1
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Xiang H, Bai L, Zhang X, Dan T, Cheng P, Yang X, Ai H, Li K, Lei X. A facile strategy for the construction of a phage display cyclic peptide library for the selection of functional macrocycles. Chem Sci 2024; 15:11847-11855. [PMID: 39092106 PMCID: PMC11290325 DOI: 10.1039/d4sc03207a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/16/2024] [Indexed: 08/04/2024] Open
Abstract
Cyclic peptides represent invaluable scaffolds in biological affinity, providing diverse collections for discovering functional molecules targeting challenging biological entities and protein-protein interactions. The field increasingly focuses on developing cyclization strategies and chemically modified combinatorial libraries in conjunction with M13 phage display, to identify macrocyclic peptide inhibitors for traditionally challenging targets. Here, we introduce a cyclization strategy utilizing ortho-phthalaldehyde (OPA) for the discovery of active macrocycles characterized by asymmetric scaffolds with side-chain cyclization. Through this approach, aldehyde groups attached to free molecules sequentially attack the ε-amine of lysine and the thiol of cysteine, facilitating the rapid cyclization of genetically encoded linear precursor libraries displayed on phage particles. The construction of a 109-member library and subsequent screening successfully identified cyclic peptide binders targeting three therapeutically relevant proteins: PTP1B, NEK7, and hKeap1. The results confirm the efficacy in rapidly obtaining active ligands with micromolar potency. This work provides a fast and efficient operable high-throughput platform for screening functional peptide macrocycles, which hold promise for broad application in therapeutics, chemically biological probes, and disease diagnosis.
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Affiliation(s)
- Hua Xiang
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 China
| | - Liwen Bai
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 China
| | - Xindan Zhang
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 China
| | - Ting Dan
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 China
| | - Peng Cheng
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 China
| | - Xiaoqin Yang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou Magnetic Resonance Center, College of Chemistry and Chemical Engineering, Lanzhou University Lanzhou 730000 China
| | - Honglian Ai
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 China
| | - Kai Li
- College of Life Sciences, South-Central Minzu University Wuhan 430074 China
| | - Xinxiang Lei
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 China
- State Key Laboratory of Applied Organic Chemistry, Lanzhou Magnetic Resonance Center, College of Chemistry and Chemical Engineering, Lanzhou University Lanzhou 730000 China
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2
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Zhang YN, Wan XC, Tang Y, Chen Y, Zheng FH, Cui ZH, Zhang H, Zhou Z, Fang GM. Employing unnatural promiscuity of sortase to construct peptide macrocycle libraries for ligand discovery. Chem Sci 2024; 15:9649-9656. [PMID: 38939140 PMCID: PMC11206207 DOI: 10.1039/d4sc01992j] [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: 03/26/2024] [Accepted: 05/11/2024] [Indexed: 06/29/2024] Open
Abstract
With the increasing attention paid to macrocyclic scaffolds in peptide drug development, genetically encoded peptide macrocycle libraries have become invaluable sources for the discovery of high-affinity peptide ligands targeting disease-associated proteins. The traditional phage display technique of constructing disulfide-tethered macrocycles by cysteine oxidation has the inherent drawback of reduction instability of the disulfide bond. Chemical macrocyclization solves the problem of disulfide bond instability, but the involved highly electrophilic reagents are usually toxic to phages and may bring undesirable side reactions. Here, we report a unique Sortase-mediated Peptide Ligation and One-pot Cyclization strategy (SPLOC) to generate peptide macrocycle libraries, avoiding the undesired reactions of electrophiles with phages. The key to this platform is to mine the unnatural promiscuity of sortase on the X residue of the pentapeptide recognition sequence (LPXTG). Low reactive electrophiles are incorporated into the X-residue side chain, enabling intramolecular cyclization with the cysteine residue of the phage-displayed peptide library. Utilizing the genetically encoded peptide macrocycle library constructed by the SPLOC platform, we found a high-affinity bicyclic peptide binding TEAD4 with a nanomolar KD value (63.9 nM). Importantly, the binding affinity of the bicyclic peptide ligand is 102-fold lower than that of the acyclic analogue. To our knowledge, this is the first time to mine the unnatural promiscuity of ligases to generate peptide macrocycles, providing a new avenue for the construction of genetically encoded cyclic peptide libraries.
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Affiliation(s)
- Yan-Ni Zhang
- School of Life Sciences, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Xiao-Cui Wan
- School of Life Sciences, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Yang Tang
- Department of Medical Ultrasound, Department of Stomatology, Shanghai Tenth People's Hospital, Tongji University Cancer Center, Tongji University School of Medicine Shanghai 200072 P. R. China
| | - Ying Chen
- School of Life Sciences, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Feng-Hao Zheng
- School of Life Sciences, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Zhi-Hui Cui
- School of Life Sciences, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Hua Zhang
- School of Life Sciences, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Zhaocai Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University Shanghai 200438 P. R. China
| | - Ge-Min Fang
- School of Life Sciences, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
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3
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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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4
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Wan XC, Zhang YN, Zhang H, Chen Y, Cui ZH, Zhu WJ, Fang GM. Asparaginyl Endopeptidase-Mediated Peptide Cyclization for Phage Display. Org Lett 2024; 26:2601-2605. [PMID: 38529932 DOI: 10.1021/acs.orglett.4c00602] [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: 03/27/2024]
Abstract
We report here an enzymatic strategy for asparaginyl endopeptidase-mediated peptide cyclization. Incorporation of chloroacetyl groups into the recognition sequence of OaAEP1 enabled intramolecular cyclization with Cys residues. Combining this strategy and phage display, we identified nanomolar macrocyclic peptide ligands targeting TEAD4. One of the bicyclic peptides binds to TEAD4 with a KD value of 139 nM, 16 times lower than its linear analogue, demonstrating the utility of this platform in discovering high-affinity macrocyclic peptide ligands.
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Affiliation(s)
- Xiao-Cui Wan
- School of Life Science, Institutes of Physical Science and Information Technology, Institute of Health Sciences, Anhui University, Hefei 230601, P.R. China
| | - Yan-Ni Zhang
- School of Life Science, Institutes of Physical Science and Information Technology, Institute of Health Sciences, Anhui University, Hefei 230601, P.R. China
| | - Hua Zhang
- School of Life Science, Institutes of Physical Science and Information Technology, Institute of Health Sciences, Anhui University, Hefei 230601, P.R. China
| | - Ying Chen
- School of Life Science, Institutes of Physical Science and Information Technology, Institute of Health Sciences, Anhui University, Hefei 230601, P.R. China
| | - Zhi-Hui Cui
- School of Life Science, Institutes of Physical Science and Information Technology, Institute of Health Sciences, Anhui University, Hefei 230601, P.R. China
| | - Wen-Jing Zhu
- School of Life Science, Institutes of Physical Science and Information Technology, Institute of Health Sciences, Anhui University, Hefei 230601, P.R. China
| | - Ge-Min Fang
- School of Life Science, Institutes of Physical Science and Information Technology, Institute of Health Sciences, Anhui University, Hefei 230601, P.R. China
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5
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Koutsopetras I, Vaur V, Benazza R, Diemer H, Sornay C, Ersoy Y, Rochet L, Longo C, Hernandez-Alba O, Erb S, Detappe A, Skerra A, Wagner A, Cianferani S, Chaubet G. Site-Selective Protein Conjugation by a Multicomponent Ugi Reaction. Chemistry 2024; 30:e202303242. [PMID: 38050774 DOI: 10.1002/chem.202303242] [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: 10/03/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
The chemical bioconjugation of proteins has seen tremendous applications in the past decades, with the booming of antibody-drug conjugates and their use in oncology. While genetic engineering has permitted to produce bespoke proteins featuring key (un-)natural amino acid residues poised for site-selective modifications, the conjugation of native proteins is riddled with selectivity issues. Chemoselective strategies are plentiful and enable the precise modification of virtually any residue with a reactive side-chain; site-selective methods are less common and usually most effective on small and medium-sized proteins. In this context, we studied the application of the Ugi multicomponent reaction for the site-selective conjugation of amine and carboxylate groups on proteins, and antibodies in particular. Through an in-depth mechanistic methodology work supported by peptide mapping studies, we managed to develop a set of conditions allowing the highly selective modification of antibodies bearing N-terminal glutamate and aspartate residues. We demonstrated that this strategy did not alter their affinity toward their target antigen and produced an antibody-drug conjugate with subnanomolar potency. Excitingly, we showed that the high site selectivity of our strategy was maintained on other protein formats, especially on anticalins, for which directed mutagenesis helped to highlight the key importance of a single lysine residue.
