1
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Bruce A, Adebomi V, Czabala P, Palmer J, McFadden WM, Lorson ZC, Slack RL, Bhardwaj G, Sarafianos SG, Raj M. A Tag-Free Platform for Synthesis and Screening of Cyclic Peptide Libraries. Angew Chem Int Ed Engl 2024; 63:e202320045. [PMID: 38529717 DOI: 10.1002/anie.202320045] [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: 12/26/2023] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
In the realm of high-throughput screening (HTS), macrocyclic peptide libraries traditionally necessitate decoding tags, essential for both library synthesis and identifying hit peptide sequences post-screening. Our innovation introduces a tag-free technology platform for synthesizing cyclic peptide libraries in solution and facilitates screening against biological targets to identify peptide binders through unconventional intramolecular CyClick and DeClick chemistries (CCDC) discovered through our research. This combination allows for the synthesis of diverse cyclic peptide libraries, the incorporation of various amino acids, and facile linearization and decoding of cyclic peptide binder sequences. Our sensitivity-enhancing derivatization method, utilized in tandem with nano LC-MS/MS, enables the sequencing of peptides even at exceedingly low picomolar concentrations. Employing our technology platform, we have successfully unearthed novel cyclic peptide binders against a monoclonal antibody and the first cyclic peptide binder of HIV capsid protein responsible for viral infections as validated by microscale thermal shift assays (TSA), biolayer interferometry (BLI) and functional assays.
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Affiliation(s)
- Angele Bruce
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
| | - Victor Adebomi
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States, 98195
| | - Patrick Czabala
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
| | - Jonathan Palmer
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States, 98195
| | - William M McFadden
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA, 30322, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - Zachary C Lorson
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA, 30322, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - Ryan L Slack
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA, 30322, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - Gaurav Bhardwaj
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States, 98195
| | - Stefan G Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA, 30322, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
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2
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Hampton JT, Liu WR. Diversification of Phage-Displayed Peptide Libraries with Noncanonical Amino Acid Mutagenesis and Chemical Modification. Chem Rev 2024; 124:6051-6077. [PMID: 38686960 PMCID: PMC11082904 DOI: 10.1021/acs.chemrev.4c00004] [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: 01/02/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Sitting on the interface between biologics and small molecules, peptides represent an emerging class of therapeutics. Numerous techniques have been developed in the past 30 years to take advantage of biological methods to generate and screen peptide libraries for the identification of therapeutic compounds, with phage display being one of the most accessible techniques. Although traditional phage display can generate billions of peptides simultaneously, it is limited to expression of canonical amino acids. Recently, several groups have successfully undergone efforts to apply genetic code expansion to introduce noncanonical amino acids (ncAAs) with novel reactivities and chemistries into phage-displayed peptide libraries. In addition to biological methods, several different chemical approaches have also been used to install noncanonical motifs into phage libraries. This review focuses on these recent advances that have taken advantage of both biological and chemical means for diversification of phage libraries with ncAAs.
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Affiliation(s)
- J. Trae Hampton
- Texas
A&M Drug Discovery Center and Department of Chemistry, College
of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe Ray Liu
- Texas
A&M Drug Discovery Center and Department of Chemistry, College
of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States
- Institute
of Biosciences and Technology and Department of Translational Medical
Sciences, College of Medicine, Texas A&M
University, Houston, Texas 77030, United States
- Department
of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas 77843, United States
- Department
of Cell Biology and Genetics, College of Medicine, Texas A&M University, College
Station, Texas 77843, United States
- Department
of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas 77843, United States
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3
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Chen FJ, Pinnette N, Gao J. Strategies for the Construction of Multicyclic Phage Display Libraries. Chembiochem 2024; 25:e202400072. [PMID: 38466139 DOI: 10.1002/cbic.202400072] [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: 01/27/2024] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/12/2024]
Abstract
Peptide therapeutics have gained great interest due to their multiple advantages over small molecule and antibody-based drugs. Peptide drugs are easier to synthesize, have the potential for oral bioavailability, and are large enough to target protein-protein interactions that are undruggable by small molecules. However, two major limitations have made it difficult to develop novel peptide therapeutics not derived from natural products, including the metabolic instability of peptides and the difficulty of reaching antibody-like potencies and specificities. Compared to linear and disulfide-monocyclized peptides, multicyclic peptides can provide increased conformational rigidity, enhanced metabolic stability, and higher potency in inhibiting protein-protein interactions. The identification of novel multicyclic peptide binders can be difficult, however, recent advancements in the construction of multicyclic phage libraries have greatly advanced the process of identifying novel multicyclic peptide binders for therapeutically relevant protein targets. This review will describe the current approaches used to create multicyclic peptide libraries, highlighting the novel chemistries developed and the proof-of-concept work done on validating these libraries against different protein targets.
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Affiliation(s)
- Fa-Jie Chen
- College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Nicole Pinnette
- Department of Chemistry, Boston College, Merkert Chemistry Center 2609 Beacon Street, Chestnut Hill, MA-02467, USA
| | - Jianmin Gao
- Department of Chemistry, Boston College, Merkert Chemistry Center 2609 Beacon Street, Chestnut Hill, MA-02467, USA
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4
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Chen FJ, Lin W, Chen FE. Non-symmetric stapling of native peptides. Nat Rev Chem 2024; 8:304-318. [PMID: 38575678 DOI: 10.1038/s41570-024-00591-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 04/06/2024]
Abstract
Stapling has emerged as a powerful technique in peptide chemistry. It enables precise control over peptide conformation leading to enhanced properties such as improved stability and enhanced binding affinity. Although symmetric stapling methods have been extensively explored, the field of non-symmetric stapling of native peptides has received less attention, largely as a result of the formidable challenges it poses - in particular the complexities involved in achieving the high chemo-selectivity and site-selectivity required to simultaneously modify distinct proteinogenic residues. Over the past 5 years, there have been significant breakthroughs in addressing these challenges. In this Review, we describe the latest strategies for non-symmetric stapling of native peptides, elucidating the protocols, reaction mechanisms and underlying design principles. We also discuss current challenges and opportunities this field offers for future applications, such as ligand discovery and peptide-based therapeutics.
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Affiliation(s)
- Fa-Jie Chen
- College of Chemistry, Fuzhou University, Fuzhou, P. R. China.
| | - Wanzhen Lin
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, P. R. China
| | - Fen-Er Chen
- College of Chemistry, Fuzhou University, Fuzhou, P. R. China.
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, P. R. China.
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, Fudan University, Shanghai, P. R. China.
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5
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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 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.
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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, North Carolina 27599, United States
| | - Joshua E Hochuli
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Patric W Sadecki
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - 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, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Eugene N Muratov
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alexander Tropsha
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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6
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Zhang YW, Lin NP, Guo X, Szabo-Fresnais N, Ortoleva PJ, Chou DHC. Omniligase-1-Mediated Phage-Peptide Library Modification and Insulin Engineering. ACS Chem Biol 2024; 19:506-515. [PMID: 38266161 DOI: 10.1021/acschembio.3c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Chemical and enzymatic modifications of peptide-displayed libraries have been successfully employed to expand the phage display library. However, the requirement of specific epitopes and scaffolds has limited the scope of protein engineering using phage display. In this study, we present a novel approach utilizing omniligase-1-mediated selective and specific ligation on the phage pIII protein, offering a high conversion rate and compatibility with commercially available phage libraries. We applied this method to perform high-throughput engineering of insulin analogues with randomized B chain C-terminal regions. Insulin analogues with different B chain C-terminal segments were selected and exhibited biological activity equivalent to that of human insulin. Molecular dynamics studies of insulin analogues revealed a novel interaction between the insulin B27 residue and insulin receptor L1 domain. In summary, our findings highlight the potential of omniligase-1-mediated phage display in the development and screening of disulfide-rich peptides and proteins. This approach holds promise for the creation of novel insulin analogues with enhanced therapeutic properties and exhibits potential for the development of other therapeutic compounds.
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Affiliation(s)
- Yi Wolf Zhang
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, California 94304, United States
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Nai-Pin Lin
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, California 94304, United States
| | - Xu Guo
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Nicolas Szabo-Fresnais
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Peter J Ortoleva
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Danny Hung-Chieh Chou
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, California 94304, United States
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7
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Liu Y, Lu X, Chen M, Wei Z, Peng G, Yang J, Tang C, Yu P. Advances in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. Biofactors 2024; 50:33-57. [PMID: 37646383 DOI: 10.1002/biof.2001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
Peptides and peptide aptamers have emerged as promising molecules for a wide range of biomedical applications due to their unique properties and versatile functionalities. The screening strategies for identifying peptides and peptide aptamers with desired properties are discussed, including high-throughput screening, display screening technology, and in silico design approaches. The synthesis methods for the efficient production of peptides and peptide aptamers, such as solid-phase peptide synthesis and biosynthesis technology, are described, along with their advantages and limitations. Moreover, various modification techniques are explored to enhance the stability, specificity, and pharmacokinetic properties of peptides and peptide aptamers. This includes chemical modifications, enzymatic modifications, biomodifications, genetic engineering modifications, and physical modifications. Furthermore, the review highlights the diverse biomedical applications of peptides and peptide aptamers, including targeted drug delivery, diagnostics, and therapeutic. This review provides valuable insights into the advancements in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. A comprehensive understanding of these aspects will aid researchers in the development of novel peptide-based therapeutics and diagnostic tools for various biomedical challenges.
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Affiliation(s)
- Yijie Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Xiaoling Lu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Meilun Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Zheng Wei
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Guangnan Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Jie Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Chunhua Tang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Peng Yu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
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8
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Iskandar SE, Chiou LF, Leisner TM, Shell DJ, Norris-Drouin JL, Vaziri C, Pearce KH, Bowers AA. Identification of Covalent Cyclic Peptide Inhibitors in mRNA Display. J Am Chem Soc 2023; 145:15065-15070. [PMID: 37395736 DOI: 10.1021/jacs.3c04833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Peptides have historically been underutilized for covalent inhibitor discovery, despite their unique abilities to interact with protein surfaces and interfaces. This is in part due to a lack of methods for screening and identifying covalent peptide ligands. Here, we report a method to identify covalent cyclic peptide inhibitors in mRNA display. We combine co- and post-translational library diversification strategies to create cyclic libraries with reactive dehydroalanines (Dhas), which we employ in selections against two model targets. The most potent hits exhibit low nanomolar inhibitory activities and disrupt known protein-protein interactions with their selected targets. Overall, we establish Dhas as electrophiles for covalent inhibition and showcase how separate library diversification methods can work synergistically to dispose mRNA display to novel applications like covalent inhibitor discovery.
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Affiliation(s)
- Sabrina E Iskandar
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Lilly F Chiou
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Tina M Leisner
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Devan J Shell
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Jacqueline L Norris-Drouin
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Cyrus Vaziri
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Curriculum in Toxicology, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H Pearce
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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9
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Fricke R, Swenson CV, Roe LT, Hamlish NX, Shah B, Zhang Z, Ficaretta E, Ad O, Smaga S, Gee CL, Chatterjee A, Schepartz A. Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase enzymes to include non-α-amino acids in vitro and in vivo. Nat Chem 2023:10.1038/s41557-023-01224-y. [PMID: 37264106 DOI: 10.1038/s41557-023-01224-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/28/2023] [Indexed: 06/03/2023]
Abstract
The absence of orthogonal aminoacyl-transfer RNA (tRNA) synthetases that accept non-L-α-amino acids is a primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers and biomaterials. Here we report that pyrrolysyl-tRNA synthetase (PylRS) and certain PylRS variants accept α-hydroxy, α-thio and N-formyl-L-α-amino acids, as well as α-carboxy acid monomers that are precursors to polyketide natural products. These monomers are accommodated and accepted by the translation apparatus in vitro; those with reactive nucleophiles are incorporated into proteins in vivo. High-resolution structural analysis of the complex formed between one PylRS enzyme and a m-substituted 2-benzylmalonic acid derivative revealed an active site that discriminates prochiral carboxylates and accommodates the large size and distinct electrostatics of an α-carboxy substituent. This work emphasizes the potential of PylRS-derived enzymes for acylating tRNA with monomers whose α-substituent diverges substantially from the α-amine of proteinogenic amino acids. These enzymes or derivatives thereof could synergize with natural or evolved ribosomes and/or translation factors to generate diverse sequence-defined non-protein heteropolymers.
