncAAs with natural enzymes. We also discuss how new-to-nature enzymes can contribute to this effort by catalyzing reactions inspired by the vast repertoire of chemical catalysis and acting on substrates that would otherwise not be used in synthesizing ncAAs. Abiotic enzyme-catalyzed reactions exploit the selectivity afforded by a macromolecular catalyst to access molecules not available to natural enzymes and perhaps not even chemical catalysis.
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Affiliation(s)
- Edwin Alfonzo
- Division of Chemistry and Chemical Engineering, 210-41, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA
| | - Anuvab Das
- Division of Chemistry and Chemical Engineering, 210-41, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, 210-41, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA
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Feng D, Liu L, Shi Y, Du P, Xu S, Zhu Z, Xu J, Yao H. Current development of bicyclic peptides. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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