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Affiliation(s)
- Ilias Koutsopetras
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Valentine Vaur
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Rania Benazza
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | - Charlotte Sornay
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Yağmur Ersoy
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany
| | - Léa Rochet
- Department of Chemistry, University College London, London, UK
| | - Carmen Longo
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | - Stéphane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | | | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
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6
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Li F, Liu J, Liu C, Liu Z, Peng X, Huang Y, Chen X, Sun X, Wang S, Chen W, Xiong D, Diao X, Wang S, Zhuang J, Wu C, Wu D. Cyclic peptides discriminate BCL-2 and its clinical mutants from BCL-X L by engaging a single-residue discrepancy. Nat Commun 2024; 15:1476. [PMID: 38368459 PMCID: PMC10874388 DOI: 10.1038/s41467-024-45848-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 02/06/2024] [Indexed: 02/19/2024] Open
Abstract
Overexpressed pro-survival B-cell lymphoma-2 (BCL-2) family proteins BCL-2 and BCL-XL can render tumor cells malignant. Leukemia drug venetoclax is currently the only approved selective BCL-2 inhibitor. However, its application has led to an emergence of resistant mutations, calling for drugs with an innovative mechanism of action. Herein we present cyclic peptides (CPs) with nanomolar-level binding affinities to BCL-2 or BCL-XL, and further reveal the structural and functional mechanisms of how these CPs target two proteins in a fashion that is remarkably different from traditional small-molecule inhibitors. In addition, these CPs can bind to the venetoclax-resistant clinical BCL-2 mutants with similar affinities as to the wild-type protein. Furthermore, we identify a single-residue discrepancy between BCL-2 D111 and BCL-XL A104 as a molecular "switch" that can differently engage CPs. Our study suggests that CPs may inhibit BCL-2 or BCL-XL by delicately modulating protein-protein interactions, potentially benefiting the development of next-generation therapeutics.
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Affiliation(s)
- Fengwei Li
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Junjie Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Chao Liu
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ziyan Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Xiangda Peng
- Shanghai Zelixir Biotech Company Ltd., Shanghai, 200030, China
| | - Yinyue Huang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiaoyu Chen
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiangnan Sun
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Sen Wang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Wei Chen
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, 200127, China
| | - Dan Xiong
- Xiamen Lifeint Technology Company Ltd., Xiamen, 361005, China
| | - Xiaotong Diao
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai, 200030, China
| | - Jingjing Zhuang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Marine College, Shandong University, Weihai, 264209, China
| | - Chuanliu Wu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Dalei Wu
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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7
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He J, Ghosh P, Nitsche C. Biocompatible strategies for peptide macrocyclisation. Chem Sci 2024; 15:2300-2322. [PMID: 38362412 PMCID: PMC10866349 DOI: 10.1039/d3sc05738k] [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: 10/27/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Peptides are increasingly important drug candidates, offering numerous advantages over conventional small molecules. However, they face significant challenges related to stability, cellular uptake and overall bioavailability. While individual modifications may not address all these challenges, macrocyclisation stands out as a single modification capable of enhancing affinity, selectivity, proteolytic stability and membrane permeability. The recent successes of in situ peptide modifications during screening in combination with genetically encoded peptide libraries have increased the demand for peptide macrocyclisation reactions that can occur under biocompatible conditions. In this perspective, we aim to distinguish biocompatible conditions from those well-known examples that are fully bioorthogonal. We introduce key strategies for biocompatible peptide macrocyclisation and contextualise them within contemporary screening methods, providing an overview of available transformations.
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Affiliation(s)
- Junming He
- Research School of Chemistry, Australian National University Canberra ACT Australia
| | - Pritha Ghosh
- Research School of Chemistry, Australian National University Canberra ACT Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University Canberra ACT Australia
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8
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Mir MH, Parmar S, Singh C, Kalia D. Location-agnostic site-specific protein bioconjugation via Baylis Hillman adducts. Nat Commun 2024; 15:859. [PMID: 38286847 PMCID: PMC10825175 DOI: 10.1038/s41467-024-45124-2] [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: 07/14/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
Proteins labelled site-specifically with small molecules are valuable assets for chemical biology and drug development. The unique reactivity profile of the 1,2-aminothiol moiety of N-terminal cysteines (N-Cys) of proteins renders it highly attractive for regioselective protein labelling. Herein, we report an ultrafast Z-selective reaction between isatin-derived Baylis Hillman adducts and 1,2-aminothiols to form a bis-heterocyclic scaffold, and employ it for stable protein bioconjugation under both in vitro and live-cell conditions. We refer to our protein bioconjugation technology as Baylis Hillman orchestrated protein aminothiol labelling (BHoPAL). Furthermore, we report a lipoic acid ligase-based technology for introducing the 1,2-aminothiol moiety at any desired site within proteins, rendering BHoPAL location-agnostic (not limited to N-Cys). By using this approach in tandem with BHoPAL, we generate dually labelled protein bioconjugates appended with different labels at two distinct specific sites on a single protein molecule. Taken together, the protein bioconjugation toolkit that we disclose herein will contribute towards the generation of both mono and multi-labelled protein-small molecule bioconjugates for applications as diverse as biophysical assays, cellular imaging, and the production of therapeutic protein-drug conjugates. In addition to protein bioconjugation, the bis-heterocyclic scaffold we report herein will find applications in synthetic and medicinal chemistry.
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Affiliation(s)
- Mudassir H Mir
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Sangeeta Parmar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Chhaya Singh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Dimpy Kalia
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India.
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9
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Li J, Liu H, Xiao S, Fan S, Cheng X, Wu C. De Novo Discovery of Cysteine Frameworks for Developing Multicyclic Peptide Libraries for Ligand Discovery. J Am Chem Soc 2023; 145:28264-28275. [PMID: 38092662 DOI: 10.1021/jacs.3c11856] [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: 12/28/2023]
Abstract
Conserved cysteine frameworks are essential components of disulfide-rich peptides (DRPs), which dominantly define the structural diversity of both naturally occurring and de novo-designed DRPs. However, there are only very limited numbers of conserved cysteine frameworks, and general methods enabling de novo discovery of cysteine frameworks with robust foldability are still not available. Here, we devised a "touchstone"-based strategy that relies on chasing oxidative foldability between two individual disulfide-rich folds on the phage surface to discover new cysteine frameworks from random sequences. Unique cysteine frameworks with a high degree of compatibility with phage display systems and broad sequence tolerance were successfully identified, which were subsequently exploited for the development of multicyclic DRP libraries, enabling the rapid discovery of new peptide ligands with low-nanomolar and picomolar binding affinity. This study provides an unprecedented method for exploring and exploiting the sequence and structure space of DRPs that is not readily accessible by existing strategies, holding the potential to revolutionize the study of DRPs and significantly advance the design and discovery of multicyclic peptide ligands and drugs.
