1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Ehinger FJ, Hertweck C. Biosynthesis and recruitment of reactive amino acids in nonribosomal peptide assembly lines. Curr Opin Chem Biol 2024; 81:102494. [PMID: 38936328 DOI: 10.1016/j.cbpa.2024.102494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/29/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024]
Abstract
Reactive amino acid side chains play important roles in the binding of peptides to specific targets. In addition, their reactivity enables selective peptide conjugation and functionalization for pharmaceutical purposes. Diverse reactive amino acids are incorporated into nonribosomal peptides, which serve as a source for drug candidates. Notable examples include (poly)unsaturated (enamine, alkyne, and furyl) and halogenated residues, strained carbacycles (cyclopropyl and cyclopropanol), small heterocycles (oxirane and aziridine), and reactive N-N functionalities (hydrazones, diazo compounds, and diazeniumdiolates). Their biosynthesis requires diverse biocatalysts for sophisticated reaction mechanisms. Several avenues have been identified for their incorporation into peptides, the recruitment by adenylation domains or ligases, on-line modifications, and enzymatic tailoring reactions. Combined with protein engineering approaches, this knowledge provides new opportunities in synthetic biology and bioorthogonal chemistry.
Collapse
Affiliation(s)
- Friedrich Johannes Ehinger
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany; Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany.
| |
Collapse
|
3
|
Song L, Liu H, Li M, Yang Y, Dong H, Li J, Shao J, Zhi L, Sun H, Li Z, Sui H, Zhang Y, Wu C, Yin Y. Ribosomal Incorporation of Lithocholic Acid into Peptides for the De Novo Discovery Of Peptide-Lithocholic Acid Hybrid Macrocyclic Peptides. ACS Chem Biol 2024. [PMID: 38901034 DOI: 10.1021/acschembio.4c00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Peptide-bile acid hybrids offer promising drug candidates due to enhanced pharmacological properties, such as improved protease resistance and oral bioavailability. However, it remains unknown whether bile acids can be incorporated into peptide chains by the ribosome to produce a peptide-bile acid hybrid macrocyclic peptide library for target-based de novo screening. In this study, we achieved the ribosomal incorporation of lithocholic acid (LCA)-d-tyrosine into peptide chains. This led to the construction of a peptide-LCA hybrid macrocyclic peptide library, which enabled the identification of peptides TP-2C-4L3 (targeting Trop2) and EP-2C-4L5 (targeting EphA2) with strong binding affinities. Notably, LCA was found to directly participate in binding to EphA2 and confer on the peptides improved stability and resistance to proteases. Cell staining experiments confirmed the high specificity of the peptides for targeting Trop2 and EphA2. This study highlights the benefits of LCA in peptides and paves the way for de novo discovery of stable peptide-LCA hybrid drugs.
Collapse
Affiliation(s)
- Lulu Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Hongtan Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Maolin Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yawen Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Huilei Dong
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Jinjing Li
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Jiaqi Shao
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lixu Zhi
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Sun
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, 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
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Chuanliu Wu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. 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
| |
Collapse
|
4
|
Chen Z, Li Y, Wang X, Qiu X, Wang C, Wang Z, Chen X, Wang J. A high-throughput molecular dynamics screening (HTMDS) approach to the design of novel cyclopeptide inhibitors of ATAD2B based on the non-canonical combinatorial library. J Biomol Struct Dyn 2024; 42:2809-2824. [PMID: 37194299 DOI: 10.1080/07391102.2023.2212796] [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: 03/20/2023] [Accepted: 04/19/2023] [Indexed: 05/18/2023]
Abstract
Cyclic peptides (CPs) are a promising class of drugs because of their high biological activity and specificity. However, the design of CP remains challenging due to their conformational flexibility and difficulties in designing stable binding conformation. Herein, we present a high-throughput MD screening (HTMDS) process for the iterative design of stable CP binders with a combinatorial CP library composed of canonical and non-canonical amino acids. As a proof of concept, we apply our methods to design CP inhibitors for the bromodomain (BrD) of ATAD2B. 698,800 CP candidates with a total of 25,570 ns MD simulations were performed to study the protein-ligand binding interactions. The binding free energies (ΔGbind) estimated by MM/PBSA approach for eight lead CP designs were found to be low. CP-1st.43 was the best CP candidate with an estimated ΔGbind of -28.48 kcal/mol when compared to the standard inhibitor C-38 which has been experimentally validated and shown to exhibit ΔGbind of -17.11 kcal/mol. The major contribution of binding sites for BrD of ATAD2B involved the hydrogen-bonding anchor within the Aly-binding pocket, salt bridging, and hydrogen-bonding mediated stabilization of the ZA loop and BC loop, and the complementary Van der Waals attraction. Our methods demonstrate encouraging results by yielding conformationally stable and high-potential CP binders that should have potential applicability in future CP drug development.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Zhidong Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yongxiao Li
