1
|
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.
Collapse
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
| |
Collapse
|
2
|
Pelton JM, Hochuli JE, Sadecki PW, Katoh T, Suga H, Hicks LM, Muratov EN, Tropsha A, Bowers AA. Cheminformatics-Guided Cell-Free Exploration of Peptide Natural Products. J Am Chem Soc 2024; 146:8016-8030. [PMID: 38470819 PMCID: PMC11151186 DOI: 10.1021/jacs.3c11306] [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: 03/14/2024]
Abstract
There have been significant advances in the flexibility and power of in vitro cell-free translation systems. The increasing ability to incorporate noncanonical amino acids and complement translation with recombinant enzymes has enabled cell-free production of peptide-based natural products (NPs) and NP-like molecules. We anticipate that many more such compounds and analogs might be accessed in this way. To assess the peptide NP space that is directly accessible to current cell-free technologies, we developed a peptide parsing algorithm that breaks down peptide NPs into building blocks based on ribosomal translation logic. Using the resultant data set, we broadly analyze the biophysical properties of these privileged compounds and perform a retrobiosynthetic analysis to predict which peptide NPs could be directly synthesized in augmented cell-free translation reactions. We then tested these predictions by preparing a library of highly modified peptide NPs. Two macrocyclases, PatG and PCY1, were used to effect the head-to-tail macrocyclization of candidate NPs. This retrobiosynthetic analysis identified a collection of high-priority building blocks that are enriched throughout peptide NPs, yet they had not previously been tested in cell-free translation. To expand the cell-free toolbox into this space, we established, optimized, and characterized the flexizyme-enabled ribosomal incorporation of piperazic acids. Overall, these results demonstrate the feasibility of cell-free translation for peptide NP total synthesis while expanding the limits of the technology. This work provides a novel computational tool for exploration of peptide NP chemical space, that could be expanded in the future to allow design of ribosomal biosynthetic pathways for NPs and NP-like molecules.
Collapse
Affiliation(s)
- Jarrett M. Pelton
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joshua E. Hochuli
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Patric W. Sadecki
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Leslie M. Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC, 27599, USA
| | - Eugene N. Muratov
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexander Tropsha
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC, 27599, USA
| |
Collapse
|
3
|
Ma W, Wang Y, Xue Y, Wang M, Lu C, Guo W, Liu YH, Shu D, Shao G, Xu Q, Tu D, Yan H. Molecular engineering of AIE-active boron clustoluminogens for enhanced boron neutron capture therapy. Chem Sci 2024; 15:4019-4030. [PMID: 38487248 PMCID: PMC10935674 DOI: 10.1039/d3sc06222h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/01/2024] [Indexed: 03/17/2024] Open
Abstract
The development of boron delivery agents bearing an imaging capability is crucial for boron neutron capture therapy (BNCT), yet it has been rarely explored. Here we present a new type of boron delivery agent that integrates aggregation-induced emission (AIE)-active imaging and a carborane cluster for the first time. In doing so, the new boron delivery agents have been rationally designed by incorporating a high boron content unit of a carborane cluster, an erlotinib targeting unit towards lung cancer cells, and a donor-acceptor type AIE unit bearing naphthalimide. The new boron delivery agents demonstrate both excellent AIE properties for imaging purposes and highly selective accumulation in tumors. For example, at a boron delivery agent dose of 15 mg kg-1, the boron amount reaches over 20 μg g-1, and both tumor/blood (T/B) and tumor/normal cell (T/N) ratios reach 20-30 times higher than those required by BNCT. The neutron irradiation experiments demonstrate highly efficient tumor growth suppression without any observable physical tissue damage and abnormal behavior in vivo. This study not only expands the application scopes of both AIE-active molecules and boron clusters, but also provides a new molecular engineering strategy for a deep-penetrating cancer therapeutic protocol based on BNCT.
Collapse
Affiliation(s)
- Wenli Ma
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Yanyang Wang
- Department of Nuclear Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University Nanjing 210008 China
| | - Yilin Xue
- Department of Nuclear Medicine, Nanjing First Hospital, Nanjing Medical University Nanjing 210033 China
| | - Mengmeng Wang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Changsheng Lu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Wanhua Guo
- Department of Nuclear Medicine, Nanjing Tongren Hospital, the Affiliated Hospital of Southeast University Medical School Nanjing 210033 China
| | - Yuan-Hao Liu
- Neuboron Therapy System Ltd. Xiamen 361028 China
- Nanjing University of Aeronautics and Astronautics Nanjing 210016 China
- Neuboron Medtech Ltd. Nanjing 211112 China
| | - Diyun Shu
- Neuboron Therapy System Ltd. Xiamen 361028 China
- Nanjing University of Aeronautics and Astronautics Nanjing 210016 China
- Neuboron Medtech Ltd. Nanjing 211112 China
| | - Guoqiang Shao
- Department of Nuclear Medicine, Nanjing First Hospital, Nanjing Medical University Nanjing 210033 China
| | - Qinfeng Xu
- Department of Nuclear Medicine, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine Nanjing 210029 China
| | - Deshuang Tu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Hong Yan
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| |
Collapse
|
4
|
Li C, Jin K. Chemical Strategies towards the Development of Effective Anticancer Peptides. Curr Med Chem 2024; 31:1839-1873. [PMID: 37170992 DOI: 10.2174/0929867330666230426111157] [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: 11/01/2022] [Revised: 01/28/2023] [Accepted: 02/24/2023] [Indexed: 05/13/2023]
Abstract
Cancer is increasingly recognized as one of the primary causes of death and has become a multifaceted global health issue. Modern medical science has made significant advancements in the diagnosis and therapy of cancer over the past decade. The detrimental side effects, lack of efficacy, and multidrug resistance of conventional cancer therapies have created an urgent need for novel anticancer therapeutics or treatments with low cytotoxicity and drug resistance. The pharmaceutical groups have recognized the crucial role that peptide therapeutic agents can play in addressing unsatisfied healthcare demands and how these become great supplements or even preferable alternatives to biological therapies and small molecules. Anticancer peptides, as a vibrant therapeutic strategy against various cancer cells, have demonstrated incredible anticancer potential due to high specificity and selectivity, low toxicity, and the ability to target the surface of traditional "undruggable" proteins. This review will provide the research progression of anticancer peptides, mainly focusing on the discovery and modifications along with the optimization and application of these peptides in clinical practice.