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Affiliation(s)
- Riley Fricke
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Cameron V Swenson
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Leah Tang Roe
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Noah Xue Hamlish
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Bhavana Shah
- Process Development, Amgen, Thousand Oaks, CA, USA
| | | | - Elise Ficaretta
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Omer Ad
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Sarah Smaga
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Christine L Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Abhishek Chatterjee
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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10
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Iskandar SE, Pelton JM, Wick ET, Bolhuis DL, Baldwin AS, Emanuele MJ, Brown NG, Bowers AA. Enabling Genetic Code Expansion and Peptide Macrocyclization in mRNA Display via a Promiscuous Orthogonal Aminoacyl-tRNA Synthetase. J Am Chem Soc 2023; 145:1512-1517. [PMID: 36630539 PMCID: PMC10411329 DOI: 10.1021/jacs.2c11294] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
mRNA display is revolutionizing peptide drug discovery through its ability to quickly identify potent peptide binders of therapeutic protein targets. Methods to expand the chemical diversity of display libraries are continually needed to increase the likelihood of identifying clinically relevant peptide ligands. Orthogonal aminoacyl-tRNA synthetases (ORSs) have proven utility in cellular genetic code expansion, but are relatively underexplored for in vitro translation (IVT) and mRNA display. Herein, we demonstrate that the promiscuous ORS p-CNF-RS can incorporate noncanonical amino acids at amber codons in IVT, including the novel substrate p-cyanopyridylalanine (p-CNpyrA), to enable a pyridine-thiazoline (pyr-thn) macrocyclization in mRNA display. Pyr-thn-based selections against the deubiquitinase USP15 yielded a potent macrocyclic binder that exhibits good selectivity for USP15 and close homologues over other ubiquitin-specific proteases (USPs). Overall, this work exemplifies how promiscuous ORSs can both expand side chain diversity and provide structural novelty in mRNA display libraries through a heterocycle forming macrocyclization.
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Affiliation(s)
- Sabrina E. Iskandar
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jarrett M. Pelton
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Elizaveta T. Wick
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Derek L. Bolhuis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Albert S. Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Michael J. Emanuele
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Nicholas G. Brown
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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11
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Bowler MM, Glavatskikh M, Pecot CV, Kireev D, Bower s AA. Enzymatic Macrolactamization of mRNA Display Libraries for Inhibitor Selection. ACS Chem Biol 2023; 18:166-175. [PMID: 36490372 PMCID: PMC9868075 DOI: 10.1021/acschembio.2c00828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
mRNA display is a powerful, high-throughput technology for discovering novel, peptide ligands for protein targets. A number of methods have been used to expand the chemical diversity of mRNA display libraries beyond the 20 canonical amino acids, including genetic code reprogramming and biorthogonal chemistries. To date, however, there have been few reports using enzymes as biocompatible reagents for diversifying mRNA display libraries. Here, we report the evaluation and implementation of the common industrial enzyme, microbial transglutaminase (mTG), as a versatile biocatalyst for cyclization of mRNA display peptide libraries via lysine-to-glutamine isopeptide bonds. We establish two separate display-based assays to validate the compatibility of mTG with mRNA-linked peptide substrates. These assays indicate that mTG has a high degree of substrate tolerance and low single round bias. To demonstrate the potential benefits of mTG-mediated cyclization in ligand discovery, high diversity mTG-modified libraries were employed in two separate affinity selections: (1) one against the calcium and integrin binding protein, CIB1, and (2) the second against the immune checkpoint protein and emerging therapeutic target, B7-H3. Both selections resulted in the identification of potent, cyclic, low nanomolar binders, and subsequent structure-activity studies demonstrate the importance of the cyclization to the observed activity. Notably, cyclization in the CIB1 binder stabilizes an α-helical conformation, while the B7-H3 inhibitor employs two bridges, one mTG-derived lactam and a second disulfide to achieve its potency. Together, these results demonstrate potential benefits of enzyme-based biocatalysts in mRNA display ligand selections and establish a framework for employing mTG in mRNA display.