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Xinpei Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Xiaohui Qiu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Chenglin Wang
- Shenzhen Qiyu Biotechnology Co., Ltd, Shenzhen, China
| | - Zhe Wang
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xu Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Junqing Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| |
Collapse
|
5
|
Liu L, Yang L, Cao S, Gao Z, Yang B, Zhang G, Zhu R, Wu D. CyclicPepedia: a knowledge base of natural and synthetic cyclic peptides. Brief Bioinform 2024; 25:bbae190. [PMID: 38678388 PMCID: PMC11056021 DOI: 10.1093/bib/bbae190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/28/2024] [Accepted: 04/09/2024] [Indexed: 04/30/2024] Open
Abstract
Cyclic peptides offer a range of notable advantages, including potent antibacterial properties, high binding affinity and specificity to target molecules, and minimal toxicity, making them highly promising candidates for drug development. However, a comprehensive database that consolidates both synthetically derived and naturally occurring cyclic peptides is conspicuously absent. To address this void, we introduce CyclicPepedia (https://www.biosino.org/iMAC/cyclicpepedia/), a pioneering database that encompasses 8744 known cyclic peptides. This repository, structured as a composite knowledge network, offers a wealth of information encompassing various aspects of cyclic peptides, such as cyclic peptides' sources, categorizations, structural characteristics, pharmacokinetic profiles, physicochemical properties, patented drug applications, and a collection of crucial publications. Supported by a user-friendly knowledge retrieval system and calculation tools specifically designed for cyclic peptides, CyclicPepedia will be able to facilitate advancements in cyclic peptide drug development.
Collapse
Affiliation(s)
- Lei Liu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P. R. China
| | - Liu Yang
- National Center, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, P. R. China
| | - Suqi Cao
- National Center, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, P. R. China
| | - Zhigang Gao
- Department of General Surgery, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, P. R. China
| | - Bin Yang
- Shanghai Southgene Technology Co., Ltd., Shanghai 201203, China
| | - Guoqing Zhang
- National Genomics Data Center & Bio-Med Big Data Center, Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, P. R. China
| | - Ruixin Zhu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P. R. China
| | - Dingfeng Wu
- National Center, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, P. R. China
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Kondo S, Miyake M. Simultaneous Prediction Method for Intestinal Absorption and Metabolism Using the Mini-Ussing Chamber System. Pharmaceutics 2023; 15:2732. [PMID: 38140073 PMCID: PMC10747201 DOI: 10.3390/pharmaceutics15122732] [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: 10/12/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Many evaluation tools for predicting human absorption are well-known for using cultured cell lines such as Caco-2, MDCK, and so on. Since the combinatorial chemistry and high throughput screening system, pharmacological assay, and pharmaceutical profiling assay are mainstays of drug development, PAMPA has been used to evaluate human drug absorption. In addition, cultured cell lines from iPS cells have been attracting attention because they morphologically resemble human intestinal tissues. In this review, we used human intestinal tissues to estimate human intestinal absorption and metabolism. The Ussing chamber uses human intestinal tissues to directly assay a drug candidate's permeability and determine the electrophysiological parameters such as potential differences (PD), short circuit current (Isc), and resistance (R). Thus, it is an attractive tool for elucidating human intestinal permeability and metabolism. We have presented a novel prediction method for intestinal absorption and metabolism by utilizing a mini-Ussing chamber using human intestinal tissues and animal intestinal tissues, based on the transport index (TI). The TI value was calculated by taking the change in drug concentrations on the apical side due to precipitation and the total amounts accumulated in the tissue (Tcorr) and transported to the basal side (Xcorr). The drug absorbability in rank order, as well as the fraction of dose absorbed (Fa) in humans, was predicted, and the intestinal metabolism of dogs and rats was also predicted, although it was not quantitative. However, the metabolites formation index (MFI) values, which are included in the TI values, can predict the evaluation of intestinal metabolism and absorption by using ketoconazole. Therefore, the mini-Ussing chamber, equipped with human and animal intestinal tissues, would be an ultimate method to predict intestinal absorption and metabolism simultaneously.
Collapse
Affiliation(s)
- Satoshi Kondo
- Department of Drug Metabolism and Pharmacokinetics, Nonclinical Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., 460-10 Kagasuno Kawauchi-cho, Tokushima 771-0192, Japan;
- Department of Drug Safety Research, Nonclinical Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., 460-10 Kagasuno Kawauchi-cho, Tokushima 771-0192, Japan
| | - Masateru Miyake
- Business Integrity and External Affairs, Otsuka Pharmaceutical Co., Ltd., 2-16-4 Konan, Minato-ku, Tokyo 108-8242, Japan
| |
Collapse
|
8
|
Lipka BM, Honeycutt DS, Bassett GM, Kowal TN, Adamczyk M, Cartnick ZC, Betti VM, Goldberg JM, Wang F. Ultra-rapid Electrophilic Cysteine Arylation. J Am Chem Soc 2023; 145:23427-23432. [PMID: 37857310 DOI: 10.1021/jacs.3c10334] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Rapid bond-forming reactions are crucial for efficient bioconjugation. We describe a simple and practical strategy for facilitating ultra-rapid electrophilic cysteine arylation. Using a variety of sulfone-activated pyridinium salts, this uncatalyzed reaction proceeds with exceptionally high rate constants, ranging from 9800 to 320,000 M-1·s-1, in pH 7.0 aqueous buffer at 25 °C. Such reactions allow for stoichiometric bioconjugation of micromolar cysteine within minutes or even seconds. Even though the arylation is extremely fast, the chemistry exhibits excellent selectivity, thus furnishing functionalized peptides and proteins with both high conversion and purity.
Collapse
Affiliation(s)
- Bradley M Lipka
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd, Kingston, Rhode Island 02881, United States
| | - Daniel S Honeycutt
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd, Kingston, Rhode Island 02881, United States
| | - Gregory M Bassett
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd, Kingston, Rhode Island 02881, United States
| | - Taylor N Kowal
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd, Kingston, Rhode Island 02881, United States
| | - Max Adamczyk
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd, Kingston, Rhode Island 02881, United States
| | - Zachary C Cartnick
- Department of Chemistry, Colgate University, 13 Oak Drive, Hamilton, New York 13346, United States
| | - Vincent M Betti
- Department of Chemistry, Colgate University, 13 Oak Drive, Hamilton, New York 13346, United States
| | - Jacob M Goldberg
- Department of Chemistry, Colgate University, 13 Oak Drive, Hamilton, New York 13346, United States
| | - Fang Wang
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd, Kingston, Rhode Island 02881, United States
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
11
|
Zhai S, Tan Y, Zhang C, Hipolito CJ, Song L, Zhu C, Zhang Y, Duan H, Yin Y. PepScaf: Harnessing Machine Learning with In Vitro Selection toward De Novo Macrocyclic Peptides against IL-17C/IL-17RE Interaction. J Med Chem 2023; 66:11187-11200. [PMID: 37480587 DOI: 10.1021/acs.jmedchem.3c00627] [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: 07/24/2023]
Abstract
The combination of library-based screening and artificial intelligence (AI) has been accelerating the discovery and optimization of hit ligands. However, the potential of AI to assist in de novo macrocyclic peptide ligand discovery has yet to be fully explored. In this study, an integrated AI framework called PepScaf was developed to extract the critical scaffold relative to bioactivity based on a vast dataset from an initial in vitro selection campaign against a model protein target, interleukin-17C (IL-17C). Taking the generated scaffold, a focused macrocyclic peptide library was rationally constructed to target IL-17C, yielding over 20 potent peptides that effectively inhibited IL-17C/IL-17RE interaction. Notably, the top two peptides displayed exceptional potency with IC50 values of 1.4 nM. This approach presents a viable methodology for more efficient macrocyclic peptide discovery, offering potential time and cost savings. Additionally, this is also the first report regarding the discovery of macrocyclic peptides against IL-17C/IL-17RE interaction.