Collapse
Affiliation(s)
- Cuicui Li
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Kang Jin
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| |
Collapse
|
5
|
Fu Q, Shen S, Sun P, Gu Z, Bai Y, Wang X, Liu Z. Bioorthogonal chemistry for prodrug activation in vivo. Chem Soc Rev 2023; 52:7737-7772. [PMID: 37905601 DOI: 10.1039/d2cs00889k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Prodrugs have emerged as a major strategy for addressing clinical challenges by improving drug pharmacokinetics, reducing toxicity, and enhancing treatment efficacy. The emergence of new bioorthogonal chemistry has greatly facilitated the development of prodrug strategies, enabling their activation through chemical and physical stimuli. This "on-demand" activation using bioorthogonal chemistry has revolutionized the research and development of prodrugs. Consequently, prodrug activation has garnered significant attention and emerged as an exciting field of translational research. This review summarizes the latest advancements in prodrug activation by utilizing bioorthogonal chemistry and mainly focuses on the activation of small-molecule prodrugs and antibody-drug conjugates. In addition, this review also discusses the opportunities and challenges of translating these advancements into clinical practice.
Collapse
Affiliation(s)
- Qunfeng Fu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
- Changping Laboratory, Beijing 102206, China
| | - Siyong Shen
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Pengwei Sun
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Zhi Gu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Yifei Bai
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Xianglin Wang
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Zhibo Liu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
- Changping Laboratory, Beijing 102206, China
- Peking University-Tsinghua University Center for Life Sciences, Peking University, Beijing 100871, China
- Key Laboratory of Carcinogenesis and Translational Research of Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Peking University Cancer Hospital & Institute, Beijing 100142, China
| |
Collapse
|
6
|
Chen H, Katoh T, Suga H. Macrocyclic Peptides Closed by a Thioether-Bipyridyl Unit That Grants Cell Membrane Permeability. ACS BIO & MED CHEM AU 2023; 3:429-437. [PMID: 37876498 PMCID: PMC10591297 DOI: 10.1021/acsbiomedchemau.3c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 10/26/2023]
Abstract
Membrane permeability is an important factor that determines the virtue of peptides targeting intracellular molecules. By introducing a membrane penetration motif, some peptides exhibit better membrane permeabilities. Previous choices for such motifs have usually been polycationic sequences, but their protease vulnerabilities and modest endosome escapability remain challenging. Here, we report a strategy for macrocyclization of peptides closed by a hydrophobic bipyridyl (BPy) unit, which grants an improvement of their membrane permeability and proteolytic stability compared with the conventional polycationic peptides. We chemically prepared model macrocyclic peptides closed by a thioether-BPy unit and determined their cell membrane permeability, giving 200 nM CP50 (an indicative value of membrane permeability), which is 40-fold better than that of the ordinary thioether macrocycle consisting of the same sequence composition. To discover potent target binders consisting of the BPy unit, we reprogrammed the initiator with chloromethyl-BPy (ClMeBPy) for the peptide library synthesis with a downstream Cys residue(s) and executed RaPID (Random nonstandard Peptide Integrated Discovery) against the bromodomains of BRD4. One of the obtained sequences exhibited a single-digit nanomolar dissociation constant against BRD4 in vitro and showed approximately 2-fold and 10-fold better membrane permeability than positive controls, R9 and Tat peptides, respectively. Moreover, we observed an intracellular activity of the BPy macrocycle tagged with a proteasome target peptide motif (RRRG), resulting in modest but detectable degradation of BRD4. The present demonstration indicates that the combination of the RaPID system with an appropriate hydrophobic unit, such as BPy, would provide a potential approach for devising cell penetrating macrocycles targeting various intracellular proteins.
Collapse
Affiliation(s)
- Hongxue Chen
- 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
| |
Collapse
|
7
|
Sun F, Tan S, Cao HJ, Lu CS, Tu D, Poater J, Solà M, Yan H. Facile Construction of New Hybrid Conjugation via Boron Cage Extension. J Am Chem Soc 2023; 145:3577-3587. [PMID: 36744315 DOI: 10.1021/jacs.2c12526] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aromatic polycyclic systems have been extensively utilized as structural subunits for the preparation of various functional molecules. Currently, aromatics-based polycyclic systems are predominantly generated from the extension of two-dimensional (2D) aromatic rings. In contrast, polycyclic compounds based on the extension of three-dimensional (3D) aromatics such as boron clusters are less studied. Here, we report three types of boron cluster-cored tricyclic molecular systems, which are constructed from a 2D aromatic ring, a 3D aromatic nido-carborane, and an alkyne. These new tricyclic compounds can be facilely accessed by Pd-catalyzed B-H activation and the subsequent cascade heteroannulation of carborane and pyridine with an alkyne in an isolated yield of up to 85% under mild conditions without any additives. Computational results indicate that the newly generated ring from the fusion of the 3D carborane, the 2D pyridyl ring, and an alkyne is non-aromatic. However, such fusion not only leads to a 1H chemical shift considerably downfield shifted owing to the strong diatropic ring current of the embedded carborane but also devotes to new/improved physicochemical properties including increased thermal stability, the emergence of a new absorption band, and a largely red-shifted emission band and enhanced emission efficiency. Besides, a number of bright, color-tunable solid emitters spanning over all visible light are obtained with absolute luminescence efficiency of up to 61%, in contrast to aggregation-caused emission quenching of, e.g., Rhodamine B containing a 2D-aromatics-fused structure. This work demonstrates that the new hybrid conjugated tricyclic systems might be promising structural scaffolds for the construction of functional molecules.
Collapse
Affiliation(s)
- Fangxiang Sun
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shuaimin Tan
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hou-Ji Cao
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Chang-Sheng Lu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Deshuang Tu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jordi Poater
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, Barcelona 08028, Spain.,ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany, 69, Girona 17003, Catalonia, Spain
| | - Hong Yan
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| |
Collapse
|
8
|
Yang J, Zhu Q, Wu Y, Qu X, Liu H, Jiang B, Ge D, Song X. Utilization of macrocyclic peptides to target protein-protein interactions in cancer. Front Oncol 2022; 12:992171. [PMID: 36465350 PMCID: PMC9714258 DOI: 10.3389/fonc.2022.992171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/24/2022] [Indexed: 07/30/2023] Open
Abstract
Protein-protein interactions (PPIs) play vital roles in normal cellular processes. Dysregulated PPIs are involved in the process of various diseases, including cancer. Thus, these PPIs may serve as potential therapeutic targets in cancer treatment. However, despite rapid advances in small-molecule drugs and biologics, it is still hard to target PPIs, especially for those intracellular PPIs. Macrocyclic peptides have gained growing attention for their therapeutic properties in targeting dysregulated PPIs. Macrocyclic peptides have some unique features, such as moderate sizes, high selectivity, and high binding affinities, which make them good drug candidates. In addition, some oncology macrocyclic peptide drugs have been approved by the US Food and Drug Administration (FDA) for clinical use. Here, we reviewed the recent development of macrocyclic peptides in cancer treatment. The opportunities and challenges were also discussed to inspire new perspectives.