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Affiliation(s)
- Jinjing Li
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Hongtan Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Shuling Xiao
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Shihui Fan
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Xueting Cheng
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Chuanliu Wu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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10
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Dengler S, Howard RT, Morozov V, Tsiamantas C, Huang WE, Liu Z, Dobrzanski C, Pophristic V, Brameyer S, Douat C, Suga H, Huc I. Display Selection of a Hybrid Foldamer-Peptide Macrocycle. Angew Chem Int Ed Engl 2023; 62:e202308408. [PMID: 37707879 DOI: 10.1002/anie.202308408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/15/2023]
Abstract
Expanding the chemical diversity of peptide macrocycle libraries for display selection is desirable to improve their potential to bind biomolecular targets. We now have implemented a considerable expansion through a large aromatic helical foldamer inclusion. A foldamer was first identified that undergoes flexizyme-mediated tRNA acylation and that is capable of initiating ribosomal translation with yields sufficiently high to perform an mRNA display selection of macrocyclic foldamer-peptide hybrids. A hybrid macrocyclic nanomolar binder to the C-lobe of the E6AP HECT domain was selected that showed a highly converged peptide sequence. A crystal structure and molecular dynamics simulations revealed that both the peptide and foldamer are helical in an intriguing reciprocal stapling fashion. The strong residue convergence could be rationalized based on their involvement in specific interactions with the target protein. The foldamer stabilizes the peptide helix through stapling and through contacts with key residues. These results altogether represent a significant extension of the chemical space amenable to display selection and highlight possible benefits of inserting an aromatic foldamer into a peptide macrocycle for the purpose of protein recognition.
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Affiliation(s)
- Sebastian Dengler
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Ryan T Howard
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Vasily Morozov
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Christos Tsiamantas
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, 113-0033, Tokyo, Japan
| | - Wei-En Huang
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, 113-0033, Tokyo, Japan
| | - Zhiwei Liu
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Road, 08028, Glassboro, New Jersey, USA
| | - Christopher Dobrzanski
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Road, 08028, Glassboro, New Jersey, USA
| | - Vojislava Pophristic
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Road, 08028, Glassboro, New Jersey, USA
| | - Sophie Brameyer
- Biozentrum, Microbiology, Ludwig-Maximilians-Universität, Großhaderner Str. 2-4, 82152, Martinsried, Germany
| | - Céline Douat
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Hiroaki Suga
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, 113-0033, Tokyo, Japan
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
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11
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Chen B, Liu C, Cong W, Gao F, Zou Y, Su L, Liu L, Hillisch A, Lehmann L, Bierer D, Li X, Hu HG. Cyclobutane-bearing restricted anchoring residues enabled geometry-specific hydrocarbon peptide stapling. Chem Sci 2023; 14:11499-11506. [PMID: 37886087 PMCID: PMC10599482 DOI: 10.1039/d3sc04279k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Stapled peptides are regarded as the promising next-generation therapeutics because of their improved secondary structure, membrane permeability and metabolic stability as compared with the prototype linear peptides. Usually, stapled peptides are obtained by a hydrocarbon stapling technique, anchoring from paired olefin-terminated unnatural amino acids and the consequent ring-closing metathesis (RCM). To investigate the adaptability of the rigid cyclobutane structure in RCM and expand the chemical diversity of hydrocarbon peptide stapling, we herein described the rational design and efficient synthesis of cyclobutane-based conformationally constrained amino acids, termed (E)-1-amino-3-(but-3-en-1-yl)cyclobutane-1-carboxylic acid (E7) and (Z)-1-amino-3-(but-3-en-1-yl)cyclobutane-1-carboxylic acid (Z7). All four combinations including E7-E7, E7-Z7, Z7-Z7 and Z7-E7 were proven to be applicable in RCM-mediated peptide stapling to afford the corresponding geometry-specific stapled peptides. With the aid of the combined quantum and molecular mechanics, the E7-E7 combination was proven to be optimal in both the RCM reaction and helical stabilization. With the spike protein of SARS-CoV-2 as the target, a series of cyclobutane-bearing stapled peptides were obtained. Among them, E7-E7 geometry-specific stapled peptides indeed exhibit higher α-helicity and thus stronger biological activity than canonical hydrocarbon stapled peptides. We believe that this methodology possesses great potential to expand the scope of the existing peptide stapling strategy. These cyclobutane-bearing restricted anchoring residues served as effective supplements for the existing olefin-terminated unnatural amino acids and the resultant geometry-specific hydrocarbon peptide stapling provided more potential for peptide therapeutics.
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Affiliation(s)
- Baobao Chen
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Chao Liu
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Wei Cong
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Fei Gao
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Yan Zou
- School of Pharmacy, Second Military Medical University Shanghai 200433 China
| | - Li Su
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Lei Liu
- Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Alexander Hillisch
- Bayer AG, Pharma Division, Drug Discovery Sciences Aprather Weg 18A Wuppertal 42096 Germany
- UCB BioSciences GmbH Alfred-Nobel-Straße 10 40789 Monheim am Rhein Germany
| | - Lutz Lehmann
- Bayer AG, Pharma Division, Drug Discovery Sciences Aprather Weg 18A Wuppertal 42096 Germany
| | - Donald Bierer
- Bayer AG, Pharma Division, Drug Discovery Sciences Aprather Weg 18A Wuppertal 42096 Germany
| | - Xiang Li
- School of Pharmacy, Second Military Medical University Shanghai 200433 China
| | - Hong-Gang Hu
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
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12
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Zhang P, Wang X, Wang X, Huang C, James TD, Sun X, Qian X. Chemoselective Fluorogenic Bioconjugation of Vicinal Dithiol-Containing Proteins for Live Cellular Imaging via Small Molecular Conjugate Acceptors. Anal Chem 2023; 95:11953-11959. [PMID: 37490273 DOI: 10.1021/acs.analchem.3c01518] [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: 07/26/2023]
Abstract
To develop small molecular fluorogenic tools for the chemoselective labeling of vicinal dithiol-containing proteins (VDPs) in live cells is important for studying intracellular redox homeostasis. With this research, we developed small molecule-based fluorescent probes, achieving selective labeling of VDPs through thiol-thiol substitutions on bisvinylogous thioester conjugated acceptors (IDAs). Initially, IDAs demonstrated its ability to bridge vicinal cysteine-sulfhydryls on a peptide as a mimic. Then, the peptide complex could be decoupled to recover the original peptide-SH in the presence of dithiothreitol. Furthermore, fluorometric signal amplification of the fluorescent probes occurred with high sensitivity, low limit of detection, and selectivity toward vicinal dithiols on reduced bovine serum albumin, as an example of real world VDPs. More importantly, the probes were utilized successfully for labeling of endogenous VDPs at different redox states in live cells. Thus, the bisvinylogous thioester-based receptor as a functional probe represents a new platform for uncovering the function of VDPs in live cells.