Collapse
Affiliation(s)
- Silong Zhai
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yahong Tan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Chengyun Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Christopher John Hipolito
- Screening & Compound Profiling, Quantitative Biosciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Lulu Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Cheng Zhu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Hongliang Duan
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, 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
| |
Collapse
|
12
|
Melander E, Eriksson C, Wellens S, Hosseini K, Fredriksson R, Gosselet F, Culot M, Göransson U, Hammarlund-Udenaes M, Loryan I. Differential Blood-Brain Barrier Transport and Cell Uptake of Cyclic Peptides In Vivo and In Vitro. Pharmaceutics 2023; 15:pharmaceutics15051507. [PMID: 37242750 DOI: 10.3390/pharmaceutics15051507] [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: 04/06/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
The blood-brain barrier (BBB) poses major challenges to drug delivery to the CNS. SFTI-1 and kalata B1 are cyclic cell-penetrating peptides (cCPPs) with high potential to be used as scaffolds for drug delivery. We here studied their transport across the BBB and distribution within the brain to gauge the potential of these two cCPPs as scaffolds for CNS drugs. In a rat model, SFTI-1 exhibited, for a peptide, high extent of BBB transport with a partitioning of unbound SFTI-1 across the BBB, Kp,uu,brain, of 13%, while only 0.5% of kalata B1 equilibrated across the BBB. By contrast, kalata B1, but not SFTI-1, readily entered neural cells. SFTI-1, but not kalata B1, could be a potential CNS delivery scaffold for drugs directed to extracellular targets. These findings indicate that differences between the BBB transport and cellular uptake abilities of CPPs are crucial in the development of peptide scaffolds.
Collapse
Affiliation(s)
- Erik Melander
- Department of Pharmacy, Uppsala University, 75123 Uppsala, Sweden
| | - Camilla Eriksson
- Department of Pharmaceutical Biosciences, Uppsala University, 75123 Uppsala, Sweden
| | - Sara Wellens
- Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Faculté des Sciences Jean Perrin, University of Artois, UR 2465, Rue Jean Souvraz SP18, F-62300 Lens, France
| | - Kimia Hosseini
- Department of Pharmaceutical Biosciences, Uppsala University, 75123 Uppsala, Sweden
| | - Robert Fredriksson
- Department of Pharmaceutical Biosciences, Uppsala University, 75123 Uppsala, Sweden
| | - Fabien Gosselet
- Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Faculté des Sciences Jean Perrin, University of Artois, UR 2465, Rue Jean Souvraz SP18, F-62300 Lens, France
| | - Maxime Culot
- Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Faculté des Sciences Jean Perrin, University of Artois, UR 2465, Rue Jean Souvraz SP18, F-62300 Lens, France
| | - Ulf Göransson
- Department of Pharmaceutical Biosciences, Uppsala University, 75123 Uppsala, Sweden
| | | | - Irena Loryan
- Department of Pharmacy, Uppsala University, 75123 Uppsala, Sweden
| |
Collapse
|
13
|
Hickey J, Sindhikara D, Zultanski SL, Schultz DM. Beyond 20 in the 21st Century: Prospects and Challenges of Non-canonical Amino Acids in Peptide Drug Discovery. ACS Med Chem Lett 2023; 14:557-565. [PMID: 37197469 PMCID: PMC10184154 DOI: 10.1021/acsmedchemlett.3c00037] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/29/2023] [Indexed: 05/19/2023] Open
Abstract
Life is constructed primarily using a toolbox of 20 canonical amino acids-relying upon these building blocks for the assembly of proteins and peptides that regulate nearly every cellular task, including cell structure, function, and maintenance. While Nature continues to be a source of inspiration for drug discovery, medicinal chemists are not beholden to only 20 canonical amino acids and have begun to explore non-canonical amino acids (ncAAs) for the construction of designer peptides with improved drug-like properties. However, as our toolbox of ncAAs expands, drug hunters are encountering new challenges in approaching the iterative peptide design-make-test-analyze cycle with a seemingly boundless set of building blocks. This Microperspective focuses on new technologies that are accelerating ncAA interrogation in peptide drug discovery (including HELM notation, late-stage functionalization, and biocatalysis) while shedding light on areas where further investment could not only accelerate the discovery of new medicines but also improve downstream development.
Collapse
Affiliation(s)
- Jennifer
L. Hickey
- Department
of Medicinal Chemistry, Merck & Co.,
Inc., Kenilworth, New Jersey 07033, United States
| | - Dan Sindhikara
- Department
of Modeling and Informatics, Merck &
Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Susan L. Zultanski
- Department
of Process Research & Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Danielle M. Schultz
- Department
of Process Research & Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| |
Collapse
|
14
|
Liu M, Yoshisada R, Amedi A, Hopstaken AJP, Pascha MN, de Haan CAM, Geerke DP, Poole DA, Jongkees SAK. An Efficient, Site-Selective and Spontaneous Peptide Macrocyclisation During in vitro Translation. Chemistry 2023; 29:e202203923. [PMID: 36529683 DOI: 10.1002/chem.202203923] [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: 12/15/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
Macrocyclisation provides a means of stabilising the conformation of peptides, often resulting in improved stability, selectivity, affinity, and cell permeability. In this work, a new approach to peptide macrocyclisation is reported, using a cyanobenzothiazole-containing amino acid that can be incorporated into peptides by both in vitro translation and solid phase peptide synthesis, meaning it should be applicable to peptide discovery by mRNA display. This cyclisation proceeds rapidly, with minimal by-products, is selective over other amino acids including non N-terminal cysteines, and is compatible with further peptide elaboration exploiting such an additional cysteine in bicyclisation and derivatisation reactions. Molecular dynamics simulations show that the new cyclisation group is likely to influence the peptide conformation as compared to previous thioether-based approaches, through rigidity and intramolecular aromatic interactions, illustrating their complementarity.