Collapse
Affiliation(s)
- Jiawen Yang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Qiaoliang Zhu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yifan Wu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojuan Qu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haixia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Di Ge
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaoling Song
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| |
Collapse
|
9
|
Sun F, Tan S, Cao H, Xu J, Bregadze VI, Tu D, Lu C, Yan H. Palladium‐Catalyzed Hydroboration of Alkynes with Carboranes: Facile Construction of a Library of Boron Cluster‐Based AIE‐Active Luminogens. Angew Chem Int Ed Engl 2022; 61:e202207125. [DOI: 10.1002/anie.202207125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Fangxiang Sun
- State Key Laboratory of Coordination Chemistry School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 P. R. China
| | - Shuaimin Tan
- State Key Laboratory of Coordination Chemistry School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 P. R. China
| | - Hou‐Ji Cao
- State Key Laboratory of Coordination Chemistry School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 P. R. China
| | - Jingkai Xu
- State Key Laboratory of Coordination Chemistry School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 P. R. China
| | - Vladimir I. Bregadze
- A. N. Nesmeyanov Institute of Organoelement Compounds (INEOS) Russian Academy of Sciences Moscow 119991 Russia
| | - Deshuang Tu
- State Key Laboratory of Coordination Chemistry School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 P. R. China
| | - Changsheng Lu
- State Key Laboratory of Coordination Chemistry School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 P. R. China
| | - Hong Yan
- State Key Laboratory of Coordination Chemistry School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 P. R. China
| |
Collapse
|
10
|
Wu WH, Guo J, Zhang L, Zhang WB, Gao W. Peptide/protein-based macrocycles: from biological synthesis to biomedical applications. RSC Chem Biol 2022; 3:815-829. [PMID: 35866174 PMCID: PMC9257627 DOI: 10.1039/d1cb00246e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/08/2022] [Indexed: 11/21/2022] Open
Abstract
Living organisms have evolved cyclic or multicyclic peptides and proteins with enhanced stability and high bioactivity superior to their linear counterparts for diverse purposes. Herein, we review recent progress in applying this concept to artificial peptides and proteins to exploit the functional benefits of these macrocycles. Not only have simple cyclic forms been prepared, numerous macrocycle variants, such as knots and links, have also been developed. The chemical tools and synthetic strategies are summarized for the biological synthesis of these macrocycles, demonstrating it as a powerful alternative to chemical synthesis. Its further application to therapeutic peptides/proteins has led to biomedicines with profoundly improved pharmaceutical performances. Finally, we present our perspectives on the field and its future developments.
Collapse
Affiliation(s)
- Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Jianwen Guo
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 P. R. China
| | - Longshuai Zhang
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Weiping Gao
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 P. R. China
| |
Collapse
|
11
|
Carboranes in drug discovery, chemical biology and molecular imaging. Nat Rev Chem 2022; 6:486-504. [PMID: 37117309 DOI: 10.1038/s41570-022-00400-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2022] [Indexed: 11/08/2022]
Abstract
There exists a paucity of structural innovation and limited molecular diversity associated with molecular frameworks in drug discovery and biomolecular imaging/chemical probe design. The discovery and exploitation of new molecular entities for medical and biological applications will necessarily involve voyaging into previously unexplored regions of chemical space. Boron clusters, notably the carboranes, offer an alternative to conventional (poly)cyclic organic frameworks that may address some of the limitations associated with the use of novel molecular frameworks in chemical biology or medicine. The high thermal stability, unique 3D structure and aromaticity, kinetic inertness to metabolism and ability to engage in unusual types of intermolecular interactions, such as dihydrogen bonds, with biological receptors make carboranes exquisite frameworks in the design of probes for chemical biology, novel drug candidates and biomolecular imaging agents. This Review highlights the key developments of carborane derivatives made over the last decade as new design tools in medicinal chemistry and chemical biology, showcasing the versatility of this unique family of boron compounds.
Collapse
|
12
|
Sun F, Tan S, Cao HJ, Xu J, Bregadze V, Tu D, Lu C, Yan H. Palladium‐Catalyzed Hydroboration of Alkynes with Carboranes: Facile Construction of a Library of Boron Cluster‐Based AIE‐Active Luminogens. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Fangxiang Sun
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Shuaimin Tan
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Hou-Ji Cao
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Jingkai Xu
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Vladimir Bregadze
- Russian Academy of Science A. N. Nesmeyanov Institute of Organoelement Compounds (INEOS) RUSSIAN FEDERATION
| | - Deshuang Tu
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Changsheng Lu
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Hong Yan
- Nanjing University School of Chemistry and Chemical Engineering 22 Hankou Rd. 210093 Nanjing CHINA
| |
Collapse
|
13
|
Gazvoda M, Dhanjee HH, Rodriguez J, Brown JS, Farquhar CE, Truex NL, Loas A, Buchwald SL, Pentelute BL. Palladium-Mediated Incorporation of Carboranes into Small Molecules, Peptides, and Proteins. J Am Chem Soc 2022; 144:7852-7860. [PMID: 35438502 PMCID: PMC9881053 DOI: 10.1021/jacs.2c01932] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Carboranes represent a class of compounds with increasing therapeutic potential. However, few general approaches to readily embed carboranes into small molecules, peptides, and proteins are available. We report a strategy based on palladium-mediated C-X (X = C, S, and N) bond formation for the installation of carborane-containing moieties onto small molecules and peptides. We demonstrate the ability of Pd-based reagents with appropriate ligands to overcome the high hydrophobicity of the carborane group and enable chemoselective conjugation of cysteine residues at room temperature in aqueous buffer. Accordingly, carboranes can be efficiently installed on proteins by employing a combination of a bis-sulfonated biarylphosphine-ligated Pd reagent in an aqueous histidine buffer. This method is successfully employed on nanobodies, a fully synthetic affibody, and the antibody therapeutics trastuzumab and cetuximab. The conjugates of the affibody ZHER2 and the trastuzumab antibody retained binding to their target antigens. Conjugated proteins maintain their activity in cell-based functional assays in HER2-positive BT-474 cell lines. This approach enables the rapid incorporation of carborane moieties into small molecules, peptides, and proteins for further exploration in boron neutron capture therapy, which requires the targeted delivery of boron-dense groups.
