1
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Liu Z, Li H, Yu Q, Song Q, Peng B, Wang K, Li Z. Heterologous Expression Facilitates the Production and Characterization of a Class III Lanthipeptide with Coupled Labionin Cross-Links in Sponge-Associated Streptomyces rochei MB037. ACS Chem Biol 2024. [PMID: 39145437 DOI: 10.1021/acschembio.4c00428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Cyclic peptides, with remarkable stability, cellular permeability, and proteolysis resistance, display promising potential in pharmaceutical applications. Labionin (Lab), a unique bicyclic cross-link containing both C-C and C-S bonds, provides high rigidity and better control of conformation compared to monocyclic cross-links. To discover more Lab-containing scaffolds with highly rigid conformation for cyclic peptide drug development, herein, a cryptic class III lanthipeptide biosynthetic gene cluster (BGC) (i.e., rcs) was identified in the sponge-associated Streptomyces rochei MB037 and expressed in Escherichia coli, incorporating an N-terminal SUMO-tag on the RcsA precursor peptide to prevent proteolysis. Subsequently, a novel class III lanthipeptide, i.e., rochsin A, exhibiting a highly rigid conformation with coupled Lab cross-links crowded by bulky aromatic amino acids, was produced. Three AplP-like proteases outside the rcs BGC were proven to remove the leader peptide of rochsin A through their dual endo- and aminopeptidase activities, resulting in mature rochsin A in vitro. Ala mutation experiments revealed the C to N cyclization direction, like most class III lanthipeptides. However, RcsKC displays a high substrate breadth, enabling various ring topologies that are rarely observed in other class III lanthipeptides. Overall, the established expression system broadens the chemical diversity of cyclic peptides with unique Lab cross-links and offers a highly rigid scaffold for cyclic peptide drug development.
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Affiliation(s)
- Zhengjie Liu
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qianzhe Yu
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qianqian Song
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo Peng
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kang Wang
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
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2
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Chaudhary S, Ali Z, Mahfouz M. Molecular farming for sustainable production of clinical-grade antimicrobial peptides. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2282-2300. [PMID: 38685599 PMCID: PMC11258990 DOI: 10.1111/pbi.14344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/26/2024] [Accepted: 03/11/2024] [Indexed: 05/02/2024]
Abstract
Antimicrobial peptides (AMPs) are emerging as next-generation therapeutics due to their broad-spectrum activity against drug-resistant bacterial strains and their ability to eradicate biofilms, modulate immune responses, exert anti-inflammatory effects and improve disease management. They are produced through solid-phase peptide synthesis or in bacterial or yeast cells. Molecular farming, i.e. the production of biologics in plants, offers a low-cost, non-toxic, scalable and simple alternative platform to produce AMPs at a sustainable cost. In this review, we discuss the advantages of molecular farming for producing clinical-grade AMPs, advances in expression and purification systems and the cost advantage for industrial-scale production. We further review how 'green' production is filling the sustainability gap, streamlining patent and regulatory approvals and enabling successful clinical translations that demonstrate the future potential of AMPs produced by molecular farming. Finally, we discuss the regulatory challenges that need to be addressed to fully realize the potential of molecular farming-based AMP production for therapeutics.
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Affiliation(s)
- Shahid Chaudhary
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences4700 King Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences4700 King Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences4700 King Abdullah University of Science and TechnologyThuwalSaudi Arabia
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3
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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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4
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Smith FR, Meehan D, Griffiths RC, Knowles HJ, Zhang P, Williams HEL, Wilson AJ, Mitchell NJ. Peptide macrocyclisation via intramolecular interception of visible-light-mediated desulfurisation. Chem Sci 2024; 15:9612-9619. [PMID: 38939126 PMCID: PMC11206203 DOI: 10.1039/d3sc05865d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/30/2024] [Indexed: 06/29/2024] Open
Abstract
Synthetic methods that enable the macrocyclisation of peptides facilitate the development of effective therapeutic and diagnostic tools. Herein we report a peptide cyclisation strategy based on intramolecular interception of visible-light-mediated cysteine desulfurisation. This method allows cyclisation of unprotected peptides in an aqueous solution via the installation of a hydrocarbon linkage. We explore the limits of this chemistry using a range of model peptides of increasing length and complexity, including peptides of biological/therapeutic relevance. The method is applied to replace the native disulfide of the peptide hormone, oxytocin, with a proteolytically/redox-stable hydrocarbon, and internal macrocyclisation of an MCL-1-binding peptide.
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Affiliation(s)
- Frances R Smith
- School of Chemistry, University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Declan Meehan
- School of Chemistry, University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Rhys C Griffiths
- School of Chemistry, University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Harriet J Knowles
- School of Chemistry, University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Peiyu Zhang
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Huw E L Williams
- Biodiscovery Institute, University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Nicholas J Mitchell
- School of Chemistry, University of Nottingham, University Park Nottingham NG7 2RD UK
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5
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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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6
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He RN, Zhang MJ, Dai B, Kong XD. Selection of Peptide-Bismuth Bicycles Using Phage Display. ACS Chem Biol 2024; 19:1040-1044. [PMID: 38620022 DOI: 10.1021/acschembio.4c00099] [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: 04/17/2024]
Abstract
Cysteine conjugation is widely used to constrain phage displayed peptides for the selection of cyclic peptides against specific targets. In this study, the nontoxic Bi3+ ion was used as a cysteine conjugation reagent to cross-link peptide libraries without compromising phage infectivity. We constructed a randomized 3-cysteine peptide library and cyclized it with Bi3+, followed by a selection against the maltose-binding protein as a model target. Next-generation sequencing of selection samples revealed the enrichment of peptides containing clear consensus sequences. Chemically synthesized linear and Bi3+ cyclized peptides were used for affinity validation. The cyclized peptide showed a hundred-fold better affinity (0.31 ± 0.04 μM) than the linear form (39 ± 6 μM). Overall, our study proved the feasibility of developing Bi3+ constrained bicyclic peptides against a specific target using phage display, which would potentially accelerate the development of new peptide-bismuth bicycles for therapeutic or diagnostic applications.
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Affiliation(s)
- Ruo-Nan He
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai 201203, China
| | - Meng-Jie Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai 201203, China
| | - Bin Dai
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xu-Dong Kong
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai 201203, China
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7
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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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8
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Merz ML, Habeshian S, Li B, David JAGL, Nielsen AL, Ji X, Il Khwildy K, Duany Benitez MM, Phothirath P, Heinis C. De novo development of small cyclic peptides that are orally bioavailable. Nat Chem Biol 2024; 20:624-633. [PMID: 38155304 PMCID: PMC11062899 DOI: 10.1038/s41589-023-01496-y] [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: 03/31/2023] [Accepted: 11/02/2023] [Indexed: 12/30/2023]
Abstract
Cyclic peptides can bind challenging disease targets with high affinity and specificity, offering enormous opportunities for addressing unmet medical needs. However, as with biological drugs, most cyclic peptides cannot be applied orally because they are rapidly digested and/or display low absorption in the gastrointestinal tract, hampering their development as therapeutics. In this study, we developed a combinatorial synthesis and screening approach based on sequential cyclization and one-pot peptide acylation and screening, with the possibility of simultaneously interrogating activity and permeability. In a proof of concept, we synthesized a library of 8,448 cyclic peptides and screened them against the disease target thrombin. Our workflow allowed multiple iterative cycles of library synthesis and yielded cyclic peptides with nanomolar affinities, high stabilities and an oral bioavailability (%F) as high as 18% in rats. This method for generating orally available peptides is general and provides a promising push toward unlocking the full potential of peptides as therapeutics.