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Affiliation(s)
- Peng Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, No. 28, West Xianning Road, Xi'an 710049, People's Republic of China
| | - Xuechuan Wang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science & Technology, Xi'an 710021, People's Republic of China
| | - Xiao Wang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science & Technology, Xi'an 710021, People's Republic of China
| | - Chusen Huang
- The Education Ministry Key Laboratory of Resource Chemistry, Shanghai Normal University, No. 100 Guilin Road, Shanghai 200234, People's Republic of China
| | - Tony D James
- Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Xiaolong Sun
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, No. 28, West Xianning Road, Xi'an 710049, People's Republic of China
| | - Xuhong Qian
- State Key Laboratory of Bioreactor Engineering; Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, No. 130 Meilong Road, Shanghai 200237, People's Republic of China
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13
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Spears RJ, Chudasama V. Recent advances in N- and C-terminus cysteine protein bioconjugation. Curr Opin Chem Biol 2023; 75:102306. [PMID: 37236135 DOI: 10.1016/j.cbpa.2023.102306] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/12/2023] [Accepted: 03/20/2023] [Indexed: 05/28/2023]
Abstract
Advances in the site-specific chemical modification of proteins, also referred to as protein bioconjugation, have proved instrumental in revolutionary approaches to designing new protein-based therapeutics. Of the sites available for protein modification, cysteine residues or the termini of proteins have proved especially popular owing to their favorable properties for site-specific modification. Strategies that, therefore, specifically target cysteine at the termini offer a combination of these favorable properties of cysteine and termini bioconjugation. In this review, we discuss these strategies with a particular focus on those reported recently and provide our opinion on the future direction of the field.
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Affiliation(s)
- Richard J Spears
- Department of Chemistry, University College London, 20 Gordon Street, London, UK
| | - Vijay Chudasama
- Department of Chemistry, University College London, 20 Gordon Street, London, UK.
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14
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Proj M, Strašek N, Pajk S, Knez D, Sosič I. Tunable Heteroaromatic Nitriles for Selective Bioorthogonal Click Reaction with Cysteine. Bioconjug Chem 2023. [PMID: 37354098 PMCID: PMC10360065 DOI: 10.1021/acs.bioconjchem.3c00163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2023]
Abstract
The binucleophilic properties of 1,2-aminothiol and its rare occurrence in nature make it a useful reporter for tracking molecules in living systems. The 1,2-aminothiol moiety is present in cysteine, which is a substrate for a biocompatible click reaction with heteroaromatic nitriles. Despite the wide range of applications for this reaction, the scope of nitrile substrates has been explored only to a limited extent. In this study, we expand the chemical space of heteroaromatic nitriles for bioconjugation under physiologically relevant conditions. We systematically assembled a library of 116 2-cyanobenzimidazoles, 1-methyl-2-cyanobenzimidazoles, 2-cyanobenzothiazoles, and 2-cyanobenzoxazoles containing electron-donating and electron-withdrawing substituents at all positions of the benzene ring. The compounds were evaluated for their stability, reactivity, and selectivity toward the N-terminal cysteine of model oligopeptides. In comparison to the benchmark 6-hydroxy-2-cyanobenzothiazole or 6-amino-2-cyanobenzothiazole, we provide highly selective and moderately reactive nitriles as well as highly reactive yet less selective analogs with a variety of enabling attachment chemistries to aid future applications in bioconjugation, chemical biology, and nanomaterial science.
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Affiliation(s)
- Matic Proj
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Nika Strašek
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Stane Pajk
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Damijan Knez
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
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15
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Fischer NH, Oliveira MT, Diness F. Chemical modification of proteins - challenges and trends at the start of the 2020s. Biomater Sci 2023; 11:719-748. [PMID: 36519403 DOI: 10.1039/d2bm01237e] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribosomally expressed proteins perform multiple, versatile, and specialized tasks throughout Nature. In modern times, chemically modified proteins, including improved hormones, enzymes, and antibody-drug-conjugates have become available and have found advanced industrial and pharmaceutical applications. Chemical modification of proteins is used to introduce new functionalities, improve stability or drugability. Undertaking chemical reactions with proteins without compromising their native function is still a core challenge as proteins are large conformation dependent multifunctional molecules. Methods for functionalization ideally should be chemo-selective, site-selective, and undertaken under biocompatible conditions in aqueous buffer to prevent denaturation of the protein. Here the present challenges in the field are discussed and methods for modification of the 20 encoded amino acids as well as the N-/C-termini and protein backbone are presented. For each amino acid, common and traditional modification methods are presented first, followed by more recent ones.
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Affiliation(s)
- Niklas Henrik Fischer
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Maria Teresa Oliveira
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Frederik Diness
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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16
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Tantipanjaporn A, Wong MK. Development and Recent Advances in Lysine and N-Terminal Bioconjugation for Peptides and Proteins. Molecules 2023; 28:molecules28031083. [PMID: 36770752 PMCID: PMC9953373 DOI: 10.3390/molecules28031083] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
The demand for creation of protein diversity and regulation of protein function through native protein modification and post-translational modification has ignited the development of selective chemical modification methods for peptides and proteins. Chemical bioconjugation offers selective functionalization providing bioconjugates with desired properties and functions for diverse applications in chemical biology, medicine, and biomaterials. The amino group existing at the lysine residue and N-terminus of peptides and proteins has been extensively studied in bioconjugation because of its good nucleophilicity and high surface exposure. Herein, we review the development of chemical methods for modification of the amino groups on lysine residue and N-terminus featuring excellent selectivity, mild reaction conditions, short reaction time, high conversion, biocompatibility, and preservation of protein integrity. This review is organized based on the chemoselectivity and site-selectivity of the chemical bioconjugation reagents to the amino acid residues aiming to provide guidance for the selection of appropriate bioconjugation methods.
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17
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Sun H, Huang Y, Tsai YH. Genetically Encoded 1,2-Aminothiol for Site-Specific Modification of a Cellular Membrane Protein via TAMM Condensation. Methods Mol Biol 2023; 2676:191-199. [PMID: 37277634 DOI: 10.1007/978-1-0716-3251-2_14] [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: 06/07/2023]
Abstract
Site-specific modification of proteins has wide applications in probing and perturbing biological systems. A popular means to achieve such a modification on a target protein is through a reaction between bioorthogonal functionalities. Indeed, various bioorthogonal reactions have been developed, including a recently reported reaction between 1,2-aminothiol and ((alkylthio)(aryl)methylene)malononitrile (TAMM). Here, we describe the procedure that combines genetic code expansion and TAMM condensation for site-specific modification of cellular membrane proteins. The 1,2-aminothiol functionality is introduced through a genetically incorporated noncanonical amino acid to a model membrane protein on mammalian cells. Treatment of the cells with a fluorophore-TAMM conjugate leads to fluorescent labeling of the target protein. This method can be applied to modify different membrane proteins on live mammalian cells.
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Affiliation(s)
- Han Sun
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yang Huang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yu-Hsuan Tsai
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China.
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18
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Hempfling JP, Sekera ER, Sarkar A, Hummon AB, Pei D. Generation of Proteins with Free N-Terminal Cysteine by Aminopeptidases. J Am Chem Soc 2022; 144:21763-21771. [PMID: 36378906 PMCID: PMC9923720 DOI: 10.1021/jacs.2c10194] [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] [Indexed: 11/16/2022]
Abstract
Efficient, site-specific, and bio-orthogonal conjugation of chemical functionalities to proteins is of great utility in fundamental research as well as industrial processes (e.g., the production of antibody-drug conjugates and immobilization of enzymes for biocatalysis). A popular approach involves reacting a free N-terminal cysteine with a variety of electrophilic reagents. However, current methods for generating proteins with N-terminal cysteines have significant limitations. Herein we report a novel, efficient, and convenient method for producing recombinant proteins with free N-terminal cysteines by genetically fusing a Met-Pro-Cys sequence to the N-terminus of a protein of interest and subjecting the recombinant protein to the sequential action of methionine and proline aminopeptidases. The resulting protein was site-specifically labeled at the N-terminus with fluorescein and a cyclic cell-penetrating peptide through native chemical ligation and a 2-cyanobenzothiazole moiety, respectively. In addition, the optimal recognition sequence of Aeromonas sobria proline aminopeptidase was determined by screening a combinatorial peptide library and incorporated into the N-terminus of a protein of interest for most efficient N-terminal processing.