Collapse
Affiliation(s)
| | | | - Jacob Rodriguez
- Department of Chemistry, Massachusetts, Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Joseph S. Brown
- Department of Chemistry, Massachusetts, Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Charlotte E. Farquhar
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicholas L. Truex
- Department of Chemistry, Massachusetts, Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Andrei Loas
- Department of Chemistry, Massachusetts, Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stephen L. Buchwald
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bradley L. Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States,Center for Environmental Health Sciences, Massachusetts, Institute of Technology, Cambridge, Massachusetts 02139, United States,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
14
|
Coronado JN, Ngo P, Anslyn EV, Ellington AD. Chemical insights into flexizyme-mediated tRNA acylation. Cell Chem Biol 2022; 29:1071-1112. [PMID: 35413283 DOI: 10.1016/j.chembiol.2022.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/12/2022] [Accepted: 03/23/2022] [Indexed: 11/03/2022]
Abstract
A critical step in repurposing the cellular translation machinery for the synthesis of polymeric products is the acylation of transfer RNA (tRNA) with unnatural monomers. Toward this goal, flexizymes, ribozymes capable of aminoacylation, have emerged as a uniquely adept tool for charging tRNA with ever increasingly diverse substrates. In this review, we present a library of monomer substrates that have been tested for tRNA acylation with the flexizyme system. From this mile-high view, we provide insights for understanding the chemical factors that influence flexizyme-mediated tRNA acylation. We conclude that flexizymes are primitive esterification catalysts that display a modest binding affinity to the monomer's aromatic recognition element. Together, these robust, yet flexible, flexizyme systems provide researchers with unprecedented access for preparing unnatural acyl-tRNA and the opportunity to repurpose the translation machinery for the synthesis of novel biologically derived structures beyond native proteins and peptides.
Collapse
Affiliation(s)
- Jaime N Coronado
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Phuoc Ngo
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
15
|
Chen Y, Du F, Tang L, Xu J, Zhao Y, Wu X, Li M, Shen J, Wen Q, Cho CH, Xiao Z. Carboranes as unique pharmacophores in antitumor medicinal chemistry. Mol Ther Oncolytics 2022; 24:400-416. [PMID: 35141397 PMCID: PMC8807988 DOI: 10.1016/j.omto.2022.01.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Carborane is a carbon-boron molecular cluster that can be viewed as a 3D analog of benzene. It features special physical and chemical properties, and thus has the potential to serve as a new type of pharmacophore for drug design and discovery. Based on the relative positions of two cage carbons, icosahedral closo-carboranes can be classified into three isomers, ortho-carborane (o-carborane, 1,2-C2B10H12), meta-carborane (m-carborane, 1,7-C2B10H12), and para-carborane (p-carborane, 1,12-C2B10H12), and all of them can be deboronated to generate their nido- forms. Cage compound carborane and its derivatives have been demonstrated as useful chemical entities in antitumor medicinal chemistry. The applications of carboranes and their derivatives in the field of antitumor research mainly include boron neutron capture therapy (BNCT), as BNCT/photodynamic therapy dual sensitizers, and as anticancer ligands. This review summarizes the research progress on carboranes achieved up to October 2021, with particular emphasis on signaling transduction pathways, chemical structures, and mechanistic considerations of using carboranes.
Collapse
Affiliation(s)
- Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Liyao Tang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Jinrun Xu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Qinglian Wen
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Luzhou Key Laboratory of Cell Therapy & Cell Drugs, Southwest Medical University, Luzhou 646000, China
| | - Chi Hin Cho
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Luzhou Key Laboratory of Cell Therapy & Cell Drugs, Southwest Medical University, Luzhou 646000, China
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Zhangang Xiao
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Luzhou Key Laboratory of Cell Therapy & Cell Drugs, Southwest Medical University, Luzhou 646000, China
| |
Collapse
|
16
|
Messner K, Vuong B, Tranmer GK. The Boron Advantage: The Evolution and Diversification of Boron’s Applications in Medicinal Chemistry. Pharmaceuticals (Basel) 2022; 15:ph15030264. [PMID: 35337063 PMCID: PMC8948683 DOI: 10.3390/ph15030264] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/10/2022] [Accepted: 02/13/2022] [Indexed: 12/13/2022] Open
Abstract
In this review, the history of boron’s early use in drugs, and the history of the use of boron functional groups in medicinal chemistry applications are discussed. This includes diazaborines, boronic acids, benzoxaboroles, boron clusters, and carboranes. Furthermore, critical developments from these functional groups are highlighted along with recent developments, which exemplify potential prospects. Lastly, the application of boron in the form of a prodrug, softdrug, and as a nanocarrier are discussed to showcase boron’s emergence into new and exciting fields. Overall, we emphasize the evolution of organoboron therapeutic agents as privileged structures in medicinal chemistry and outline the impact that boron has had on drug discovery and development.
Collapse
Affiliation(s)
- Katia Messner
- Rady Faculty of Health Science, College of Pharmacy, University of Manitoba, Winnipeg, MB R3E 0T5, Canada; (K.M.); (B.V.)
| | - Billy Vuong
- Rady Faculty of Health Science, College of Pharmacy, University of Manitoba, Winnipeg, MB R3E 0T5, Canada; (K.M.); (B.V.)
| | - Geoffrey K. Tranmer
- Rady Faculty of Health Science, College of Pharmacy, University of Manitoba, Winnipeg, MB R3E 0T5, Canada; (K.M.); (B.V.)
- Department of Chemistry, Faculty of Science, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
- Correspondence:
| |
Collapse
|
17
|
Recent trends and tactics in facile functionalization of neutral icosahedral carboranes (C2B10H12) and nido-carborane (7,8-C2B9H12−). ADVANCES IN CATALYSIS 2022. [DOI: 10.1016/bs.acat.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
18
|
Cao HJ, Wei X, Sun F, Zhang X, Lu C, Yan H. Metal-catalyzed B-H acylmethylation of pyridylcarboranes: access to carborane-fused indoliziniums and quinoliziniums. Chem Sci 2021; 12:15563-15571. [PMID: 35003585 PMCID: PMC8654026 DOI: 10.1039/d1sc05296a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 11/19/2021] [Indexed: 12/11/2022] Open
Abstract
Metal-catalyzed mono-acylmethylation of pyridylcarboranes has been realized using α-carbonyl sulfoxonium ylides as a coupling partner. The reaction features high efficiency, excellent site-selectivity and good functional group tolerance. In the presence of pyridyl and enolizable acylmethyl groups, a post-coordination mode has been proposed and validated by in situ high resolution mass spectroscopy (HRMS) to rationalize the unique mono-substitution. Post-functionalization at the newly incorporated alkyl site provides additional utility of this method, including the construction of carborane-fused indoliziniums and quinoliziniums. We believe that these mono-alkylated carboranes, together with their post-functionalized derivatives, may find applications in luminescent materials and drug discovery in the near future.