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Affiliation(s)
- Manuel L Merz
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sevan Habeshian
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bo Li
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jean-Alexandre G L David
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Xinjian Ji
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Khaled Il Khwildy
- Center of Phenogenomics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Maury M Duany Benitez
- Center of Phenogenomics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Phoukham Phothirath
- Center of Phenogenomics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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9
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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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10
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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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11
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Wang Y, Zhao L, Dai Y, Xu M, Zhou R, Zhou B, Gou K, Zeng R, Xu L, Li H. Enantioselective Oral Absorption of Molecular Chiral Mesoporous Silica Nanoparticles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2307900. [PMID: 37839052 DOI: 10.1002/adma.202307900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/10/2023] [Indexed: 10/17/2023]
Abstract
Inspired by the unique pharmacological effects of chiral drugs in the asymmetrical body environments, it is assumed that the chirality of nanocarriers is also a key factor to determine their oral adsorption efficiency, apart from their size, shape, etc. Herein, l/d-tartaric acid modified mesoporous silica nanoparticles (l/d-CMSNs) are fabricated via a one-pot cocondensation method, and focused on whether the oral adsorption of nanocarriers will be benefited from their chirality. It is found that l-CMSN performed better in the sequential oral absorption processes, including mucus permeation, mucosa bio-adhesion, cellular uptake, intestinal transport and gastrointestinal tract (GIT) retention, than those of the d-chiral (d-CMSN), racemic (dl-CMSN), and achiral (MSN) counterparts. The multiple chiral recognition mechanisms are experimentally and theoretically demonstrated following simple differential adsorption on biointerfaces, wherein electrostatic interaction is the dominant energy. During the oral delivery task, l-CMSN, which is proven to be stable, nonirritative, biocompatible, and biodegradable, is efficiently absorbed into the blood (1.72-2.05-fold higher than other nanocarriers), and helps the loaded doxorubicin (DOX) to achieve better intestinal transport (2.32-27.03-times higher than other samples), satisfactory bioavailability (449.73%) and stronger antitumor effect (up to 95.43%). These findings validated the dominant role of chirality in determining the biological fate of nanocarriers.
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Affiliation(s)
- Yuxin Wang
- School of Pharmacy, China Medical University, Shenyang, 110122, China
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Lin Zhao
- School of Pharmacy, China Medical University, Shenyang, 110122, China
| | - Yibo Dai
- School of Pharmacy, China Medical University, Shenyang, 110122, China
| | - Miao Xu
- School of Pharmacy, China Medical University, Shenyang, 110122, China
| | - Ruilin Zhou
- School of Pharmacy, China Medical University, Shenyang, 110122, China
| | - Bingxin Zhou
- School of Pharmacy, China Medical University, Shenyang, 110122, China
| | - Kaijun Gou
- Institute of Tibetan Plateau, Southwest Minzu University, Chengdu, 610225, China
| | - Rui Zeng
- Institute of Tibetan Plateau, Southwest Minzu University, Chengdu, 610225, China
| | - Lu Xu
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Heran Li
- School of Pharmacy, China Medical University, Shenyang, 110122, China
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12
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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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13
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Yang Y, Wu H, Gao Y, Tong W, Li K. MFPPDB: a comprehensive multi-functional plant peptide database. FRONTIERS IN PLANT SCIENCE 2023; 14:1224394. [PMID: 37908832 PMCID: PMC10613858 DOI: 10.3389/fpls.2023.1224394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/29/2023] [Indexed: 11/02/2023]
Abstract
Plants produce a wide range of bioactive peptides as part of their innate defense mechanisms. With the explosive growth of plant-derived peptides, verifying the therapeutic function using traditional experimental methods are resources and time consuming. Therefore, it is necessary to predict the therapeutic function of plant-derived peptides more effectively and accurately with reduced waste of resources and thus expedite the development of plant peptides. We herein developed a repository of plant peptides predicted to have multiple therapeutic functions, named as MFPPDB (multi-functional plant peptide database). MFPPDB including 1,482,409 single or multiple functional plant origin therapeutic peptides derived from 121 fundamental plant species. The functional categories of these therapeutic peptides include 41 different features such as anti-bacterial, anti-fungal, anti-HIV, anti-viral, and anti-cancer. The detailed physicochemical information of these peptides was presented in functional search and physicochemical property search module, which can help users easily access the peptide information by the plant peptide species, ID, and functions, or by their peptide ID, isoelectric point, peptide sequence, and molecular weight through web-friendly interface. We further matched the predicted peptides to nine state-of-the-art curated functional peptide databases and found that at least 293,408 of the peptides possess functional potentials. Overall, MFPPDB integrated a massive number of plant peptides have single or multiple therapeutic functions, which will facilitate the comprehensive research in plant peptidomics. MFPPDB can be freely accessed through http://124.223.195.214:9188/mfppdb/index.
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Affiliation(s)
- Yaozu Yang
- School of Information and Computer, Anhui Agricultural University, Hefei, China
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Anhui University, Hefei, Anhui, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Hongwei Wu
- School of Information and Computer, Anhui Agricultural University, Hefei, China
| | - Yu Gao
- School of Information and Computer, Anhui Agricultural University, Hefei, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Ke Li
- School of Information and Computer, Anhui Agricultural University, Hefei, China
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Anhui University, Hefei, Anhui, China
- Anhui Provincial Engineering Laboratory for Beidou Precision Agriculture Information, Anhui Agricultural University, Hefei, Anhui, China
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14
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Yang J, Li D, Zhang M, Lin G, Hu S, Xu H. From the updated landscape of the emerging biologics for IBDs treatment to the new delivery systems. J Control Release 2023; 361:568-591. [PMID: 37572962 DOI: 10.1016/j.jconrel.2023.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/06/2023] [Accepted: 08/06/2023] [Indexed: 08/14/2023]
Abstract
Inflammatory bowel diseases (IBDs) treatments have shifted from small-molecular therapeutics to the oncoming biologics. The first-line biologics against the moderate-to-severe IBDs are mainly involved in antibodies against integrins, cytokines and cell adhesion molecules. Besides, other biologics including growth factors, antioxidative enzyme, anti-inflammatory peptides, nucleic acids, stem cells and probiotics have also been explored at preclinical or clinical studies. Biologics with variety of origins have their unique potentials in attenuating immune inflammation or gut mucosa healing. Great advances in use of biologics for IBDs treatments have been archived in recent years. But delivering issues for biologic have also been confronted due to their liable nature. In this review, we will focus on biologics for IBDs treatments in the recent publications; summarize the current landscapes of biologics and their promise to control disease progress. Alternatively, the confronted challenges for delivering biologics will also be analyzed. To combat these drawbacks, some new delivering strategies are provided: firstly, designing the functional materials with high affinity toward biologics; secondly, the delivering vehicle systems to encapsulate the liable biologics; thirdly, the topical adhering delivery systems as enema. To our knowledge, this review is the first study to summarize the updated usage of the oncoming biologics for IBDs, their confronted challenges in term of delivery and the potential combating strategies.
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Affiliation(s)
- Jiaojiao Yang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou City, Zhejiang Province 325035, China
| | - Dingwei Li
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou City, Zhejiang Province 325035, China
| | - Mengjiao Zhang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou City, Zhejiang Province 325035, China
| | - Gaolong Lin
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou City, Zhejiang Province 325035, China
| | - Sunkuan Hu
- Department of Gastroenterology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province 325000, China
| | - Helin Xu
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou City, Zhejiang Province 325035, China.
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15
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Wang L, Li H, Wang X, Yang X, Tian C, Sun D, Liu L, Li J. Modification of Low-Energy Surfaces Using Bicyclic Peptides Discovered by Phage Display. J Am Chem Soc 2023; 145:17613-17620. [PMID: 37531461 DOI: 10.1021/jacs.3c02943] [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: 08/04/2023]
Abstract
Solid-binding peptides are a simple and versatile tool for the non-covalent modification of solid material surfaces, and a variety of peptides have been developed by reference to natural proteins or de novo design. Here, for the first time, we report the discovery of a bicyclic peptide targeting the heterogeneous material polypropylene by combining phage display technology and next-generation sequencing. We find that the enrichment properties of bicyclic peptides capable of binding to polypropylene are distinct from linear peptides, as reflected in amino acid abundance and a trend toward negative net charges and high hydrophobicity. The selected bicyclic peptide has a higher binding affinity for polypropylene compared with a previously reported linear peptide, enabling the hydrophilic and adhesive properties of the polypropylene to be more effectively enhanced. Our work paves the way for the exploration and utilization of conformational-restricted cyclic peptides as a new family of functionally evolvable agents for material surface modification.
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Affiliation(s)
- Lingxiao Wang
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Haodong Li
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Xinyan Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xichu Yang
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Changlin Tian
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Demeng Sun
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jinghong Li
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
- New Cornerstone Science Laboratory, Shenzhen 518054, China
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16
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Peng H, Wang J, Chen J, Peng Y, Wang X, Chen Y, Kaplan DL, Wang Q. Challenges and opportunities in delivering oral peptides and proteins. Expert Opin Drug Deliv 2023; 20:1349-1369. [PMID: 37450427 PMCID: PMC10990675 DOI: 10.1080/17425247.2023.2237408] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
INTRODUCTION Rapid advances in bioengineering enable the use of complex proteins as therapeutic agents to treat diseases. Compared with conventional small molecule drugs, proteins have multiple advantages, including high bioactivity and specificity with low toxicity. Developing oral dosage forms with active proteins is a route to improve patient compliance and significantly reduce production costs. However, the gastrointestinal environment remains a challenge to this delivery path due to enzymatic degradation, low permeability, and weak absorption, leading to reduced delivery efficiency and poor clinical outcomes. AREAS COVERED This review describes the barriers to oral delivery of peptides and complex proteins, current oral delivery strategies utilized and the opportunities and challenges ahead to try and circumvent these barriers. Oral protein drugs on the market and clinical trials provide insights and approaches for advancing delivery strategies. EXPERT OPINION Although most current studies on oral protein delivery rely on in vitro and in vivo animal data, the safety and limitations of the approach in humans remain uncertain. The shortage of clinical data limits the development of new or alternative strategies. Therefore, designing appropriate oral delivery strategies remains a significant challenge and requires new ideas, innovative design strategies and novel model systems.
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Affiliation(s)
- Haisheng Peng
- Department of Pharmacology, Medical College, University of Shaoxing, Shaoxing, China
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
| | - Jiahe Wang
- Department of Humanities, Daqing Branch, Harbin Medical University, Daqing, China
| | - Jiayu Chen
- Department of Pharmacology, Medical College, University of Shaoxing, Shaoxing, China
| | - Yanbo Peng
- Department of Pharmaceutical Engineering, China Pharmaceutical University, 639 Longmian Rd, Nanjing 211198, China
| | - Xiaoxian Wang
- The Affiliated Hospital of Medical College, University of Shaoxing, Shaoxing, Zhejiang Province, China
| | - Ying Chen
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - Qun Wang
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
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17
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Yang S, Wang M, Wang T, Sun M, Huang H, Shi X, Duan S, Wu Y, Zhu J, Liu F. Self-assembled short peptides: Recent advances and strategies for potential pharmaceutical applications. Mater Today Bio 2023; 20:100644. [PMID: 37214549 PMCID: PMC10199221 DOI: 10.1016/j.mtbio.2023.100644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/10/2023] [Accepted: 04/23/2023] [Indexed: 05/24/2023] Open
Abstract
Self-assembled short peptides have intrigued scientists due to the convenience of synthesis, good biocompatibility, low toxicity, inherent biodegradability and fast response to change in the physiological environment. Therefore, it is necessary to present a comprehensive summary of the recent advances in the last decade regarding the construction, route of administration and application of self-assembled short peptides based on the knowledge on their unique and specific ability of self-assembly. Herein, we firstly explored the molecular mechanisms of self-assembly of short peptides, such as non-modified amino acids, as well as Fmoc-modified, N-functionalized, and C-functionalized peptides. Next, cell penetration, fusion, and peptide targeting in peptide-based drug delivery were characterized. Then, the common administration routes and the potential pharmaceutical applications (drug delivery, antibacterial activity, stabilizers, imaging agents, and applications in bioengineering) of peptide drugs were respectively summarized. Last but not least, some general conclusions and future perspectives in the relevant fields were briefly listed. Although with certain challenges, great opportunities are offered by self-assembled short peptides to the fascinating area of drug development.
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Affiliation(s)
- Shihua Yang
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, China Medical University, Ministry of Education, Shenyang, 110001, China
- Department of Phase I Clinical Trials Center, The First Hospital of China Medical University, Shenyang, 110102, China
| | - Mingge Wang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Tianye Wang
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, China Medical University, Ministry of Education, Shenyang, 110001, China
- Department of Anus and Intestine Surgery, The First Hospital of Dalian Medical University, Dalian, 116000, China
| | - Mengchi Sun
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Hanwei Huang
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, China Medical University, Ministry of Education, Shenyang, 110001, China
- Department of Phase I Clinical Trials Center, The First Hospital of China Medical University, Shenyang, 110102, China
| | - Xianbao Shi
- Department of Pharmacy, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121001, China
| | - Shijie Duan
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, China Medical University, Ministry of Education, Shenyang, 110001, China
- Department of Phase I Clinical Trials Center, The First Hospital of China Medical University, Shenyang, 110102, China
| | - Ying Wu
- Department of Phase I Clinical Trials Center, The First Hospital of China Medical University, Shenyang, 110102, China
| | - Jiaming Zhu
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, China Medical University, Ministry of Education, Shenyang, 110001, China
| | - Funan Liu
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, China Medical University, Ministry of Education, Shenyang, 110001, China
- Department of Phase I Clinical Trials Center, The First Hospital of China Medical University, Shenyang, 110102, China
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18
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Lay CS, Isidro-Llobet A, Kilpatrick LE, Craggs PD, Hill SJ. Characterisation of IL-23 receptor antagonists and disease relevant mutants using fluorescent probes. Nat Commun 2023; 14:2882. [PMID: 37208328 PMCID: PMC10199020 DOI: 10.1038/s41467-023-38541-2] [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: 10/06/2022] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
Association of single nucleotide polymorphisms in the IL-23 receptor with several auto-inflammatory diseases, led to the heterodimeric receptor and its cytokine-ligand IL-23, becoming important drug targets. Successful antibody-based therapies directed against the cytokine have been licenced and a class of small peptide antagonists of the receptor have entered clinical trials. These peptide antagonists may offer therapeutic advantages over existing anti-IL-23 therapies, but little is known about their molecular pharmacology. In this study, we use a fluorescent version of IL-23 to characterise antagonists of the full-length receptor expressed by living cells using a NanoBRET competition assay. We then develop a cyclic peptide fluorescent probe, specific to the IL23p19:IL23R interface and use this molecule to characterise further receptor antagonists. Finally, we use the assays to study the immunocompromising C115Y IL23R mutation, demonstrating that the mechanism of action is a disruption of the binding epitope for IL23p19.
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Affiliation(s)
- Charles S Lay
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Birmingham and Nottingham, The Midlands, UK
- Chemical Biology, Medicine Design, GlaxoSmithKline, Stevenage, SG1 2NY, UK
| | | | - Laura E Kilpatrick
- Centre of Membrane Proteins and Receptors, University of Birmingham and Nottingham, The Midlands, UK
- Division of Bimolecular Science and Medicinal Chemistry, School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Peter D Craggs
- Chemical Biology, Medicine Design, GlaxoSmithKline, Stevenage, SG1 2NY, UK.
- Crick-GSK Biomedical Linklabs, Medicine Design, GlaxoSmithKline, Stevenage, SG1 2NY, UK.
| | - Stephen J Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK.
- Centre of Membrane Proteins and Receptors, University of Birmingham and Nottingham, The Midlands, UK.
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19
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Díaz-Perlas C, Ricken B, Farrera-Soler L, Guschin D, Pojer F, Lau K, Gerhold CB, Heinis C. High-affinity peptides developed against calprotectin and their application as synthetic ligands in diagnostic assays. Nat Commun 2023; 14:2774. [PMID: 37198182 DOI: 10.1038/s41467-023-38075-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
Common inflammatory disorders such as ulcerative colitis and Crohn's disease are non-invasively diagnosed or monitored by the biomarker calprotectin. However, current quantitative tests for calprotectin are antibody-based and vary depending on the type of antibody and assay used. Additionally, the binding epitopes of applied antibodies are not characterized by structures and for most antibodies it is unclear if they detect calprotectin dimer, tetramer, or both. Herein, we develop calprotectin ligands based on peptides, that offer advantages such as homogenous chemical composition, heat-stability, site-directed immobilization, and chemical synthesis at high purity and at low cost. By screening a 100-billion peptide phage display library against calprotectin, we identified a high-affinity peptide (Kd = 26 ± 3 nM) that binds to a large surface region (951 Å2) as shown by X-ray structure analysis. The peptide uniquely binds the calprotectin tetramer, which enabled robust and sensitive quantification of a defined species of calprotectin by ELISA and lateral flow assays in patient samples, and thus offers an ideal affinity reagent for next-generation inflammatory disease diagnostic assays.
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Affiliation(s)
- Cristina Díaz-Perlas
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Benjamin Ricken
- BÜHLMANN Laboratories AG, Baselstrasse 55, CH-4124, Schönenbuch, Switzerland
| | - Lluc Farrera-Soler
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Dmitrii Guschin
- BÜHLMANN Laboratories AG, Baselstrasse 55, CH-4124, Schönenbuch, Switzerland
| | - Florence Pojer
- Protein Production and Structure Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Kelvin Lau
- Protein Production and Structure Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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20
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Speltz TE, Qiao Z, Swenson CS, Shangguan X, Coukos JS, Lee CW, Thomas DM, Santana J, Fanning SW, Greene GL, Moellering RE. Targeting MYC with modular synthetic transcriptional repressors derived from bHLH DNA-binding domains. Nat Biotechnol 2023; 41:541-551. [PMID: 36302987 PMCID: PMC10392954 DOI: 10.1038/s41587-022-01504-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 09/08/2022] [Indexed: 01/16/2023]
Abstract
Despite unequivocal roles in disease, transcription factors (TFs) remain largely untapped as pharmacologic targets due to the challenges in targeting protein-protein and protein-DNA interactions. Here we report a chemical strategy to generate modular synthetic transcriptional repressors (STRs) derived from the bHLH domain of MAX. Our synthetic approach yields chemically stabilized tertiary domain mimetics that cooperatively bind the MYC/MAX consensus E-box motif with nanomolar affinity, exhibit specificity that is equivalent to or beyond that of full-length TFs and directly compete with MYC/MAX protein for DNA binding. A lead STR directly inhibits MYC binding in cells, downregulates MYC-dependent expression programs at the proteome level and inhibits MYC-dependent cell proliferation. Co-crystallization and structure determination of a STR:E-box DNA complex confirms retention of DNA recognition in a near identical manner as full-length bHLH TFs. We additionally demonstrate structure-blind design of STRs derived from alternative bHLH-TFs, confirming that STRs can be used to develop highly specific mimetics of TFs targeting other gene regulatory elements.
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Affiliation(s)
- Thomas E Speltz
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Zeyu Qiao
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Colin S Swenson
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Xianghang Shangguan
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - John S Coukos
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Christopher W Lee
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Deborah M Thomas
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Jesse Santana
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Sean W Fanning
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
- Department of Cancer Biology, Loyola University Chicago, Chicago, IL, USA
| | - Geoffrey L Greene
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, Chicago, IL, USA.
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
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21
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Chaudhary S, Ali Z, Tehseen M, Haney EF, Pantoja-Angles A, Alshehri S, Wang T, Clancy GJ, Ayach M, Hauser C, Hong PY, Hamdan SM, Hancock REW, Mahfouz M. Efficient in planta production of amidated antimicrobial peptides that are active against drug-resistant ESKAPE pathogens. Nat Commun 2023; 14:1464. [PMID: 36928189 PMCID: PMC10020429 DOI: 10.1038/s41467-023-37003-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
Antimicrobial peptides (AMPs) are promising next-generation antibiotics that can be used to combat drug-resistant pathogens. However, the high cost involved in AMP synthesis and their short plasma half-life render their clinical translation a challenge. To address these shortcomings, we report efficient production of bioactive amidated AMPs by transient expression of glycine-extended AMPs in Nicotiana benthamiana line expressing the mammalian enzyme peptidylglycine α-amidating mono-oxygenase (PAM). Cationic AMPs accumulate to substantial levels in PAM transgenic plants compare to nontransgenic N. benthamiana. Moreover, AMPs purified from plants exhibit robust killing activity against six highly virulent and antibiotic resistant ESKAPE pathogens, prevent their biofilm formation, analogous to their synthetic counterparts and synergize with antibiotics. We also perform a base case techno-economic analysis of our platform, demonstrating the potential economic advantages and scalability for industrial use. Taken together, our experimental data and techno-economic analysis demonstrate the potential use of plant chassis for large-scale production of clinical-grade AMPs.
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Affiliation(s)
- Shahid Chaudhary
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Evan F Haney
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Aarón Pantoja-Angles
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Salwa Alshehri
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Biochemistry Department, Faculty of Science, University of Jeddah, Jeddah, 21577, Saudi Arabia
| | - Tiannyu Wang
- Water Desalination and Reuse Center, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Gerard J Clancy
- Analytical Chemistry Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Maya Ayach
- Imaging & Characterization Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Charlotte Hauser
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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22
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Yang Y, Zhou R, Wang Y, Zhang Y, Yu J, Gu Z. Recent Advances in Oral and Transdermal Protein Delivery Systems. Angew Chem Int Ed Engl 2023; 62:e202214795. [PMID: 36478123 DOI: 10.1002/anie.202214795] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Protein and peptide drugs are predominantly administered by injection to achieve high bioavailability, but this greatly compromises patient compliance. Oral and transdermal drug delivery with minimal invasiveness and high adherence represent attractive alternatives to injection administration. However, oral and transdermal administration of bioactive proteins must overcome biological barriers, namely the gastrointestinal and skin barriers, respectively. The rapid development of new materials and technologies promises to address these physiological obstacles. This review provides an overview of the latest advances in oral and transdermal protein delivery, including chemical strategies, synthetic nanoparticles, medical microdevices, and biomimetic systems for oral administration, as well as chemical enhancers, physical approaches, and microneedles in transdermal delivery. We also discuss challenges and future perspectives of the field with a focus on innovation and translation.
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Affiliation(s)
- Yinxian Yang
- Zhejiang Provincial Key Laboratory for Advanced Drug Delivery Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ruyi Zhou
- Zhejiang Provincial Key Laboratory for Advanced Drug Delivery Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanfang Wang
- Zhejiang Provincial Key Laboratory for Advanced Drug Delivery Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yuqi Zhang
- Zhejiang Provincial Key Laboratory for Advanced Drug Delivery Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.,Department of Burns and Wound Center, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Jicheng Yu
- Zhejiang Provincial Key Laboratory for Advanced Drug Delivery Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China.,Jinhua Institute of Zhejiang University, Jinhua, 321299, China.,Department of General Surgery, Sir Run Run Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Zhen Gu
- Zhejiang Provincial Key Laboratory for Advanced Drug Delivery Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China.,Jinhua Institute of Zhejiang University, Jinhua, 321299, China.,Department of General Surgery, Sir Run Run Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.,MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, China
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23
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Yin M, Chen Y, Liu X, Tian S, Zhao L, Bai Y, Wang H, Lin J, Jiang D, Lei Z, Meng F, Tian D, Luo L. Targeted Computed Tomography Visualization and Healing of Inflammatory Bowel Disease by Orally Delivered Bacterial-Flagella-Inspired Polydiiododiacetylene Nanofibers. ACS NANO 2023; 17:3873-3888. [PMID: 36791326 DOI: 10.1021/acsnano.2c12154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Accurate diagnosis and timely therapeutic intervention of inflammatory bowel disease (IBD) is essential in preventing the progression of the disease, although it still represents an insurmountable challenge. Here we report the design of bacterial-flagella-inspired polydiiododiacetylene (PIDA) nanofibers and its performance in targeted computed tomography (CT) imaging and on-demand therapeutic intervention of IBD. With a morphology mimicking bacterial flagella, PIDA nanofibers attach on the mucus layer of the gastrointestinal (GI) tract after oral administration, evenly distributing on the GI surface to portray the GI lining under CT scan within 2 h. PIDA can retain for a longer time in the damaged mucosa at the inflamed lesions than in normal GI tissues to enable the targeted CT visualization of IBD. PIDA also scavenges reactive oxygen species and ameliorates gut dysbiosis attributed to its iodine-substituted polydiacetylene structure, so that the enriched PIDA nanofibers at the targeted IBD lesions can alleviate the inflammation while maintaining the gut microbiota homeostasis, thus promoting the rebalance of GI microenvironment and the mucosal healing.
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Affiliation(s)
- Mingming Yin
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yu Chen
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaoming Liu
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
| | - Sidan Tian
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Liyuan Zhao
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yaowei Bai
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hao Wang
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jinfeng Lin
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Dawei Jiang
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ziqiao Lei
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
| | - Fanling Meng
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - De'an Tian
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Liang Luo
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
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24
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Zhang Y, Guo J, Cheng J, Zhang Z, Kang F, Wu X, Chu Q. High-Throughput Screening of Stapled Helical Peptides in Drug Discovery. J Med Chem 2023; 66:95-106. [PMID: 36580278 DOI: 10.1021/acs.jmedchem.2c01541] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Therapeutic peptides have revolutionized treatment for a number of human diseases. In particular, the past two decades have witnessed rapid progress of stapled helical peptides in drug discovery. Stapled helical peptides are chemically modified and constrained in their bioactive α-helical conformation. Compared to unstabilized linear peptides, stapled helical peptides exhibit superior binding affinity and selectivity, enhanced membrane permeability, and improved metabolic stability, presenting exciting promise for targeting otherwise challenging protein-protein interfaces. In this Perspective, we summarize recent applications of high-throughput screening technologies for identification of potent stapled helical peptides with optimized binding properties. We expect to provide a broad reference to accelerate the development of stapled helical peptides as the next generation of therapeutic peptides for various human diseases.
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Affiliation(s)
- Yiwei Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiabei Guo
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, Nanjing Xiaozhuang University, Nanjing 211171, China
| | - Zhenghua Zhang
- Department of Chemistry, School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Fenghua Kang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Xiaoxing Wu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Qian Chu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
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25
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Mordhorst S, Ruijne F, Vagstad AL, Kuipers OP, Piel J. Emulating nonribosomal peptides with ribosomal biosynthetic strategies. RSC Chem Biol 2023; 4:7-36. [PMID: 36685251 PMCID: PMC9811515 DOI: 10.1039/d2cb00169a] [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: 07/19/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Peptide natural products are important lead structures for human drugs and many nonribosomal peptides possess antibiotic activity. This makes them interesting targets for engineering approaches to generate peptide analogues with, for example, increased bioactivities. Nonribosomal peptides are produced by huge mega-enzyme complexes in an assembly-line like manner, and hence, these biosynthetic pathways are challenging to engineer. In the past decade, more and more structural features thought to be unique to nonribosomal peptides were found in ribosomally synthesised and posttranslationally modified peptides as well. These streamlined ribosomal pathways with modifying enzymes that are often promiscuous and with gene-encoded precursor proteins that can be modified easily, offer several advantages to produce designer peptides. This review aims to provide an overview of recent progress in this emerging research area by comparing structural features common to both nonribosomal and ribosomally synthesised and posttranslationally modified peptides in the first part and highlighting synthetic biology strategies for emulating nonribosomal peptides by ribosomal pathway engineering in the second part.
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Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Fleur Ruijne
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
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26
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Dou Q, Yuan J, Yu R, Yang J, Wang J, Zhu Y, Zhong J, Long H, Liu Z, Wang X, Li Y, Xiao Y, Liang J, Zhang X, Wang Y. MomL inhibits bacterial antibiotic resistance through the starvation stringent response pathway. MLIFE 2022; 1:428-442. [PMID: 38818489 PMCID: PMC10989899 DOI: 10.1002/mlf2.12016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/20/2022] [Accepted: 02/27/2022] [Indexed: 06/01/2024]
Abstract
Antibiotic resistance in gram-negative pathogens has become one of the most serious global public health threats. The role of the N-acyl homoserine lactone (AHL)-mediated signaling pathway, which is widespread in gram-negative bacteria, in the bacterial resistance process should be studied in depth. Here, we report a degrading enzyme of AHLs, MomL, that inhibits the antibiotic resistance of Pseudomonas aeruginosa through a novel mechanism. The MomL-mediated reactivation of kanamycin is highly associated with the relA-mediated starvation stringent response. The degradation of AHLs by MomL results in the inability of LasR to activate relA, which, in turn, stops the activation of downstream rpoS. Further results show that rpoS directly regulates the type VI secretion system H2-T6SS. Under MomL treatment, inactivated RpoS fails to regulate H2-T6SS; therefore, the expression of effector phospholipase A is reduced, and the adaptability of bacteria to antibiotics is weakened. MomL in combination with kanamycin is effective against a wide range of gram-negative pathogenic bacteria. Therefore, this study reports a MomL-antibiotic treatment strategy on antibiotic-resistant bacteria and reveals its mechanism of action.
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Affiliation(s)
- Qin Dou
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Jin Yuan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐Sen UniversityGuangzhouChina
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and PharmacyOcean University of ChinaQingdaoChina
| | - Jiahui Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐Sen UniversityGuangzhouChina
| | - Jiayi Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Yuxiang Zhu
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Jing Zhong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐Sen UniversityGuangzhouChina
| | - Hongan Long
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Zhiqing Liu
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Xianghong Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Yuying Li
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Yichen Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐Sen UniversityGuangzhouChina
| | - Jiazhen Liang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and PharmacyOcean University of ChinaQingdaoChina
| | - Xiao‐Hua Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Ecology and Environmental ScienceQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Yan Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Ecology and Environmental ScienceQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
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27
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Synergetic collision and space separation in microfluidic chip for efficient affinity-discriminated molecular selection. Proc Natl Acad Sci U S A 2022; 119:e2211538119. [PMID: 36191233 PMCID: PMC9565315 DOI: 10.1073/pnas.2211538119] [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: 11/18/2022] Open
Abstract
Efficient molecular selection is a prerequisite for generating molecular tools used in diagnosis, pathology, vaccinology, and therapeutics. Selection efficiency is thermodynamically highly dependent on the dissociation equilibrium that can be reached in a single round. Extreme shifting of equilibrium towards dissociation favors the retention of high-affinity ligands over those with lower affinity, thus improving the selection efficiency. We propose to synergize dual effects by deterministic lateral-displacement microfluidics, including the collision-based force effect and the two-dimensional (2D) separation-based concentration effect, to greatly shift the equilibrium. Compared with previous approaches, this system can remove more low- or moderate-affinity ligands and maintain most high-affinity ligands, thereby improving affinity discrimination in selection. This strategy is demonstrated on phage display in both experiment and simulation, and two peptides against tumor markers ephrin type-A receptor 2 (EphA2) and CD71 were obtained with high affinity and specificity within a single round of selection, which offers a promising direction for discovery of robust binding ligands for a wide range of biomedical applications.
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28
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Truncated Pleurocidin Derivative with High Pepsin Hydrolysis Resistance to Combat Multidrug-Resistant Pathogens. Pharmaceutics 2022; 14:pharmaceutics14102025. [PMID: 36297458 PMCID: PMC9610943 DOI: 10.3390/pharmaceutics14102025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/13/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022] Open
Abstract
The global prevalence of antimicrobial resistance calls for the development of novel antimicrobial agents, particularly for these orally available drugs. Structural modifications of the natural antimicrobial peptides (AMPs) provide a straightforward approach to develop potent antimicrobial agents with high specificity and low toxicity. In this study, we truncated 11-amino-acids at the C-terminus of Pleurocidin, an AMP produced by Pleuronectes americanus, and obtained four peptide analogues termed GK-1, GK-2, GK-3 and GK-4. Minimum inhibitory concentration (MIC) tests showed that GK-1 obtained by direct truncation of Pleurocidin has no antibacterial activity, while GK-2, GK-3 and GK-4 show considerable antibacterial activity with Pleurocidin. Notably, GK-4 displays rapid bacteriostatic activity, great stability and low hemolysis, as well as enhanced hydrolytic resistance to pepsin treatment. Mechanistic studies showed that GK-4 induces membrane damage by interacting with bacterial membrane-specific components, dissipates bacterial membrane potential and promotes the generation of ROS. SEM and CD analysis further confirmed the ability of GK-4 to resist pepsin hydrolysis, which may be attributed to its stable helicity structure. Collectively, our findings reveal that GK-4 is a potential orally available candidate to treat infections caused by multidrug-resistant pathogens.
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29
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Anapindi KDB, Romanova EV, Checco JW, Sweedler JV. Mass Spectrometry Approaches Empowering Neuropeptide Discovery and Therapeutics. Pharmacol Rev 2022; 74:662-679. [PMID: 35710134 DOI: 10.1124/pharmrev.121.000423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The discovery of insulin in the early 1900s ushered in the era of research related to peptides acting as hormones and neuromodulators, among other regulatory roles. These essential gene products are found in all organisms, from the most primitive to the most evolved, and carry important biologic information that coordinates complex physiology and behavior; their misregulation has been implicated in a variety of diseases. The evolutionary origins of at least 30 neuropeptide signaling systems have been traced to the common ancestor of protostomes and deuterostomes. With the use of relevant animal models and modern technologies, we can gain mechanistic insight into orthologous and paralogous endogenous peptides and translate that knowledge into medically relevant insights and new treatments. Groundbreaking advances in medicine and basic science influence how signaling peptides are defined today. The precise mechanistic pathways for over 100 endogenous peptides in mammals are now known and have laid the foundation for multiple drug development pipelines. Peptide biologics have become valuable drugs due to their unique specificity and biologic activity, lack of toxic metabolites, and minimal undesirable interactions. This review outlines modern technologies that enable neuropeptide discovery and characterization, and highlights lessons from nature made possible by neuropeptide research in relevant animal models that is being adopted by the pharmaceutical industry. We conclude with a brief overview of approaches/strategies for effective development of peptides as drugs. SIGNIFICANCE STATEMENT: Neuropeptides, an important class of cell-cell signaling molecules, are involved in maintaining a range of physiological functions. Since the discovery of insulin's activity, over 100 bioactive peptides and peptide analogs have been used as therapeutics. Because these are complex molecules not easily predicted from a genome and their activity can change with subtle chemical modifications, mass spectrometry (MS) has significantly empowered peptide discovery and characterization. This review highlights contributions of MS-based research towards the development of therapeutic peptides.
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Affiliation(s)
- Krishna D B Anapindi
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois (K.D.B.A., E.V.R., J.V.S.) and Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska (J.W.C.)
| | - Elena V Romanova
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois (K.D.B.A., E.V.R., J.V.S.) and Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska (J.W.C.)
| | - James W Checco
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois (K.D.B.A., E.V.R., J.V.S.) and Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska (J.W.C.)
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois (K.D.B.A., E.V.R., J.V.S.) and Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska (J.W.C.)
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30
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Kremsmayr T, Aljnabi A, Blanco-Canosa JB, Tran HNT, Emidio NB, Muttenthaler M. On the Utility of Chemical Strategies to Improve Peptide Gut Stability. J Med Chem 2022; 65:6191-6206. [PMID: 35420805 PMCID: PMC9059125 DOI: 10.1021/acs.jmedchem.2c00094] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Inherent susceptibility
of peptides to enzymatic degradation in
the gastrointestinal tract is a key bottleneck in oral peptide drug
development. Here, we present a systematic analysis of (i) the gut
stability of disulfide-rich peptide scaffolds, orally administered
peptide therapeutics, and well-known neuropeptides and (ii) medicinal
chemistry strategies to improve peptide gut stability. Among a broad
range of studied peptides, cyclotides were the only scaffold class
to resist gastrointestinal degradation, even when grafted with non-native
sequences. Backbone cyclization, a frequently applied strategy, failed
to improve stability in intestinal fluid, but several site-specific
alterations proved efficient. This work furthermore highlights the
importance of standardized gut stability test conditions and suggests
defined protocols to facilitate cross-study comparison. Together,
our results provide a comparative overview and framework for the chemical
engineering of gut-stable peptides, which should be valuable for the
development of orally administered peptide therapeutics and molecular
probes targeting receptors within the gastrointestinal tract.
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Affiliation(s)
- Thomas Kremsmayr
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, Vienna 1090, Austria
| | - Aws Aljnabi
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, Vienna 1090, Austria
| | - Juan B Blanco-Canosa
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, Barcelona 08034, Spain
| | - Hue N T Tran
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Nayara Braga Emidio
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Markus Muttenthaler
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, Vienna 1090, Austria.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
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31
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Li Y, Zhang W, Zhao R, Zhang X. Advances in oral peptide drug nanoparticles for diabetes mellitus treatment. Bioact Mater 2022; 15:392-408. [PMID: 35386357 PMCID: PMC8958389 DOI: 10.1016/j.bioactmat.2022.02.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 12/11/2022] Open
Abstract
Peptide drugs play an important role in diabetes mellitus treatment. Oral administration of peptide drugs is a promising strategy for diabetes mellitus because of its convenience and high patient compliance compared to parenteral administration routes. However, there are a series of formidable unfavorable conditions present in the gastrointestinal (GI) tract after oral administration, which result in the low oral bioavailability of these peptide drugs. To overcome these challenges, various nanoparticles (NPs) have been developed to improve the oral absorption of peptide drugs due to their unique in vivo properties and high design flexibility. This review discusses the unfavorable conditions present in the GI tract and provides the corresponding strategies to overcome these challenges. The review provides a comprehensive overview on the NPs that have been constructed for oral peptide drug delivery in diabetes mellitus treatment. Finally, we will discuss the rational application and give some suggestions that can be utilized for the development of oral peptide drug NPs. Our aim is to provide a systemic and comprehensive review of oral peptide drug NPs that can overcome the challenges in GI tract for efficient treatment of diabetes mellitus. •Oral administration of peptide drugs is a promising strategy for diabetes mellitus treatment •A series of formidable unfavorable conditions in gastrointestinal tract result in the low oral bioavailability of peptide drugs •Nanoparticles can improve the oral bioavailability of peptide drugs
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Affiliation(s)
- Yan Li
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China
| | - Wen Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China
| | - Ruichen Zhao
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China.,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xin Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
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32
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Foundations of gastrointestinal-based drug delivery and future developments. Nat Rev Gastroenterol Hepatol 2022; 19:219-238. [PMID: 34785786 DOI: 10.1038/s41575-021-00539-w] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/07/2021] [Indexed: 12/12/2022]
Abstract
Gastrointestinal-based drug delivery is considered the preferred mode of drug administration owing to its convenience for patients, which improves adherence. However, unique characteristics of the gastrointestinal tract (such as the digestive environment and constraints on transport across the gastrointestinal mucosa) limit the absorption of drugs. As a result, many medications, in particular biologics, still exist only or predominantly in injectable form. In this Review, we examine the fundamentals of gastrointestinal drug delivery to inform clinicians and pharmaceutical scientists. We discuss general principles, including the challenges that need to be overcome for successful drug formulation, and describe the unique features to consider for each gastrointestinal compartment when designing drug formulations for topical and systemic applications. We then discuss emerging technologies that seek to address remaining obstacles to successful gastrointestinal-based drug delivery.
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Lay CS, Bridges A, Goulding J, Briddon SJ, Soloviev Z, Craggs PD, Hill SJ. Probing the binding of interleukin-23 to individual receptor components and the IL-23 heteromeric receptor complex in living cells using NanoBRET. Cell Chem Biol 2022; 29:19-29.e6. [PMID: 34038748 PMCID: PMC8790524 DOI: 10.1016/j.chembiol.2021.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/06/2021] [Accepted: 05/04/2021] [Indexed: 02/07/2023]
Abstract
Interleukin-23 (IL-23) is a pro-inflammatory cytokine involved in the host defense against pathogens but is also implicated in the development of several autoimmune disorders. The IL-23 receptor has become a key target for drug discovery, but the exact mechanism of the receptor ligand interaction remains poorly understood. In this study the affinities of IL-23 for its individual receptor components (IL23R and IL12Rβ1) and the heteromeric complex formed between them have been measured in living cells using NanoLuciferase-tagged full-length proteins. Here, we demonstrate that TAMRA-tagged IL-23 has a greater than 7-fold higher affinity for IL12Rβ1 than IL23R. However, in the presence of both receptor subunits, IL-23 affinity is increased more than three orders of magnitude to 27 pM. Furthermore, we show that IL-23 induces a potent change in the position of the N-terminal domains of the two receptor subunits, consistent with a conformational change in the heteromeric receptor structure.
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Affiliation(s)
- Charles S Lay
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, The Midlands, UK; Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Angela Bridges
- Protein and Cellular Sciences, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Joelle Goulding
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, The Midlands, UK
| | - Stephen J Briddon
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, The Midlands, UK
| | - Zoja Soloviev
- Protein and Cellular Sciences, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Peter D Craggs
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK; GSK-Francis Crick Institute Linklabs, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK.
| | - Stephen J Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, The Midlands, UK.
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34
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Chen K, Tang Y, Wu M, Wan XC, Zhang YN, Chen XX, Yu FQ, Cui ZH, Ma JM, Zhou Z, Fang GM. Head-to-Tail Cross-Linking to Generate Bicyclic Helical Peptides with Enhanced Helicity and Proteolytic Stability. Org Lett 2022; 24:53-57. [PMID: 34894695 DOI: 10.1021/acs.orglett.1c03629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new pattern of a bicyclic helical peptide constructed through head-to-tail cross-linking. The described bicyclic helical peptide has a head-to-tail cross-linking arm and a C-terminal i, i + 4 cross-linking arm. This scaffold will provide a promising scaffold for designing a proteolytically resistant helix-constrained peptide.
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Affiliation(s)
- Kai Chen
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Yang Tang
- Center of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound, Shanghai Tenth People's Hospital, and Ultrasound Research and Education Institute, Clinical Research Center for Interventional Medicine, School of Medicine, Tongji University, Shanghai 200072, P. R. China
| | - Meng Wu
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Xiao-Cui Wan
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Yan-Ni Zhang
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Xiao-Xu Chen
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Fei-Qiang Yu
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Zhi-Hui Cui
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong 518055, P. R. China
| | - Jin-Ming Ma
- School of Life Science, Institute 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, Fudan University, Shanghai 200438, P. R. China
| | - Ge-Min Fang
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
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35
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Plais L, Scheuermann J. Macrocyclic DNA-encoded chemical libraries: a historical perspective. RSC Chem Biol 2022; 3:7-17. [PMID: 35128404 PMCID: PMC8729180 DOI: 10.1039/d1cb00161b] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/19/2021] [Indexed: 12/25/2022] Open
Abstract
While macrocyclic peptides are extensively researched for therapeutically relevant protein targets, DNA-encoded chemical libraries (DELs) are developed at a quick pace to discover novel small molecule binders. The combination of both fields has been explored since 2004 and the number of macrocyclic peptide DELs is steadily increasing. Macrocycles with high affinity and potency were identified for diverse classes of proteins, revealing DEL's huge potential. By giving a historical perspective, we would like to review the methods which permitted the rise of macrocyclic peptide DELs, describe the different DELs which were created and discuss the achievements and challenges of this emerging field.
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Affiliation(s)
- Louise Plais
- Department of Chemistry and Applied Biosciences, ETH Zürich (Swiss Federal Institute of Technology) Vladimir-Prelog-Weg 4 CH-8093 Zürich Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, ETH Zürich (Swiss Federal Institute of Technology) Vladimir-Prelog-Weg 4 CH-8093 Zürich Switzerland
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36
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Clark RJ, Phan TH, Song A, Ouellette AJ, Conibear AC, Rosengren KJ. A conserved β‐bulge glycine residue facilitates folding and increases stability of the mouse α‐defensin cryptdin‐4. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24250] [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)
- Richard J. Clark
- The University of Queensland, School of Biomedical Sciences Brisbane Queensland Australia
| | - Thanh Huyen Phan
- The University of Queensland, School of Biomedical Sciences Brisbane Queensland Australia
| | - Angela Song
- The University of Queensland, School of Biomedical Sciences Brisbane Queensland Australia
| | - André J. Ouellette
- Department of Pathology and Laboratory Medicine and USC Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California Los Angeles California USA
| | - Anne C. Conibear
- The University of Queensland, School of Biomedical Sciences Brisbane Queensland Australia
| | - K. Johan Rosengren
- The University of Queensland, School of Biomedical Sciences Brisbane Queensland Australia
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37
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Patel DK, Menon DV, Patel DH, Dave G. Linkers: A synergistic way for the synthesis of chimeric proteins. Protein Expr Purif 2021; 191:106012. [PMID: 34767950 DOI: 10.1016/j.pep.2021.106012] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 11/15/2022]
Abstract
In the cell, the protein domains are attached with the short oligopeptide, commonly known as linker peptide. Besides bridging, the linker assists in the domain-domain interaction and protein folding into the peculiar conformations. Linkers allow or control the movement of protein domains in the dynamic cellular environment. The recent advances in the recombinant DNA technology enable the construction of multiple gene constructs in an open reading frame. The express sequences can work in a cascade to cater for myriad functions. This trend has given momentum to incorporating bridge sequences (linker) that essentially separates the independent domains. According to the cellular need, the bridging partner can be spaced at a secure gap or requires attaching or interacting physically. The flexible or rigid linker can help to achieve such conformations in chimeric fusion proteins. The linker can improve solubility, proteolytic resistance and stability of such fusion proteins. Recently, linker aided protein switches and antibody-drug conjugates are gaining the attention of researchers worldwide. Here, we thoroughly reviewed the types of the linker, strategies for linker engineering and the composition of a linker.
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Affiliation(s)
- Dharti Keyur Patel
- PD Patel Institute of Applied Sciences, CHARUSAT, Changa, 388421, Gujarat, India
| | - Dhanya V Menon
- Tata Institute of Fundamental Research, NCBS, Bangalore, 560065, India
| | - Darshan H Patel
- Charotar Institute of Paramedical Sciences, CHARUSAT, Changa, 388421, Gujarat, India
| | - Gayatri Dave
- PD Patel Institute of Applied Sciences, CHARUSAT, Changa, 388421, Gujarat, India.
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38
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Georgieva M, Heinonen T, Vitale A, Hargraves S, Causevic S, Pillonel T, Eberl L, Widmann C, Jacquier N. Bacterial surface properties influence the activity of the TAT-RasGAP 317-326 antimicrobial peptide. iScience 2021; 24:102923. [PMID: 34430812 PMCID: PMC8365389 DOI: 10.1016/j.isci.2021.102923] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/05/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance is an increasing threat for public health, underscoring the need for new antibacterial agents. Antimicrobial peptides (AMPs) represent an alternative to classical antibiotics. TAT-RasGAP317-326 is a recently described AMP effective against a broad range of bacteria, but little is known about the conditions that may influence its activity. Using RNA-sequencing and screening of mutant libraries, we show that Escherichia coli and Pseudomonas aeruginosa respond to TAT-RasGAP317-326 by regulating metabolic and stress response pathways, possibly implicating two-component systems. Our results also indicate that bacterial surface properties, in particular integrity of the lipopolysaccharide layer, influence peptide binding and entry. Finally, we found differences between bacterial species with respect to their rate of resistance emergence against this peptide. Our findings provide the basis for future investigation on the mode of action of TAT-RasGAP317-326, which may help developing antimicrobial treatments based on this peptide.
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Affiliation(s)
- Maria Georgieva
- Department of Biomedical Sciences, University of Lausanne, Lausanne 1005, Switzerland
| | - Tytti Heinonen
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
| | - Alessandra Vitale
- Department of Plant and Microbial Biology, University of Zurich, Zurich 8008, Switzerland
| | - Simone Hargraves
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
| | - Senka Causevic
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich 8008, Switzerland
| | - Christian Widmann
- Department of Biomedical Sciences, University of Lausanne, Lausanne 1005, Switzerland
- Corresponding author
| | - Nicolas Jacquier
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
- Corresponding author
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39
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Wicke N, Bedford MR, Howarth M. Gastrobodies are engineered antibody mimetics resilient to pepsin and hydrochloric acid. Commun Biol 2021; 4:960. [PMID: 34381153 PMCID: PMC8358037 DOI: 10.1038/s42003-021-02487-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 07/23/2021] [Indexed: 02/04/2023] Open
Abstract
Protein-based targeting reagents, such as antibodies and non-antibody scaffold proteins, are rapidly inactivated in the upper gastrointestinal (GI) tract. Hydrochloric acid in gastric juice denatures proteins and activates pepsin, concentrations of which reach 1 mg/mL in the mammalian stomach. Two stable scaffold proteins (nanobody and nanofitin), previously developed to be protease-resistant, were completely digested in less than 10 min at 100-fold lower concentration of pepsin than found in the stomach. Here we present gastrobodies, a protein scaffold derived from Kunitz soybean trypsin inhibitor (SBTI). SBTI is highly resistant to the challenges of the upper GI tract, including digestive proteases, pH 2 and bile acids. Computational prediction of SBTI's evolvability identified two nearby loops for randomization, to create a potential recognition surface which was experimentally validated by alanine scanning. We established display of SBTI on full-length pIII of M13 phage. Phage selection of gastrobody libraries against the glucosyltransferase domain of Clostridium difficile toxin B (GTD) identified hits with nanomolar affinity and enzyme inhibitory activity. Anti-GTD binders retained high stability to acid, digestive proteases and heat. Gastrobodies show resilience to exceptionally harsh conditions, which should provide a foundation for targeting and modulating function within the GI tract.
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Affiliation(s)
- Niels Wicke
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford, UK.
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40
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Wong JYK, Mukherjee R, Miao J, Bilyk O, Triana V, Miskolzie M, Henninot A, Dwyer JJ, Kharchenko S, Iampolska A, Volochnyuk DM, Lin YS, Postovit LM, Derda R. Genetically-encoded discovery of proteolytically stable bicyclic inhibitors for morphogen NODAL. Chem Sci 2021; 12:9694-9703. [PMID: 34349940 PMCID: PMC8294009 DOI: 10.1039/d1sc01916c] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/25/2021] [Indexed: 12/19/2022] Open
Abstract
In this manuscript, we developed a two-fold symmetric linchpin (TSL) that converts readily available phage-displayed peptides libraries made of 20 common amino acids to genetically-encoded libraries of bicyclic peptides displayed on phage. TSL combines an aldehyde-reactive group and two thiol-reactive groups; it bridges two side chains of cysteine [C] with an N-terminal aldehyde group derived from the N-terminal serine [S], yielding a novel bicyclic topology that lacks a free N-terminus. Phage display libraries of SX1CX2X3X4X5X6X7C sequences, where X is any amino acid but Cys, were converted to a library of bicyclic TSL-[S]X1[C]X2X3X4X5X6X7[C] peptides in 45 ± 15% yield. Using this library and protein morphogen NODAL as a target, we discovered bicyclic macrocycles that specifically antagonize NODAL-induced signaling in cancer cells. At a 10 μM concentration, two discovered bicyclic peptides completely suppressed NODAL-induced phosphorylation of SMAD2 in P19 embryonic carcinoma cells. The TSL-[S]Y[C]KRAHKN[C] bicycle inhibited NODAL-induced proliferation of NODAL-TYK-nu ovarian carcinoma cells with apparent IC50 of 1 μM. The same bicycle at 10 μM concentration did not affect the growth of the control TYK-nu cells. TSL-bicycles remained stable over the course of the 72 hour-long assays in a serum-rich cell-culture medium. We further observed general stability in mouse serum and in a mixture of proteases (Pronase™) for 21 diverse bicyclic macrocycles of different ring sizes, amino acid sequences, and cross-linker geometries. TSL-constrained peptides to expand the previously reported repertoire of phage-displayed bicyclic architectures formed by cross-linking Cys side chains. We anticipate that it will aid the discovery of proteolytically stable bicyclic inhibitors for a variety of protein targets.
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Affiliation(s)
- Jeffrey Y-K Wong
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Raja Mukherjee
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Jiayuan Miao
- Department of Chemistry, Tufts University Medford MA 02155 USA
| | - Olena Bilyk
- Department of Experimental Oncology, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Vivian Triana
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Mark Miskolzie
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | | | - John J Dwyer
- Ferring Research Institute San Diego California 92121 USA
| | | | - Anna Iampolska
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
| | | | - Yu-Shan Lin
- Department of Chemistry, