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Ullrich S, Somathilake U, Shang M, Nitsche C. Phage-encoded bismuth bicycles enable instant access to targeted bioactive peptides. Commun Chem 2024; 7:143. [PMID: 38937646 PMCID: PMC11211329 DOI: 10.1038/s42004-024-01232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024] Open
Abstract
Genetically encoded libraries play a crucial role in discovering structurally rigid, high-affinity macrocyclic peptide ligands for therapeutic applications. Bicyclic peptides with metal centres like bismuth were recently developed as a new type of constrained peptide with notable affinity, stability and membrane permeability. This study represents the genetic encoding of peptide-bismuth and peptide-arsenic bicycles in phage display. We introduce bismuth tripotassium dicitrate (gastrodenol) as a water-soluble bismuth(III) reagent for phage library modification and in situ bicyclic peptide preparation, eliminating the need for organic co-solvents. Additionally, we explore arsenic(III) as an alternative thiophilic element that is used analogously to our previously introduced bicyclic peptides with a bismuth core. The modification of phage libraries and peptides with these elements is instantaneous and entirely biocompatible, offering an advantage over conventional alkylation-based methods. In a pilot display screening campaign aimed at identifying ligands for the biotin-binding protein streptavidin, we demonstrate the enrichment of bicyclic peptides with dissociation constants two orders of magnitude lower than those of their linear counterparts, underscoring the impact of structural constraint on binding affinity.
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Affiliation(s)
- Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Upamali Somathilake
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Minghao Shang
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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Cao X, Liu T, Wang T, Wang X, Xu Z, Zhou L, Tian C, Sun D. De Novo Screening and Mirror Image Isomerization of Linear Peptides Targeting α7 Nicotinic Acetylcholine Receptor. ACS Chem Biol 2024; 19:592-598. [PMID: 38380973 DOI: 10.1021/acschembio.3c00674] [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: 02/22/2024]
Abstract
As ligand-gated ion channels, nicotinic acetylcholine receptors (nAChRs) are widely distributed in the central and peripheral nervous systems and are associated with the pathogenesis of various degenerative neurological diseases. Here, we report the results of phage display-based de novo screening of an 11-residue linear peptide (named LKP1794) that targets the α7 nAChR, which is among the most abundant nAChR subtypes in the brain. Moreover, two d-peptides were generated through mirror image and/or primary sequence inverso isomerization (termed DRKP1794 and DKP1794) and displayed improved inhibitory effects (IC50 = 0.86 and 0.35 μM, respectively) on α7 nAChR compared with the parent l-peptide LKP1794 (IC50 = 2.48 μM), which markedly enhanced serum stability. A peptide-based fluorescence probe was developed using proteolytically resistant DKP1794 to specifically image the α7 nAChR in living cells. This work provides a new peptide tool to achieve inhibitory modulation and specifically image the α7 nAChR.
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Affiliation(s)
- Xiuxiu Cao
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, P. R. China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Tianqi Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Tao Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Xudong Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Ziyan Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Li Zhou
- Anhui Provincial Peptide Drug Laboratory, Hefei 230026, P. R. China
| | - Changlin Tian
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, P. R. China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
- Anhui Provincial Peptide Drug Laboratory, Hefei 230026, P. R. China
- School of Biomedical Engineering, Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, P. R. China
- Beijing Life Science Academy, Beijing 102200, P. R. China
| | - Demeng Sun
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
- Anhui Provincial Peptide Drug Laboratory, Hefei 230026, P. R. China
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Zhang YW, Lin NP, Guo X, Szabo-Fresnais N, Ortoleva PJ, Chou DHC. Omniligase-1-Mediated Phage-Peptide Library Modification and Insulin Engineering. ACS Chem Biol 2024; 19:506-515. [PMID: 38266161 DOI: 10.1021/acschembio.3c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Chemical and enzymatic modifications of peptide-displayed libraries have been successfully employed to expand the phage display library. However, the requirement of specific epitopes and scaffolds has limited the scope of protein engineering using phage display. In this study, we present a novel approach utilizing omniligase-1-mediated selective and specific ligation on the phage pIII protein, offering a high conversion rate and compatibility with commercially available phage libraries. We applied this method to perform high-throughput engineering of insulin analogues with randomized B chain C-terminal regions. Insulin analogues with different B chain C-terminal segments were selected and exhibited biological activity equivalent to that of human insulin. Molecular dynamics studies of insulin analogues revealed a novel interaction between the insulin B27 residue and insulin receptor L1 domain. In summary, our findings highlight the potential of omniligase-1-mediated phage display in the development and screening of disulfide-rich peptides and proteins. This approach holds promise for the creation of novel insulin analogues with enhanced therapeutic properties and exhibits potential for the development of other therapeutic compounds.
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Affiliation(s)
- Yi Wolf Zhang
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, California 94304, United States
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Nai-Pin Lin
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, California 94304, United States
| | - Xu Guo
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Nicolas Szabo-Fresnais
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Peter J Ortoleva
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Danny Hung-Chieh Chou
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, California 94304, United States
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Zhang YW, Zheng N, Chou DHC. Serine-mediated hydrazone ligation displaying insulin-like peptides on M13 phage pIII. Org Biomol Chem 2023; 21:8902-8909. [PMID: 37905463 DOI: 10.1039/d3ob01487h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Phage display has emerged as a tool for the discovery of therapeutic antibodies and proteins. However, the effective display and engineering of structurally complex proteins, such as insulin, pose significant challenges due to the sequence of insulin, which is composed of two peptide chains linked by three disulfide bonds. In this study, we developed a new approach for the display of insulin-like peptides on M13 phage pIII, employing N-terminal serine-mediated hydrazone ligation. The insulin-displaying phage retains the biological binding affinity of human insulin. To address the viability loss after ligation, we introduced a trypsin-cleavable spacer on pIII, enabling insulin-displayed phage library selection. This method offers a general pathway for the display of structurally complex proteins on pIII, enhancing the practicality of selecting chemically modified phage libraries and opening avenues for the engineering of new insulin analogs for the treatment of diabetes by using phage display.
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Affiliation(s)
- Yi Wolf Zhang
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, CA 94304, USA.
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Nan Zheng
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Danny Hung-Chieh Chou
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, CA 94304, USA.
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Veeranarayanan S, Azam AH, Kiga K, Watanabe S, Cui L. Bacteriophages as Solid Tumor Theragnostic Agents. Int J Mol Sci 2021; 23:402. [PMID: 35008840 PMCID: PMC8745063 DOI: 10.3390/ijms23010402] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 12/16/2022] Open
Abstract
Cancer, especially the solid tumor sub-set, poses considerable challenges to modern medicine owing to the unique physiological characteristics and substantial variations in each tumor's microenvironmental niche fingerprints. Though there are many treatment methods available to treat solid tumors, still a considerable loss of life happens, due to the limitation of treatment options and the outcomes of ineffective treatments. Cancer cells evolve with chemo- or radiation-treatment strategies and later show adaptive behavior, leading to failed treatment. These challenges demand tailored and individually apt personalized treatment methods. Bacteriophages (or phages) and phage-based theragnostic vectors are gaining attention in the field of modern cancer medicine, beyond their bactericidal ability. With the invention of the latest techniques to fine-tune phages, such as in the field of genetic engineering, synthetic assembly methods, phage display, and chemical modifications, noteworthy progress in phage vector research for safe cancer application has been realized, including use in pre-clinical studies. Herein, we discuss the distinct fingerprints of solid tumor physiology and the potential for bacteriophage vectors to exploit specific tumor features for improvised tumor theragnostic applications.
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Affiliation(s)
| | | | | | | | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke-shi 3290498, Japan; (S.V.); (A.H.A.); (K.K.); (S.W.)
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