Collapse
Affiliation(s)
- Hou-Ji Cao
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Xing Wei
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Fangxiang Sun
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Xiaolei Zhang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Changsheng Lu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Hong Yan
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| |
Collapse
|
19
|
Goto Y, Suga H. The RaPID Platform for the Discovery of Pseudo-Natural Macrocyclic Peptides. Acc Chem Res 2021; 54:3604-3617. [PMID: 34505781 DOI: 10.1021/acs.accounts.1c00391] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although macrocyclic peptides bearing exotic building blocks have proven their utility as pharmaceuticals, the sources of macrocyclic peptide drugs have been largely limited to mimetics of native peptides or natural product peptides. However, the recent emergence of technologies for discovering de novo bioactive peptides has led to their reconceptualization as a promising therapeutic modality. For the construction and screening of libraries of such macrocyclic peptides, our group has devised a platform to conduct affinity-based selection of massive libraries (>1012 unique sequences) of in vitro expressed macrocyclic peptides, which is referred to as the random nonstandard peptides integrated discovery (RaPID) system. The RaPID system integrates genetic code reprogramming using the FIT (flexible in vitro translation) system, which is largely facilitated by flexizymes (flexible tRNA-aminoacylating ribozymes), with mRNA display technology.We have demonstrated that the RaPID system enables rapid discovery of various de novo pseudo-natural peptide ligands for protein targets of interest. Many examples discussed in this Account prove that thioether-closed macrocyclic peptides (teMPs) obtained by the RaPID system generally exhibit remarkably high affinity and specificity, thereby potently inhibiting or activating a specific function(s) of the target. Moreover, such teMPs are used for a wide range of biochemical applications, for example, as crystallization chaperones for intractable transmembrane proteins and for in vivo recognition of specific cell types. Furthermore, recent studies demonstrate that some teMPs exhibit pharmacological activities in animal models and that even intracellular proteins can be inhibited by teMPs, illustrating the potential of this class of peptides as drug leads.Besides the ring-closing thioether linkage in the teMPs, genetic code reprogramming by the FIT system allows for incorporation of a variety of other exotic building blocks. For instance, diverse nonproteinogenic amino acids, hydroxy acids (ester linkage), amino carbothioic acid (thioamide linkage), and abiotic foldamer units have been successfully incorporated into ribosomally synthesized peptides. Despite such enormous successes in the conventional FIT system, multiple or consecutive incorporation of highly exotic amino acids, such as d- and β-amino acids, is yet challenging, and particularly the synthesis of peptides bearing non-carbonyl backbone structures remains a demanding task. To upgrade the RaPID system to the next generation, we have engaged in intensive manipulation of the FIT system to expand the structural diversity of peptides accessible by our in vitro biosynthesis strategy. Semilogical engineering of tRNA body sequences led to a new suppressor tRNA (tRNAPro1E2) capable of effectively recruiting translation factors, particularly EF-Tu and EF-P. The use of tRNAPro1E2 in the FIT system allows for not only single but also consecutive and multiple elongation of exotic amino acids, such as d-, β-, and γ-amino acids as well as aminobenzoic acids. Moreover, the integration of the FIT system with various chemical or enzymatic posttranslational modifications enables us to expand the range of accessible backbone structures to non-carbonyl moieties prominent in natural products and peptidomimetics. In such systems, FIT-expressed peptides undergo multistep backbone conversions in a one-pot manner to yield designer peptides composed of modified backbones such as azolines, azoles, and ring-closing pyridines. Our current research endeavors focus on applying such in vitro biosynthesis systems for the discovery of bioactive de novo pseudo-natural products.
Collapse
Affiliation(s)
- Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| |
Collapse
|
20
|
Huang R, Zhao W, Xu S, Xu J, Li C, Lu C, Yan H. Photoredox B-H functionalization to selective B-N(sp 3) coupling of nido-carborane with primary and secondary amines. Chem Commun (Camb) 2021; 57:8580-8583. [PMID: 34369517 DOI: 10.1039/d1cc03326c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Access to nido-carborane site-selective B-N(sp3) coupling by photoredox catalysed B-H activation has been achieved for the first time, which leads to the synthesis of a series of nitrogen-containing nido-carboranes with moderate to good yields. This protocol is applicable to primary and secondary amines containing alkyl, or heteroaryl groups as well as sulfonamides. Furthermore, the open to air and metal-free conditions with excellent site-selectivity represent a significant improvement for B-H functionalization of nido-carboranes with organic functionalities.
Collapse
Affiliation(s)
- Ronghui Huang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China.
| | | | | | | | | | | | | |
Collapse
|
21
|
Waddington MA, Zheng X, Stauber JM, Hakim Moully E, Montgomery HR, Saleh LMA, Král P, Spokoyny AM. An Organometallic Strategy for Cysteine Borylation. J Am Chem Soc 2021; 143:8661-8668. [PMID: 34060827 DOI: 10.1021/jacs.1c02206] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Synthetic bioconjugation at cysteine (Cys) residues in peptides and proteins has emerged as a powerful tool in chemistry. Soft nucleophilicity of the sulfur in Cys renders an exquisite chemoselectivity with which various functional groups can be placed onto this residue under benign conditions. While a variety of reactions have been successful at producing Cys-based bioconjugates, the majority of these feature sulfur-carbon bonds. We report Cys-borylation, wherein a benchtop stable Pt(II)-based organometallic reagent can be used to transfer a boron-rich cluster onto a sulfur moiety in unprotected peptides forging a boron-sulfur bond. Cys-borylation proceeds at room temperature and tolerates a variety of functional groups present in complex polypeptides. Further, the bioconjugation strategy can be applied to a model protein modification of Cys-containing DARPin (designed ankyrin repeat protein). The resultant bioconjugates show no additional toxicity compared to their Cys alkyl-based congeners. Finally, we demonstrate how the developed Cys-borylation can enhance the proteolytic stability of the resultant peptide bioconjugates while maintaining the binding affinity to a protein target.