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Affiliation(s)
- Matthew M. Bowler
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Marta Glavatskikh
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Chad V. Pecot
- UNC Lineberger Comprehensive Cancer Center, Curriculum in Genetics and Molecular Biology and Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Albert A. Bower s
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA,Authors to whom correspondence should be addressed:
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12
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Cowell T, Han HS. Double Emulsion Flow Cytometry for Rapid Single Genome Detection. Methods Mol Biol 2023; 2689:155-167. [PMID: 37430053 DOI: 10.1007/978-1-0716-3323-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Established techniques in droplet microfluidics have utilized single emulsion (SE) drops to compartmentalize and analyze single cells achieving high-throughput, low input analysis. Building upon this foundation, double emulsion (DE) droplet microfluidics has emerged with distinct advantages in terms of stable compartmentalization, resistance to merging, and most importantly direct compatibility with flow cytometry. In this chapter, we describe a simple-to-fabricate, single-layer DE drop generation device that achieves spatial control over surface wetting with a plasma treatment step. This easy-to-operate device allows for the robust production of single-core DEs with excellent control over the monodispersity. We further explain the use of these DE drops for single-molecule and single-cell assays. Detailed protocols are described to perform single molecule detection using droplet digital PCR in DE drops and automated detection of DE drops on a fluorescence-activated cell sorter (FACS). Due to the wide availability of FACS instruments, DE methods can facilitate the broader adoption of drop-based screening. As the applications of FACS-compatible DE droplets are immensely varied and extend well beyond what can be explored here, this chapter should be seen as an introduction to DE microfluidics.
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Affiliation(s)
- Thomas Cowell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hee-Sun Han
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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13
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Iskandar S, Bowers AA. mRNA Display Reaches for the Clinic with New PCSK9 Inhibitor. ACS Med Chem Lett 2022; 13:1379-1383. [PMID: 36105330 PMCID: PMC9465826 DOI: 10.1021/acsmedchemlett.2c00319] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/16/2022] [Indexed: 11/30/2022] Open
Abstract
Merck & Co. recently reported one of the first mRNA display-derived clinical candidates in a bioavailable inhibitor of proprotein convertase subtilisin/kexin type 9 (PCSK9). Herein, we discuss the chemical and pharmacological challenges surmounted in bringing this compound to trials and the current outlook for mRNA display-based therapeutic development.
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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
| | - 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, Chapel
Hill, North Carolina 27599, United States
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14
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Ng S, Brueckner AC, Bahmanjah S, Deng Q, Johnston JM, Ge L, Duggal R, Habulihaz B, Barlock B, Ha S, Sadruddin A, Yeo C, Strickland C, Peier A, Henry B, Sherer EC, Partridge AW. Discovery and Structure-Based Design of Macrocyclic Peptides Targeting STUB1. J Med Chem 2022; 65:9789-9801. [PMID: 35853179 DOI: 10.1021/acs.jmedchem.2c00406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent evidence suggests that deletion of STUB1─a pivotal negative regulator of interferon-γ sensing─may potentially clear malignant cells. However, current studies rely primarily on genetic approaches, as pharmacological inhibitors of STUB1 are lacking. Identifying a tool compound will be a step toward validating the target in a broader therapeutic sense. Herein, screening more than a billion macrocyclic peptides resulted in STUB1 binders, which were further optimized by a structure-enabled in silico design. The strategy to replace the macrocyclic peptides' hydrophilic and solvent-exposed region with a hydrophobic scaffold improved cellular permeability while maintaining the binding conformation. Further substitution of the permeability-limiting terminal aspartic acid with a tetrazole bioisostere retained the binding to a certain extent while improving permeability, suggesting a path forward. Although not optimal for cellular study, the current lead provides a valuable template for further development into selective tool compounds for STUB1 to enable target validation.