Collapse
Affiliation(s)
- Minglong Liu
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Ryoji Yoshisada
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Avand Amedi
- Department Chemical Biology and Drug Discovery and Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, 3584 CG, the Netherlands
| | - Antonius J P Hopstaken
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Mirte N Pascha
- Section Virology Division of Infectious Diseases and Immunology Department of Biomolecular Health Sciences Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, the Netherlands
| | - Cornelis A M de Haan
- Section Virology Division of Infectious Diseases and Immunology Department of Biomolecular Health Sciences Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, the Netherlands
| | - Daan P Geerke
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - David A Poole
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Seino A K Jongkees
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands.,Department Chemical Biology and Drug Discovery and Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, 3584 CG, the Netherlands
| |
Collapse
|
15
|
Komar AA. Molecular Peptide Grafting as a Tool to Create Novel Protein Therapeutics. Molecules 2023; 28:2383. [PMID: 36903628 PMCID: PMC10005171 DOI: 10.3390/molecules28052383] [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: 02/11/2023] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
The study of peptides (synthetic or corresponding to discrete regions of proteins) has facilitated the understanding of protein structure-activity relationships. Short peptides can also be used as powerful therapeutic agents. However, the functional activity of many short peptides is usually substantially lower than that of their parental proteins. This is (as a rule) due to their diminished structural organization, stability, and solubility often leading to an enhanced propensity for aggregation. Several approaches have emerged to overcome these limitations, which are aimed at imposing structural constraints into the backbone and/or sidechains of the therapeutic peptides (such as molecular stapling, peptide backbone circularization and molecular grafting), therefore enforcing their biologically active conformation and thus improving their solubility, stability, and functional activity. This review provides a short summary of approaches aimed at enhancing the biological activity of short functional peptides with a particular focus on the peptide grafting approach, whereby a functional peptide is inserted into a scaffold molecule. Intra-backbone insertions of short therapeutic peptides into scaffold proteins have been shown to enhance their activity and render them a more stable and biologically active conformation.
Collapse
Affiliation(s)
- Anton A. Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA; ; Tel.: +1-216-687-2516
- Department of Biochemistry and Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| |
Collapse
|
16
|
Functional Peptides from One-bead One-compound High-throughput Screening Technique. Chem Res Chin Univ 2023. [DOI: 10.1007/s40242-023-2356-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
17
|
Lai S, Zhang Q, Jin L. Natural and Man-Made Cyclic Peptide-Based Antibiotics. Antibiotics (Basel) 2022; 12:antibiotics12010042. [PMID: 36671244 PMCID: PMC9855121 DOI: 10.3390/antibiotics12010042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
In recent years, an increasing number of drug-resistant bacterial strains have been identified due to the abuse of antibiotics, which seriously threatens human and animal health. Antimicrobial peptides (AMPs) have become one of the most effective weapons to solve this problem. AMPs have little tendency to induce drug resistance and have outstanding antimicrobial effects. The study of AMPs, especially cyclic peptides, has become a hot topic. Among them, macrocyclic AMPs have received extensive attention. This mini-review discusses the structures and functions of the dominant cyclic natural and synthetic AMPs and provides a little outlook on the future direction of cyclic AMPs.
Collapse
Affiliation(s)
- Shian Lai
- Small Molecule Drugs Sichuan Key Laboratory, Institute of Materia Medica, School of Pharmacy, Chengdu Medical College, Chengdu 610500, China
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe 610-0394, Japan
| | - Quan Zhang
- Small Molecule Drugs Sichuan Key Laboratory, Institute of Materia Medica, School of Pharmacy, Chengdu Medical College, Chengdu 610500, China
| | - Lin Jin
- Small Molecule Drugs Sichuan Key Laboratory, Institute of Materia Medica, School of Pharmacy, Chengdu Medical College, Chengdu 610500, China
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
- Correspondence:
| |
Collapse
|