Collapse
Affiliation(s)
- Mary A Waddington
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Xin Zheng
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Julia M Stauber
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Elamar Hakim Moully
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Hayden R Montgomery
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Liban M A Saleh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States.,Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Alexander M Spokoyny
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States.,California NanoSystems Institute (CNSI), University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095, United States
| |
Collapse
|
22
|
Stefan E, Obexer R, Hofmann S, Vu Huu K, Huang Y, Morgner N, Suga H, Tampé R. De novo macrocyclic peptides dissect energy coupling of a heterodimeric ABC transporter by multimode allosteric inhibition. eLife 2021; 10:67732. [PMID: 33929325 PMCID: PMC8116058 DOI: 10.7554/elife.67732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/29/2021] [Indexed: 12/16/2022] Open
Abstract
ATP-binding cassette (ABC) transporters constitute the largest family of primary active transporters involved in a multitude of physiological processes and human diseases. Despite considerable efforts, it remains unclear how ABC transporters harness the chemical energy of ATP to drive substrate transport across cell membranes. Here, by random nonstandard peptide integrated discovery (RaPID), we leveraged combinatorial macrocyclic peptides that target a heterodimeric ABC transport complex and explore fundamental principles of the substrate translocation cycle. High-affinity peptidic macrocycles bind conformationally selective and display potent multimode inhibitory effects. The macrocycles block the transporter either before or after unidirectional substrate export along a single conformational switch induced by ATP binding. Our study reveals mechanistic principles of ATP binding, conformational switching, and energy transduction for substrate transport of ABC export systems. We highlight the potential of de novo macrocycles as effective inhibitors for membrane proteins implicated in multidrug resistance, providing avenues for the next generation of pharmaceuticals.
Collapse
Affiliation(s)
- Erich Stefan
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Richard Obexer
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Susanne Hofmann
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Khanh Vu Huu
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Yichao Huang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| |
Collapse
|
23
|
Gruzdev DA, Levit GL, Krasnov VP, Charushin VN. Carborane-containing amino acids and peptides: Synthesis, properties and applications. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213753] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
24
|
Discovery of De Novo Macrocyclic Peptides by Messenger RNA Display. Trends Pharmacol Sci 2021; 42:385-397. [PMID: 33771353 DOI: 10.1016/j.tips.2021.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
Macrocyclic peptides are a promising class of compounds that can often engage challenging therapeutic targets. Display technologies, such as mRNA display, allow for the efficient discovery of macrocyclic peptides. This article reviews the current approaches for generating macrocyclic peptide libraries using mRNA display and highlights some recent examples of ribosomal incorporation of nonproteinogenic amino acids into macrocyclic peptides.
Collapse
|
25
|
Mihara E, Watanabe S, Bashiruddin NK, Nakamura N, Matoba K, Sano Y, Maini R, Yin Y, Sakai K, Arimori T, Matsumoto K, Suga H, Takagi J. Lasso-grafting of macrocyclic peptide pharmacophores yields multi-functional proteins. Nat Commun 2021; 12:1543. [PMID: 33750839 PMCID: PMC7943567 DOI: 10.1038/s41467-021-21875-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/17/2021] [Indexed: 12/27/2022] Open
Abstract
Protein engineering has great potential for devising multifunctional recombinant proteins to serve as next-generation protein therapeutics, but it often requires drastic modifications of the parental protein scaffolds e.g., additional domains at the N/C-terminus or replacement of a domain by another. A discovery platform system, called RaPID (Random non-standard Peptides Integrated Discovery) system, has enabled rapid discovery of small de novo macrocyclic peptides that bind a target protein with high binding specificity and affinity. Capitalizing on the optimized binding properties of the RaPID-derived peptides, here we show that RaPID-derived pharmacophore sequences can be readily implanted into surface-exposed loops on recombinant proteins and maintain both the parental peptide binding function(s) and the host protein function. We refer to this protein engineering method as lasso-grafting and demonstrate that it can endow specific binding capacity toward various receptors into a diverse set of scaffolds that includes IgG, serum albumin, and even capsid proteins of adeno-associated virus, enabling us to rapidly formulate and produce bi-, tri-, and even tetra-specific binder molecules.
Collapse
Affiliation(s)
- Emiko Mihara
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Satoshi Watanabe
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Nasir K Bashiruddin
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nozomi Nakamura
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kyoko Matoba
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Yumi Sano
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Rumit Maini
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yizhen Yin
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Katsuya Sakai
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Takao Arimori
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kunio Matsumoto
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan.
| |
Collapse
|
26
|
Li CX, Ning Q, Zhao W, Cao HJ, Wang YP, Yan H, Lu CS, Liang Y. Rh-Catalyzed Decarbonylative Cross-Coupling between o-Carboranes and Twisted Amides: A Regioselective, Additive-Free, and Concise Late-Stage Carboranylation. Chemistry 2021; 27:2699-2706. [PMID: 32969106 DOI: 10.1002/chem.202003634] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/06/2020] [Indexed: 12/17/2022]
Abstract
The convenient cross-coupling of sp2 or sp3 carbons with a specific boron vertex on carborane cage represents significant synthetic values and insurmountable challenges. In this work, we report an Rh-catalyzed reaction between o-carborane and N-acyl-glutarimides to construct various Bcage -C bonds. Under the optimized condition, the removable imine directing group (DG) leads to B(3)- or B(3,6)-C couplings, while the pyridyl DG leads to B(3,5)-Ar coupling. In particular, an unexpected rearrangement of amide reagent is observed in pyridyl directed B(4)-C(sp3 ) formation. This scalable protocol has many advantages, including easy access, the use of cheap and widely available coupling agents, no requirement of an external ligand, base or oxidant, high efficiency, and a broad substrate scope. Leveraging the RhI dimer and twisted amides, this method enables straightforward access to diversely substituted and therapeutically important carborane derivatives at boron site, and provides a highly valuable vista for carborane-based drug screening.
Collapse
Affiliation(s)
- Chun-Xiao Li
- State Key Laboratory of Coordination Chemistry, Jiangsu Key, Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Qian Ning
- State Key Laboratory of Coordination Chemistry, Jiangsu Key, Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Wenxuan Zhao
- State Key Laboratory of Coordination Chemistry, Jiangsu Key, Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Hou-Ji Cao
- State Key Laboratory of Coordination Chemistry, Jiangsu Key, Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Yi-Ping Wang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key, Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Hong Yan
- State Key Laboratory of Coordination Chemistry, Jiangsu Key, Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Chang-Sheng Lu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key, Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key, Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| |
Collapse
|
27
|
Wu Y, Williams J, Calder EDD, Walport LJ. Strategies to expand peptide functionality through hybridisation with a small molecule component. RSC Chem Biol 2021; 2:151-165. [PMID: 34458778 PMCID: PMC8341444 DOI: 10.1039/d0cb00167h] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/09/2020] [Indexed: 02/04/2023] Open
Abstract
Combining different compound classes gives molecular hybrids that can offer access to novel chemical space and unique properties. Peptides provide ideal starting points for such molecular hybrids, which can be easily modified with a variety of molecular entities. The addition of small molecules can improve the potency, stability and cell permeability of therapeutically relevant peptides. Furthermore, they are often applied to create peptide-based tools in chemical biology. In this review, we discuss general methods that allow the discovery of this compound class and highlight key examples of peptide-small molecule hybrids categorised by the application and function of the small molecule entity.
Collapse
Affiliation(s)
- Yuteng Wu
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Jack Williams
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Ewen D D Calder
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Louise J Walport
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| |
Collapse
|
28
|
Lee J, Torres R, Kim DS, Byrom M, Ellington AD, Jewett MC. Ribosomal incorporation of cyclic β-amino acids into peptides using in vitro translation. Chem Commun (Camb) 2020; 56:5597-5600. [PMID: 32400780 DOI: 10.1039/d0cc02121k] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We demonstrate in vitro incorporation of cyclic β-amino acids into peptides by the ribosome through genetic code reprogramming. Further, we show that incorporation efficiency can be increased through the addition of elongation factor P.
Collapse
Affiliation(s)
- Joongoo Lee
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA.
| | - Rafael Torres
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA.
| | - Do Soon Kim
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA.
| | - Michelle Byrom
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, 78712 TX, USA
| | - Andrew D Ellington
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, 78712 TX, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA.
| |
Collapse
|
29
|
Iskandar SE, Haberman VA, Bowers AA. Expanding the Chemical Diversity of Genetically Encoded Libraries. ACS COMBINATORIAL SCIENCE 2020; 22:712-733. [PMID: 33167616 PMCID: PMC8284915 DOI: 10.1021/acscombsci.0c00179] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The power of ribosomes has increasingly been harnessed for the synthesis and selection of molecular libraries. Technologies, such as phage display, yeast display, and mRNA display, effectively couple genotype to phenotype for the molecular evolution of high affinity epitopes for many therapeutic targets. Genetic code expansion is central to the success of these technologies, allowing researchers to surpass the intrinsic capabilities of the ribosome and access new, genetically encoded materials for these selections. Here, we review techniques for the chemical expansion of genetically encoded libraries, their abilities and limits, and opportunities for further development. Importantly, we also discuss methods and metrics used to assess the efficiency of modification and library diversity with these new techniques.
Collapse
Affiliation(s)
- Sabrina E Iskandar
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Victoria A Haberman
- Division of 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, 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
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
30
|
Liu M, Thijssen V, Jongkees SAK. Suppression of Formylation Provides an Alternative Approach to Vacant Codon Creation in Bacterial In Vitro Translation. Angew Chem Int Ed Engl 2020; 59:21870-21874. [PMID: 32840944 PMCID: PMC7756408 DOI: 10.1002/anie.202003779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/04/2020] [Indexed: 11/22/2022]
Abstract
Genetic code reprogramming is a powerful approach to controlled protein modification. A remaining challenge, however, is the generation of vacant codons. We targeted the initiation machinery of E. coli, showing that restriction of the formyl donor or inhibition of the formyl transferase during in vitro translation is sufficient to prevent formylation of the acylated initiating tRNA and thereby create a vacant initiation codon that can be reprogrammed by exogenously charged tRNA. Our approach conveniently generates peptides and proteins tagged N‐terminally with non‐canonical functional groups at up to 99 % reprogramming efficiency, in combination with decoding the AUG elongation codons either with native methionine or with further reprogramming with azide‐ and alkyne‐containing cognates. We further show macrocyclization and intermolecular modifications with these click handles, thus emphasizing the applicability of our method to current challenges in peptide and protein chemistry.
Collapse
Affiliation(s)
- Minglong Liu
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Vito Thijssen
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Seino A K Jongkees
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| |
Collapse
|
31
|
Liu M, Thijssen V, Jongkees SAK. Suppression of Formylation Provides an Alternative Approach to Vacant Codon Creation in Bacterial In Vitro Translation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Minglong Liu
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3584CG Utrecht The Netherlands
| | - Vito Thijssen
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3584CG Utrecht The Netherlands
| | - Seino A. K. Jongkees
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3584CG Utrecht The Netherlands
| |
Collapse
|
32
|
McAllister TE, Coleman OD, Roper G, Kawamura A. Structural diversity in
de novo
cyclic peptide ligands from genetically encoded library technologies. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24204] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tom E. McAllister
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Oliver D. Coleman
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Grace Roper
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Chemistry Research Laboratory, Department of Chemistry University of Oxford Oxford UK
| | - Akane Kawamura
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Chemistry Research Laboratory, Department of Chemistry University of Oxford Oxford UK
| |
Collapse
|
33
|
Okuma R, Kuwahara T, Yoshikane T, Watanabe M, Dranchak P, Inglese J, Shuto S, Goto Y, Suga H. A Macrocyclic Peptide Library with a Structurally Constrained Cyclopropane-containing Building Block Leads to Thiol-independent Inhibitors of Phosphoglycerate Mutase. Chem Asian J 2020; 15:2631-2636. [PMID: 32633882 PMCID: PMC9547493 DOI: 10.1002/asia.202000700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/04/2020] [Indexed: 01/20/2023]
Abstract
Here we report the construction of an mRNA-encoded library of thioether-closed macrocyclic peptides by using an N-chloroacetyl-cyclopropane-containing exotic initiator whose structure is more constrained than the ordinary N-chloroacetyl-α-amino acid initiators. The use of such an initiator has led to a macrocycle library with significantly suppressed population of lariat-shaped species compared with the conventional libraries. We previously used a conventional library and identified a small lariat thioether-macrocycle with a tail peptide with a C-terminal free Cys whose sidechain plays an essential role in potent inhibitory activity against a parasitic model enzyme, phosphoglycerate mutase. On the other hand, the cyclopropane-containing macrocycle library has yielded a larger thioether-macrocycle lacking a free Cys residue, which exhibits potent inhibitory activity to the same enzyme with a different mode of action. This result indicates that such a cyclopropane-containing macrocycle library would allow us to access mechanistically distinct macrocycles.