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Affiliation(s)
- Simon Ng
- Quantitative Biosciences, MSD, 8 Biomedical Grove, Singapore 138665
| | - Alexander C Brueckner
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Soheila Bahmanjah
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Qiaolin Deng
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jennifer M Johnston
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Lan Ge
- Cell Sciences Innovation, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ruchia Duggal
- ADME Group 2, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Bahanu Habulihaz
- PPDM ADME Transporters & In Vitro Technology, Merck & Co., Inc., 126 East Lincoln Ave, Rahway, New Jersey 07065, United States
| | - Benjamin Barlock
- ADME Group 2, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Sookhee Ha
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ahmad Sadruddin
- Quantitative Biosciences, MSD, 8 Biomedical Grove, Singapore 138665
| | - Constance Yeo
- Quantitative Biosciences, MSD, 8 Biomedical Grove, Singapore 138665
| | - Corey Strickland
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Andrea Peier
- Screening & Compound Profiling, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Brian Henry
- Quantitative Biosciences, MSD, 8 Biomedical Grove, Singapore 138665
| | - Edward C Sherer
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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15
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Katsuki R, Numayama T, Tabuchi Y, Sharma J, Satake N, Sandhu A, Taki M. Solvatochromic peptidic binder obtained via extended phage display acts as a fluororeporter for fragment-based drug discovery (FBDD). Anal Bioanal Chem 2022; 414:4803-4807. [DOI: 10.1007/s00216-022-04128-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022]
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16
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Shakya B, Joyner OG, Hartman MCT. Hyperaccurate Ribosomes for Improved Genetic Code Reprogramming. ACS Synth Biol 2022; 11:2193-2201. [PMID: 35549158 PMCID: PMC10100576 DOI: 10.1021/acssynbio.2c00150] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reprogramming of the genetic code through the introduction of noncanonical amino acids (ncAAs) has enabled exciting advances in synthetic biology and peptide drug discovery. Ribosomes that function with high efficiency and fidelity are necessary for all of these efforts, but for challenging ncAAs, the competing processes of near-cognate readthrough and peptidyl-tRNA dropoff can be issues. Here we uncover the surprising extent of these competing pathways in the PURE translation system using mRNAs encoding peptides with affinity tags at the N- and C-termini. We also show that hyperaccurate or error restrictive ribosomes with mutations in ribosomal protein S12 lead to significant improvements in yield and fidelity in the context of both canonical AAs and a challenging α,α-disubstituted ncAA. Hyperaccurate ribosomes also improve yields for quadruplet codon readthrough for a tRNA containing an expanded anticodon stem-loop, although they are not able to eliminate triplet codon reading by this tRNA. The impressive improvements in fidelity and the simplicity of introducing this mutation alongside other efforts to engineer the translation apparatus make hyperaccurate ribosomes an important advance for synthetic biology.
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Affiliation(s)
- Bipasana Shakya
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23220, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23220, United States
| | - Olivia G. Joyner
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23220, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23220, United States
| | - Matthew C. T. Hartman
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23220, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23220, United States
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17
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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.
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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.
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18
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Jarosinski MA, Chen YS, Varas N, Dhayalan B, Chatterjee D, Weiss MA. New Horizons: Next-Generation Insulin Analogues: Structural Principles and Clinical Goals. J Clin Endocrinol Metab 2022; 107:909-928. [PMID: 34850005 PMCID: PMC8947325 DOI: 10.1210/clinem/dgab849] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Indexed: 11/19/2022]
Abstract
Design of "first-generation" insulin analogues over the past 3 decades has provided pharmaceutical formulations with tailored pharmacokinetic (PK) and pharmacodynamic (PD) properties. Application of a molecular tool kit-integrating protein sequence, chemical modification, and formulation-has thus led to improved prandial and basal formulations for the treatment of diabetes mellitus. Although PK/PD changes were modest in relation to prior formulations of human and animal insulins, significant clinical advantages in efficacy (mean glycemia) and safety (rates of hypoglycemia) were obtained. Continuing innovation is providing further improvements to achieve ultrarapid and ultrabasal analogue formulations in an effort to reduce glycemic variability and optimize time in range. Beyond such PK/PD metrics, next-generation insulin analogues seek to exploit therapeutic mechanisms: glucose-responsive ("smart") analogues, pathway-specific ("biased") analogues, and organ-targeted analogues. Smart insulin analogues and delivery systems promise to mitigate hypoglycemic risk, a critical barrier to glycemic control, whereas biased and organ-targeted insulin analogues may better recapitulate physiologic hormonal regulation. In each therapeutic class considerations of cost and stability will affect use and global distribution. This review highlights structural principles underlying next-generation design efforts, their respective biological rationale, and potential clinical applications.
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Affiliation(s)
- Mark A Jarosinski
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Yen-Shan Chen
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Nicolás Varas
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Balamurugan Dhayalan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Deepak Chatterjee
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Michael A Weiss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
- Correspondence: Michael A. Weiss, MD, PhD, Dept of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS 4053, Indianapolis, IN 46202-3082 USA.
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19
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Melsen PRA, Yoshisada R, Jongkees SAK. Opportunities for expanding encoded chemical diversification and improving hit enrichment in mRNA-displayed peptide libraries. Chembiochem 2022; 23:e202100685. [PMID: 35100479 PMCID: PMC9306583 DOI: 10.1002/cbic.202100685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Indexed: 11/07/2022]
Abstract
DNA‐encoded small‐molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide‐tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the ‘drug‐likeness’ of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA‐encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA‐encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA‐displayed peptide library to allow a more diversity‐oriented approach to library modification. Finally, we outline alternate approaches for enriching target‐binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA‐display based approach could be used to discover new ‘drug‐like’ modified small peptides.
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Affiliation(s)
- Paddy R A Melsen
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, NETHERLANDS
| | - Ryoji Yoshisada
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, NETHERLANDS
| | - Seino A K Jongkees
- Vrije Universiteit Amsterdam, Chemistry and Pharmaceutical Sciences, de Boelelaan 1108, 1081 HZ, Amsterdam, NETHERLANDS
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20
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Jarosinski MA, Dhayalan B, Chen YS, Chatterjee D, Varas N, Weiss MA. Structural principles of insulin formulation and analog design: A century of innovation. Mol Metab 2021; 52:101325. [PMID: 34428558 PMCID: PMC8513154 DOI: 10.1016/j.molmet.2021.101325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The discovery of insulin in 1921 and its near-immediate clinical use initiated a century of innovation. Advances extended across a broad front, from the stabilization of animal insulin formulations to the frontiers of synthetic peptide chemistry, and in turn, from the advent of recombinant DNA manufacturing to structure-based protein analog design. In each case, a creative interplay was observed between pharmaceutical applications and then-emerging principles of protein science; indeed, translational objectives contributed to a growing molecular understanding of protein structure, aggregation and misfolding. SCOPE OF REVIEW Pioneering crystallographic analyses-beginning with Hodgkin's solving of the 2-Zn insulin hexamer-elucidated general features of protein self-assembly, including zinc coordination and the allosteric transmission of conformational change. Crystallization of insulin was exploited both as a step in manufacturing and as a means of obtaining protracted action. Forty years ago, the confluence of recombinant human insulin with techniques for site-directed mutagenesis initiated the present era of insulin analogs. Variant or modified insulins were developed that exhibit improved prandial or basal pharmacokinetic (PK) properties. Encouraged by clinical trials demonstrating the long-term importance of glycemic control, regimens based on such analogs sought to resemble daily patterns of endogenous β-cell secretion more closely, ideally with reduced risk of hypoglycemia. MAJOR CONCLUSIONS Next-generation insulin analog design seeks to explore new frontiers, including glucose-responsive insulins, organ-selective analogs and biased agonists tailored to address yet-unmet clinical needs. In the coming decade, we envision ever more powerful scientific synergies at the interface of structural biology, molecular physiology and therapeutics.
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Affiliation(s)
- Mark A Jarosinski
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, 46202, IN, USA
| | - Balamurugan Dhayalan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, 46202, IN, USA
| | - Yen-Shan Chen
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, 46202, IN, USA
| | - Deepak Chatterjee
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, 46202, IN, USA
| | - Nicolás Varas
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, 46202, IN, USA
| | - Michael A Weiss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, 46202, IN, USA; Department of Chemistry, Indiana University, Bloomington, 47405, IN, USA; Weldon School of Biomedical Engineering, Purdue University, West Lafayette, 47907, IN, USA.
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21
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Wong JYK, Mukherjee R, Miao J, Bilyk O, Triana V, Miskolzie M, Henninot A, Dwyer JJ, Kharchenko S, Iampolska A, Volochnyuk DM, Lin YS, Postovit LM, Derda R. Genetically-encoded discovery of proteolytically stable bicyclic inhibitors for morphogen NODAL. Chem Sci 2021; 12:9694-9703. [PMID: 34349940 PMCID: PMC8294009 DOI: 10.1039/d1sc01916c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/25/2021] [Indexed: 12/19/2022] Open
Abstract
In this manuscript, we developed a two-fold symmetric linchpin (TSL) that converts readily available phage-displayed peptides libraries made of 20 common amino acids to genetically-encoded libraries of bicyclic peptides displayed on phage. TSL combines an aldehyde-reactive group and two thiol-reactive groups; it bridges two side chains of cysteine [C] with an N-terminal aldehyde group derived from the N-terminal serine [S], yielding a novel bicyclic topology that lacks a free N-terminus. Phage display libraries of SX1CX2X3X4X5X6X7C sequences, where X is any amino acid but Cys, were converted to a library of bicyclic TSL-[S]X1[C]X2X3X4X5X6X7[C] peptides in 45 ± 15% yield. Using this library and protein morphogen NODAL as a target, we discovered bicyclic macrocycles that specifically antagonize NODAL-induced signaling in cancer cells. At a 10 μM concentration, two discovered bicyclic peptides completely suppressed NODAL-induced phosphorylation of SMAD2 in P19 embryonic carcinoma cells. The TSL-[S]Y[C]KRAHKN[C] bicycle inhibited NODAL-induced proliferation of NODAL-TYK-nu ovarian carcinoma cells with apparent IC50 of 1 μM. The same bicycle at 10 μM concentration did not affect the growth of the control TYK-nu cells. TSL-bicycles remained stable over the course of the 72 hour-long assays in a serum-rich cell-culture medium. We further observed general stability in mouse serum and in a mixture of proteases (Pronase™) for 21 diverse bicyclic macrocycles of different ring sizes, amino acid sequences, and cross-linker geometries. TSL-constrained peptides to expand the previously reported repertoire of phage-displayed bicyclic architectures formed by cross-linking Cys side chains. We anticipate that it will aid the discovery of proteolytically stable bicyclic inhibitors for a variety of protein targets.
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Affiliation(s)
- Jeffrey Y-K Wong
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Raja Mukherjee
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Jiayuan Miao
- Department of Chemistry, Tufts University Medford MA 02155 USA
| | - Olena Bilyk
- Department of Experimental Oncology, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Vivian Triana
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Mark Miskolzie
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | | | - John J Dwyer
- Ferring Research Institute San Diego California 92121 USA
| | | | - Anna Iampolska
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
| | | | - Yu-Shan Lin
- Department of Chemistry, Tufts University Medford MA 02155 USA
| | - Lynne-Marie Postovit
- Department of Experimental Oncology, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Ratmir Derda
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
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