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Affiliation(s)
- Jordan P. Hempfling
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, United States
| | - Emily R. Sekera
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, United States
| | - Amar Sarkar
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, United States
| | - Amanda B. Hummon
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
| | - Dehua Pei
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, United States
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19
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Abstract
Cysteine bioconjugation serves as a powerful tool in biological research and has been widely used for chemical modification of proteins, constructing antibody-drug conjugates, and enabling cell imaging studies. Cysteine conjugation reactions with fast kinetics and exquisite selectivity have been under heavy pursuit as they would allow clean protein modification with just stoichiometric amounts of reagents, which minimizes side reactions, simplifies purification and broadens functional group tolerance. In this concept, we summarize the recent advances in fast cysteine bioconjugation, and discuss the mechanism and chemical principles that underlie the high efficiencies of the newly developed cysteine reactive reagents.
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Affiliation(s)
- Fa-Jie Chen
- 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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20
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Hampton JT, Lalonde TJ, Tharp JM, Kurra Y, Alugubelli YR, Roundy CM, Hamer GL, Xu S, Liu WR. Novel Regioselective Approach to Cyclize Phage-Displayed Peptides in Combination with Epitope-Directed Selection to Identify a Potent Neutralizing Macrocyclic Peptide for SARS-CoV-2. ACS Chem Biol 2022; 17:2911-2922. [PMID: 36174018 PMCID: PMC9528030 DOI: 10.1021/acschembio.2c00565] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/19/2022] [Indexed: 01/20/2023]
Abstract
Using the regioselective cyanobenzothiazole condensation reaction with an N-terminal cysteine and the chloroacetamide reaction with an internal cysteine, a phage-displayed macrocyclic 12-mer peptide library was constructed and subsequently validated. Using this library in combination with iterative selections against two epitopes from the receptor binding domain (RBD) of the novel severe acute respiratory syndrome virus 2 (SARS-CoV-2) Spike protein, macrocyclic peptides that strongly inhibit the interaction between the Spike RBD and angiotensin-converting enzyme 2 (ACE2), the human host receptor of SARS-CoV-2, were identified. The two epitopes were used instead of the Spike RBD to avoid selection of nonproductive macrocyclic peptides that bind RBD but do not directly inhibit its interactions with ACE2. Antiviral tests against SARS-CoV-2 showed that one macrocyclic peptide is highly potent against viral reproduction in Vero E6 cells with an EC50 value of 3.1 μM. The AlphaLISA-detected IC50 value for this macrocyclic peptide was 0.3 μM. The current study demonstrates that two kinetically controlled reactions toward N-terminal and internal cysteines, respectively, are highly effective in the construction of phage-displayed macrocyclic peptides, and the selection based on the SARS-CoV-2 Spike epitopes is a promising methodology in the identification of peptidyl antivirals.
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Affiliation(s)
- J. Trae Hampton
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Tyler J. Lalonde
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Jeffery M. Tharp
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Yadagiri Kurra
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Yugendar R. Alugubelli
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | | | - Gabriel L. Hamer
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Wenshe Ray Liu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA
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21
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Djaló M, Silva MJSA, Faustino H, Pinto SN, Mendonça R, Gois PMP. Multivalent NHS-activated acrylates for orthogonal site-selective functionalisation of peptides at cysteine residues. Chem Commun (Camb) 2022; 58:7928-7931. [PMID: 35758206 DOI: 10.1039/d2cc02204d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The site-selective chemical appendage of multiple functionalities on a native peptide backbone is a highly demanding and complex tool of modern chemical biology. Here, novel NHS-activated acrylates were designed to hold various payloads in a single bioconjugation handle that is able to site-selectively and orthogonally target the N-terminal cysteine of peptides.
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Affiliation(s)
- Mariama Djaló
- Research Institute for Medicines (iMed. ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
| | - Maria J S A Silva
- Research Institute for Medicines (iMed. ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
| | - Hélio Faustino
- Research Institute for Medicines (iMed. ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal. .,Association BLC3-Innovation and Technology Campus, Oliveira do Hospital, Portugal
| | - Sandra N Pinto
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | | | - Pedro M P Gois
- Research Institute for Medicines (iMed. ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
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22
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Xi Z, Kong H, Chen Y, Deng J, Xu W, Liang Y, Zhang Y. Metal- and Strain-Free Bioorthogonal Cycloaddition of o-Diones with Furan-2(3H)-one as Anionic Cycloaddend. Angew Chem Int Ed Engl 2022; 61:e202200239. [PMID: 35304810 DOI: 10.1002/anie.202200239] [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: 01/07/2022] [Indexed: 12/18/2022]
Abstract
The development of new bioorthogonal reactions with mutual orthogonality to classic bioorthogonal reactions such as the strain-promoted azide-alkyne click reaction and the inverse-electron-demand Diels-Alder reaction is of great importance in providing chemical tools for multiplex labelling of live cells. Here we report the first anionic cycloaddend-promoted bioorthogonal cycloaddition reaction between phenanthrene-9,10-dione and furan-2(3H)-one derivatives, where the high polarity of water is exploited to stabilize the highly electron-rich anionic cycloaddend. The reaction is metal- and strain-free, which proceeds rapidly in aqueous solution and on live cells with a second-order rate constant up to 119 M-1 s-1 . The combined utilization of this reaction together with the two other widely used bioorthogonal reactions allows for mutually orthogonal labelling of three types of proteins or three groups of living cells in one batch without cross-talking. Such results highlight the great potential for multiplex labelling of different biomolecules in live cells.
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Affiliation(s)
- Ziwei Xi
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Hao Kong
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Yu Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Jiafang Deng
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Wenyuan Xu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
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23
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Spear LA, Huang Y, Chen J, Nödling AR, Virdee S, Tsai YH. Selective Inhibition of Cysteine-Dependent Enzymes by Bioorthogonal Tethering. J Mol Biol 2022; 434:167524. [PMID: 35248542 DOI: 10.1016/j.jmb.2022.167524] [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: 08/20/2021] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 10/18/2022]
Abstract
A general approach for the rapid and selective inhibition of enzymes in cells using a common tool compound would be of great value for research and therapeutic development. We previously reported a chemogenetic strategy that addresses this challenge for kinases, relying on bioorthogonal tethering of a pan inhibitor to a target kinase through a genetically encoded non-canonical amino acid. However, pan inhibitors are not available for many enzyme classes. Here, we expand the scope of the chemogenetic strategy to cysteine-dependent enzymes by bioorthogonal tethering of electrophilic warheads. For proof of concept, selective inhibition of two E2 ubiquitin-conjugating enzymes, UBE2L3 and UBE2D1, was demonstrated in biochemical assays. Further development and optimization of this approach should enable its use in cells as well as with other cysteine-dependent enzymes, facilitating the investigation of their cellular function and validation as therapeutic targets.
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Affiliation(s)
- Luke A Spear
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - Yang Huang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Jinghao Chen
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | | | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom.
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, United Kingdom; Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China.
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24
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Chen FJ, Zheng M, Nobile V, Gao J. Fast and Cysteine-Specific Modification of Peptides, Proteins and Bacteriophage Using Chlorooximes. Chemistry 2022; 28:e202200058. [PMID: 35167137 PMCID: PMC8986619 DOI: 10.1002/chem.202200058] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Indexed: 12/21/2022]
Abstract
This work reports a novel chlorooxime mediated modification of native peptides and proteins under physiologic conditions. This method features fast reaction kinetics (apparent k2 =306±4 M-1 s-1 for GSH) and exquisite selectivity for cysteine residues. This cysteine conjugation reaction can be carried out with just single-digit micromolar concentrations of the labeling reagent. The conjugates show high stability towards acid, base, and external thiol nucleophiles. A nitrile oxide species generated in situ is likely involved as the key intermediate. Furthermore, a bis-chlorooxime reagent is synthesized to enable facile Cys-Cys stapling in native peptides and proteins. This highly efficient cysteine conjugation and stapling was further implemented on bacteriophage to construct chemically modified phage libraries.
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Affiliation(s)
- Fa-Jie Chen
- Department of Chemistry Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Mengmeng Zheng
- Department of Chemistry Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Vincent Nobile
- 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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25
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Xi Z, Kong H, Chen Y, Deng J, Xu W, Liang Y, Zhang Y. Metal‐ and Strain‐free Bioorthogonal Cycloaddition of o‐Diones with Furan‐2(3H)‐one as Anionic Cycloaddend. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ziwei Xi
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Hao Kong
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Yu Chen
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Jiafang Deng
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Wenyuan Xu
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Yong Liang
- Nanjing University Chemistry 163 Xianlin Ave 210023 Nanjing CHINA
| | - Yan Zhang
- Nanjing University School of Chemistry and Chemical Engineering CHINA
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26
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Wang C, Zhao Y, Zhao J. Recent Advances in Chemical Protein Modification via Cysteine. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202203008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Zheng M, Haeffner F, Gao J. N-Terminal cysteine mediated backbone-side chain cyclization for chemically enhanced phage display. Chem Sci 2022; 13:8349-8354. [PMID: 35919713 PMCID: PMC9297441 DOI: 10.1039/d2sc03241d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/24/2022] [Indexed: 11/21/2022] Open
Abstract
Phage display, an ingenious invention for evaluating peptide libraries, has been limited to natural peptides that are ribosomally assembled with proteinogenic amino acids. Recently, there has been growing interest in chemically modifying phage libraries to create nonnatural cyclic and multicyclic peptides, which are appealing for use as inhibitors of protein–protein interactions. While earlier reports largely focused on side-chain side-chain cyclization, we report herein a novel strategy for creating backbone-side chain cyclized peptide libraries on phage. Our strategy capitalizes on the unique reactivity of an N-terminal cysteine (NCys) with 2-cyanobenzothiazole (CBT) which, in conjugation with another thiol-reactive group, can elicit rapid cyclization between an NCys and an internal cysteine. The resulting library was screened against two model proteins, namely Keap1 and Sortase A. The screening readily revealed potent inhibitors for both proteins with certain Keap1 ligands reaching low nanomolar potency. The backbone-side chain cyclization strategy described herein presents a significant addition to the toolkit of creating nonnatural macrocyclic peptide libraries for phage display. An NCys–Cys crosslinker elicits rapid and clean backbone-side chain cyclization, yielding nonnatural cyclic peptide libraries for phage display.![]()
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Affiliation(s)
- Mengmeng Zheng
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA
| | - Fredrik Haeffner
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA
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28
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Jiang H, Chen W, Wang J, Zhang R. Selective N-terminal modification of peptides and proteins: Recent progresses and applications. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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29
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Shen MH, Wang YJ, Wang Y, Zhou Y, Gu J, Liu XQ, Guo J, Ouyang M, Deng L, Xu HD. α-Vinyl azide–cysteine click coupling reaction enabled bioorthogonal peptide/protein modification. Org Chem Front 2022. [DOI: 10.1039/d2qo00736c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α-Alkyl and α-aryl vinyl azides were found to be able to couple with cysteine-derived alkyl thiols chemoselectively under mild conditions, providing the corresponding β-ketosulfides with simultaneous extrusion of N2 and ammonia.
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Affiliation(s)
- Mei-Hua Shen
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Yu-Jiao Wang
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Yong Wang
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Ying Zhou
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Jie Gu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Xiao-Qian Liu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Jia Guo
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Mingxing Ouyang
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Linhong Deng
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Hua-Dong Xu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
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30
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Sornay C, Vaur V, Wagner A, Chaubet G. An overview of chemo- and site-selectivity aspects in the chemical conjugation of proteins. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211563. [PMID: 35116160 PMCID: PMC8790347 DOI: 10.1098/rsos.211563] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/20/2021] [Indexed: 05/03/2023]
Abstract
The bioconjugation of proteins-that is, the creation of a covalent link between a protein and any other molecule-has been studied for decades, partly because of the numerous applications of protein conjugates, but also due to the technical challenge it represents. Indeed, proteins possess inner physico-chemical properties-they are sensitive and polynucleophilic macromolecules-that make them complex substrates in conjugation reactions. This complexity arises from the mild conditions imposed by their sensitivity but also from selectivity issues, viz the precise control of the conjugation site on the protein. After decades of research, strategies and reagents have been developed to address two aspects of this selectivity: chemoselectivity-harnessing the reacting chemical functionality-and site-selectivity-controlling the reacting amino acid residue-most notably thanks to the participation of synthetic chemistry in this effort. This review offers an overview of these chemical bioconjugation strategies, insisting on those employing native proteins as substrates, and shows that the field is active and exciting, especially for synthetic chemists seeking new challenges.
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Affiliation(s)
- Charlotte Sornay
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Valentine Vaur
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
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31
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Zheng X, Pan D, Chen X, Wu L, Chen M, Wang W, Zhang H, Gong Q, Gu Z, Luo K. Self-Stabilized Supramolecular Assemblies Constructed from PEGylated Dendritic Peptide Conjugate for Augmenting Tumor Retention and Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102741. [PMID: 34623034 PMCID: PMC8596125 DOI: 10.1002/advs.202102741] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/22/2021] [Indexed: 02/05/2023]
Abstract
Supramolecular self-assemblies of dendritic peptides with well-organized nanostructures have great potential as multifunctional biomaterials, yet the complex self-assembly mechanism hampers their wide exploration. Herein, a self-stabilized supramolecular assembly (SSA) constructed from a PEGylated dendritic peptide conjugate (PEG-dendritic peptide-pyropheophorbide a, PDPP), for augmenting tumor retention and therapy, is reported. The supramolecular self-assembly process of PDPP is concentration-dependent with multiple morphologies. By tailoring the concentration of PDPP, the supramolecular self-assembly is driven by noncovalent interactions to form a variety of SSAs (unimolecular micelles, oligomeric aggregates, and multi-aggregates) with different sizes from nanometer to micrometer. SSAs at 100 nm with a spherical shape possess extremely high stability to prolong blood circulation about 4.8-fold higher than pyropheophorbide a (Ppa), and enhance tumor retention about eight-fold higher than Ppa on day 5 after injection, which leads to greatly boosting the in vivo photodynamic therapeutic efficiency. RNA-seq demonstrates that these effects of SSAs are related to the inhibition of MET-PI3K-Akt pathway. Overall, the supramolecular self-assembly mechanism for the synthetic PEGylated dendritic peptide conjugate sheds new light on the development of supramolecular assemblies for tumor therapy.
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Affiliation(s)
- Xiuli Zheng
- Huaxi MR Research Center (HMRRC), Department of Radiology, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease‐Related Molecular Network, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengdu610041China
- National Engineering Research Center for BiomaterialsSichuan UniversityChengdu610064China
| | - Dayi Pan
- Huaxi MR Research Center (HMRRC), Department of Radiology, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease‐Related Molecular Network, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengdu610041China
| | - Xiaoting Chen
- Animal Experimental Center of West China HospitalCore Facility of West China HospitalSichuan UniversityChengdu610041China
| | - Lei Wu
- Animal Experimental Center of West China HospitalCore Facility of West China HospitalSichuan UniversityChengdu610041China
| | - Miao Chen
- West China School of MedicineWest China College of StomatologySichuan UniversityChengdu610041China
| | - Wenjia Wang
- Huaxi MR Research Center (HMRRC), Department of Radiology, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease‐Related Molecular Network, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengdu610041China
| | - Hu Zhang
- Huaxi MR Research Center (HMRRC), Department of Radiology, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease‐Related Molecular Network, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengdu610041China
- Amgen Bioprocessing CentreKeck Graduate InstituteClaremontCA91711USA
| | - Qiyong Gong
- Huaxi MR Research Center (HMRRC), Department of Radiology, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease‐Related Molecular Network, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengdu610041China
- Functional and Molecular Imaging Key Laboratory of Sichuan ProvinceResearch Unit of PsychoradiologyChinese Academy of Medical SciencesChengdu610041China
| | - Zhongwei Gu
- Huaxi MR Research Center (HMRRC), Department of Radiology, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease‐Related Molecular Network, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengdu610041China
- National Engineering Research Center for BiomaterialsSichuan UniversityChengdu610064China
| | - Kui Luo
- Huaxi MR Research Center (HMRRC), Department of Radiology, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease‐Related Molecular Network, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengdu610041China
- National Engineering Research Center for BiomaterialsSichuan UniversityChengdu610064China
- Functional and Molecular Imaging Key Laboratory of Sichuan ProvinceResearch Unit of PsychoradiologyChinese Academy of Medical SciencesChengdu610041China
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32
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Wu Y, Li C, Fan S, Zhao Y, Wu C. Fast and Selective Reaction of 2-Benzylacrylaldehyde with 1,2-Aminothiol for Stable N-Terminal Cysteine Modification and Peptide Cyclization. Bioconjug Chem 2021; 32:2065-2072. [PMID: 34405993 DOI: 10.1021/acs.bioconjchem.1c00378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N-terminal cysteine (Cys)-specific reactions have been exploited for protein and peptide modifications. However, existing reactions for N-terminal Cys suffer from low reaction rate, unavoidable side reactions, or poor stability for reagents or products. Herein we report a fast, efficient, and selective conjugation between 2-benzylacrylaldehyde (BAA) and 1,2-aminothiol, which involves multistep reactions including aldimine condensation, Michael addition, and reduction of imine by NaBH3CN. This conjugation proceeds with a rate constant of ∼2700 M-1 s-1 under neutral condition at room temperature to produce a pair of seven-membered ring diastereoisomers, which are stable under neutral and acidic conditions. This method enables the selective modifications of the N-terminal Cys residue without interference from the internal Cys and lysine residues, providing a useful alternative to existing approaches for site-specific peptide or protein modifications and synthesis of cyclic peptides.
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Affiliation(s)
- Yaqi Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, P.R. China
| | - Cong Li
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, P.R. China
| | - Shihui Fan
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, P.R. China
| | - Yibing Zhao
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, P.R. China
| | - Chuanliu Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, P.R. China
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33
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Kumar M, Reddy NC, Rai V. Chemical technologies for precise protein bioconjugation interfacing biology and medicine. Chem Commun (Camb) 2021; 57:7083-7095. [PMID: 34180471 DOI: 10.1039/d1cc02268g] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteins provide an excellent means to monitor and regulate biological processes. Hence, a precise chemical toolbox for their modification becomes indispensable. In this perspective, this feature article outlines our efforts to establish the core principles of chemoselectivity, site-selectivity, site-specificity, site-modularity, residue-modularity, and protein-specificity. With the knowledge to systematically regulate these parameters, the field has access to technological platforms that can address multiple challenges at the interface of chemistry, biology, and medicine.
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Affiliation(s)
- Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| | - Neelesh C Reddy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
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34
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Bechtler C, Lamers C. Macrocyclization strategies for cyclic peptides and peptidomimetics. RSC Med Chem 2021; 12:1325-1351. [PMID: 34447937 PMCID: PMC8372203 DOI: 10.1039/d1md00083g] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
Peptides are a growing therapeutic class due to their unique spatial characteristics that can target traditionally "undruggable" protein-protein interactions and surfaces. Despite their advantages, peptides must overcome several key shortcomings to be considered as drug leads, including their high conformational flexibility and susceptibility to proteolytic cleavage. As a general approach for overcoming these challenges, macrocyclization of a linear peptide can usually improve these characteristics. Their synthetic accessibility makes peptide macrocycles very attractive, though traditional synthetic methods for macrocyclization can be challenging for peptides, especially for head-to-tail cyclization. This review provides an updated summary of the available macrocyclization chemistries, such as traditional lactam formation, azide-alkyne cycloadditions, ring-closing metathesis as well as unconventional cyclization reactions, and it is structured according to the obtained functional groups. Keeping peptide chemistry and screening in mind, the focus is given to reactions applicable in solution, on solid supports, and compatible with contemporary screening methods.
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Affiliation(s)
- Clément Bechtler
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
| | - Christina Lamers
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
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35
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An X, Chen C, Wang T, Huang A, Zhang D, Han MJ, Wang J. Genetic Incorporation of Selenotyrosine Significantly Improves Enzymatic Activity of Agrobacterium radiobacter Phosphotriesterase. Chembiochem 2021; 22:2535-2539. [PMID: 32789938 DOI: 10.1002/cbic.202000460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/11/2020] [Indexed: 12/16/2022]
Abstract
Tyrosine plays important roles in many enzymes. To facilitate enzyme design, mechanistic studies and minimize structural perturbation in the active site, here we report the genetic incorporation of a novel unnatural amino acid selenotyrosine (SeHF), which has single-atom replacement in comparison to tyrosine. The arPTE-(Agrobacterium radiobacter Phosphotriesterase) Tyr309SeHF mutant exhibits a significant 12-fold increase in kcat and 3.2-fold enhancement in kcat /KM at pH 7.0. Molecular dynamics simulations show that the SeHF309 mutation results in a conformational switch which opens up the product release pocket and increases the product release rate, thereby elevating the overall enzyme activity. Significant improvement of the catalytic efficiency at neutral pH by single unnatural amino acid (UAA) mutation broadens the application of this enzyme, and provides valuable insights to the mechanism. Our method represents a new approach for designing enzymes with enhanced activity.
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Affiliation(s)
- Xiaojing An
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Chao Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- University of the Chinese Academy of Sciences (UCAS), Hefei, China
| | - Tianyuan Wang
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Aiping Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Ming-Jie Han
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Jiangyun Wang
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
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36
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Asiimwe N, Al Mazid MF, Murale DP, Kim YK, Lee J. Recent advances in protein modifications techniques for the targeting
N‐terminal
cysteine. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nicholas Asiimwe
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST) Seoul Korea
- Bio‐Med Program, KIST‐School UST Seoul Korea
| | | | | | - Yun Kyung Kim
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST) Seoul Korea
- Bio‐Med Program, KIST‐School UST Seoul Korea
| | - Jun‐Seok Lee
- Department of Pharmacology Korea University College of Medicine Seoul Korea
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37
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Hayes HC, Luk LYP, Tsai YH. Approaches for peptide and protein cyclisation. Org Biomol Chem 2021; 19:3983-4001. [PMID: 33978044 PMCID: PMC8114279 DOI: 10.1039/d1ob00411e] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/01/2021] [Indexed: 12/26/2022]
Abstract
The cyclisation of polypeptides can play a crucial role in exerting biological functions, maintaining stability under harsh conditions and conferring proteolytic resistance, as demonstrated both in nature and in the laboratory. To date, various approaches have been reported for polypeptide cyclisation. These approaches range from the direct linkage of N- and C- termini to the connection of amino acid side chains, which can be applied both in reaction vessels and in living systems. In this review, we categorise the cyclisation approaches into chemical methods (e.g. direct backbone cyclisation, native chemical ligation, aldehyde-based ligations, bioorthogonal reactions, disulphide formation), enzymatic methods (e.g. subtiligase variants, sortases, asparaginyl endopeptidases, transglutaminases, non-ribosomal peptide synthetases) and protein tags (e.g. inteins, engineered protein domains for isopeptide bond formation). The features of each approach and the considerations for selecting an appropriate method of cyclisation are discussed.
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Affiliation(s)
- Heather C Hayes
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT.
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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38
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Silva MJSA, Faustino H, Coelho JAS, Pinto MV, Fernandes A, Compañón I, Corzana F, Gasser G, Gois PMP. Efficient Amino‐Sulfhydryl Stapling on Peptides and Proteins Using Bifunctional NHS‐Activated Acrylamides. Angew Chem Int Ed Engl 2021; 60:10850-10857. [DOI: 10.1002/anie.202016936] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Maria J. S. A. Silva
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
- Chimie ParisTech PSL University CNRS Institute of Chemistry for Life and Health Sciences Laboratory for Inorganic Chemical Biology 75005 Paris France
| | - Hélio Faustino
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Jaime A. S. Coelho
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Maria V. Pinto
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Adelaide Fernandes
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Ismael Compañón
- Departamento de Química Centro de Investigación en Síntesis Química Universidad de La Rioja 26006 Logroño La Rioja Spain
| | - Francisco Corzana
- Departamento de Química Centro de Investigación en Síntesis Química Universidad de La Rioja 26006 Logroño La Rioja Spain
| | - Gilles Gasser
- Chimie ParisTech PSL University CNRS Institute of Chemistry for Life and Health Sciences Laboratory for Inorganic Chemical Biology 75005 Paris France
| | - Pedro M. P. Gois
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
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39
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Silva MJSA, Faustino H, Coelho JAS, Pinto MV, Fernandes A, Compañón I, Corzana F, Gasser G, Gois PMP. Efficient Amino‐Sulfhydryl Stapling on Peptides and Proteins Using Bifunctional NHS‐Activated Acrylamides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016936] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Maria J. S. A. Silva
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
- Chimie ParisTech PSL University CNRS Institute of Chemistry for Life and Health Sciences Laboratory for Inorganic Chemical Biology 75005 Paris France
| | - Hélio Faustino
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Jaime A. S. Coelho
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Maria V. Pinto
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Adelaide Fernandes
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Ismael Compañón
- Departamento de Química Centro de Investigación en Síntesis Química Universidad de La Rioja 26006 Logroño La Rioja Spain
| | - Francisco Corzana
- Departamento de Química Centro de Investigación en Síntesis Química Universidad de La Rioja 26006 Logroño La Rioja Spain
| | - Gilles Gasser
- Chimie ParisTech PSL University CNRS Institute of Chemistry for Life and Health Sciences Laboratory for Inorganic Chemical Biology 75005 Paris France
| | - Pedro M. P. Gois
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
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40
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A versatile resin for the generation of thioether-bonded head-to-tail cyclized peptides. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.152867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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41
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Lu J, Wu Y, Li Y, Wang H. The Utilization of Lanthipeptide Synthetases Is a General Strategy for the Biosynthesis of 2‐Aminovinyl‐Cysteine Motifs in Thioamitides**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jingxia Lu
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Yuan Wu
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Yuqing Li
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
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42
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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.
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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
| | - 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
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43
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Lu J, Wu Y, Li Y, Wang H. The Utilization of Lanthipeptide Synthetases Is a General Strategy for the Biosynthesis of 2‐Aminovinyl‐Cysteine Motifs in Thioamitides**. Angew Chem Int Ed Engl 2020; 60:1951-1958. [DOI: 10.1002/anie.202012871] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Jingxia Lu
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Yuan Wu
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Yuqing Li
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
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44
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Purushottam L, V B U, Rawale DG, Gujrati M, Mishra SD, T K S, Reddy NC, Adusumalli SR, Mishra RK, Rai V. A single amino acid Gly-tag enables metal-free protein purification. Chem Sci 2020; 11:13137-13142. [PMID: 34094495 PMCID: PMC8163197 DOI: 10.1039/d0sc01153c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Analytically pure proteins are indispensable for diverse applications, including therapeutics. Here, we report a methodology where a single amino acid, glycine, enables metal-free protein purification. This robust platform is enabled by a Gly-tag resin for site-specific capture, enrichment, and release through chemically triggered C-C bond dissociation by resonance-assisted electron density polarization.
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Affiliation(s)
- Landa Purushottam
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Unnikrishnan V B
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Dattatraya Gautam Rawale
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Mansi Gujrati
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Surya Dev Mishra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India .,Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Sajeev T K
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Neelesh C Reddy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Srinivasa Rao Adusumalli
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Ram Kumar Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
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45
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Li X, Chen S, Zhang WD, Hu HG. Stapled Helical Peptides Bearing Different Anchoring Residues. Chem Rev 2020; 120:10079-10144. [DOI: 10.1021/acs.chemrev.0c00532] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiang Li
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Insititute of Translational Medicine, Shanghai University, Shanghai, China
| | - Si Chen
- School of Medicine, Shanghai University, Shanghai, China
| | - Wei-Dong Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hong-Gang Hu
- Insititute of Translational Medicine, Shanghai University, Shanghai, China
- Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
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46
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Zheng X, Liu W, Liu Z, Zhao Y, Wu C. Biocompatible and Rapid Cyclization of Peptides with 2,4-Difluoro-6-hydroxy-1,3,5-benzenetricarbonitrile for the Development of Cyclic Peptide Libraries. Bioconjug Chem 2020; 31:2085-2091. [DOI: 10.1021/acs.bioconjchem.0c00363] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xuejun Zheng
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen, 361005, P.R. China
| | - Weidong Liu
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen, 361005, P.R. China
| | - Ziyan Liu
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen, 361005, P.R. China
| | - Yibing Zhao
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen, 361005, P.R. China
| | - Chuanliu Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen, 361005, P.R. China
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47
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Reddy NC, Kumar M, Molla R, Rai V. Chemical methods for modification of proteins. Org Biomol Chem 2020; 18:4669-4691. [DOI: 10.1039/d0ob00857e] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The field of protein bioconjugation draws attention from stakeholders in chemistry, biology, and medicine. This review provides an overview of the present status, challenges, and opportunities for organic chemists.
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Affiliation(s)
- Neelesh C. Reddy
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Mohan Kumar
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Rajib Molla
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Vishal Rai
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
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