Collapse
Affiliation(s)
- Rika Okuma
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Tomoki Kuwahara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Takafumi Yoshikane
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Mizuki Watanabe
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Patricia Dranchak
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - James Inglese
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| |
Collapse
|
34
|
Pethő L, Kasza G, Lajkó E, Láng O, Kőhidai L, Iván B, Mező G. Amphiphilic drug-peptide-polymer conjugates based on poly(ethylene glycol) and hyperbranched polyglycerol for epidermal growth factor receptor targeting: the effect of conjugate aggregation on in vitro activity. SOFT MATTER 2020; 16:5759-5769. [PMID: 32530018 DOI: 10.1039/d0sm00428f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Numerous peptide-drug conjugates have been developed over the years to enhance the specificity and selectivity of chemotherapeutic agents for tumour cells. In our present work, epidermal growth factor receptor targeting drug-peptide conjugates were prepared using GE11 and D4 peptides. To ensure the drug release, the cathepsin B labile GFLG spacer was incorporated between the targeting peptide and the drug molecule (daunomycin), which significantly increased the hydrophobicity and thereby decreased the water solubility of the conjugates. To overcome the solubility problem, drug-peptide-polymer conjugates with systematic structural variations were prepared, by linking poly(ethylene glycol) (PEG) or a well-defined amino-monofunctional hyperbranched polyglycerol (HbPG) directly or via a pentaglycine spacer to the targeting peptides. All the drug-peptide-polymer conjugates were water-soluble as confirmed by turbidimetric measurements. The results of the in vitro cell viability and cellular uptake measurements on HT-29 human colon adenocarcinoma cells proved that the HbPG and the PEG highly influenced the biological activity. The conjugation of the hydrophilic polymer resulted in the amphiphilic character of the conjugates, which led to self-aggregation and nanoparticle formation that decreased the cellular uptake above a specific aggregation concentration. On the other hand, the hydrodynamic volume and the different polymer chain topology of the linear PEG and the compact hyperbranched HbPG also played an important role in the biological activity. Therefore, in similar systems, the investigation of the colloidal properties is inevitable for the better understanding of the biological activity, which can reveal the structure-activity relationship of amphiphilic drug-peptide-polymer conjugates for efficient tumour targeting.
Collapse
Affiliation(s)
- Lilla Pethő
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd University, H-1117 Budapest, Pázmány Péter sétány 1/A, Hungary.
| | - György Kasza
- Polymer Chemistry Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, H-1117 Budapest, Magyar tudósok körútja 2, Hungary.
| | - Eszter Lajkó
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, H-1089 Budapest, Nagyvárad tér 4, Hungary
| | - Orsolya Láng
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, H-1089 Budapest, Nagyvárad tér 4, Hungary
| | - László Kőhidai
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, H-1089 Budapest, Nagyvárad tér 4, Hungary
| | - Béla Iván
- Polymer Chemistry Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, H-1117 Budapest, Magyar tudósok körútja 2, Hungary.
| | - Gábor Mező
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd University, H-1117 Budapest, Pázmány Péter sétány 1/A, Hungary. and Eötvös Loránd University, Faculty of Science, Institute of Chemistry, H-1117 Budapest, Pázmány Péter sétány 1/A, Hungary
| |
Collapse
|
35
|
Kavianpour P, Gemmell MCM, Kahlert JU, Rendina LM. Histone Deacetylase 2 (HDAC2) Inhibitors Containing Boron. Chembiochem 2020; 21:2786-2791. [DOI: 10.1002/cbic.202000131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/30/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Poya Kavianpour
- School of Chemistry, The University of Sydney The University of Sydney F11, Eastern Avenue Sydney NSW 2006 Australia
| | - Madeleine C. M. Gemmell
- School of Chemistry, The University of Sydney The University of Sydney F11, Eastern Avenue Sydney NSW 2006 Australia
| | - Jan U. Kahlert
- School of Chemistry, The University of Sydney The University of Sydney F11, Eastern Avenue Sydney NSW 2006 Australia
| | - Louis M. Rendina
- School of Chemistry, The University of Sydney The University of Sydney F11, Eastern Avenue Sydney NSW 2006 Australia
- The University of Sydney Nano Institute Camperdown NSW 2050 Sydney NSW 2006 Australia
| |
Collapse
|
36
|
Tsiamantas C, Rogers JM, Suga H. Initiating ribosomal peptide synthesis with exotic building blocks. Chem Commun (Camb) 2020; 56:4265-4272. [PMID: 32267262 DOI: 10.1039/d0cc01291b] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ribosomal peptide synthesis begins almost exclusively with the amino acid methionine, across all domains of life. The ubiquity of methionine initiation raises the question; to what extent could polypeptide synthesis be realized with other amino acids, proteinogenic or otherwise? This highlight describes the breadth of building blocks now known to be accepted by the ribosome initiation machinery, from subtle methionine analogues to large exotic non-proteinogenic structures. We outline the key methodological developments that have enabled these discoveries, including the exploitation of methionyl-tRNA synthetase promiscuity, synthetase and tRNA engineering, and the utilization of artificial tRNA-loading ribozymes, flexizymes. Using these methods, the number and diversity of validated initiation building blocks is rapidly expanding permitting the use of the ribosome to synthesize ever more artificial polymers in search of new functional molecules.
Collapse
Affiliation(s)
- Christos Tsiamantas
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan.
| | | | | |
Collapse
|
37
|
Ando M, Sasaki Y, Akiyoshi K. Preparation of cationic proteoliposomes using cell-free membrane protein synthesis: the chaperoning effect of cationic liposomes. RSC Adv 2020; 10:28741-28745. [PMID: 35520093 PMCID: PMC9055869 DOI: 10.1039/d0ra05825d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 07/29/2020] [Indexed: 01/09/2023] Open
Abstract
Membrane protein reconstituted cationic liposomes are constructed using cell-free membrane protein synthesis in the presence of cationic liposomes. The chaperon effect of cationic liposomal membrane assists in folding the functional conformation of membrane protein. This preparation method enables the provision of the usage of proteoliposomes for drug delivery. The preparation method of cationic proteoliposomes is established using a cell-free membrane protein synthesis in the presence of cationic liposomes.![]()
Collapse
Affiliation(s)
- Mitsuru Ando
- Department of Polymer Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto
- Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto
- Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto
- Japan
| |
Collapse
|
38
|
Chen Y, Quan Y, Xie Z. Ir-catalyzed selective dehydrogenative cross-coupling of aryls with o-carboranes via a mixed directing-group strategy. Chem Commun (Camb) 2020; 56:7001-7004. [DOI: 10.1039/d0cc02531c] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ir-catalyzed highly selective B–H/C–H cross dehydrogenative coupling between o-carboranes and (hetero)aryls has been achieved using a mixed directing-group strategy.
Collapse
Affiliation(s)
- Yu Chen
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The Chinese University of Hong Kong
- Shatin
- China
| | - Yangjian Quan
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The Chinese University of Hong Kong
- Shatin
- China
| | - Zuowei Xie
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The Chinese University of Hong Kong
- Shatin
- China
| |
Collapse
|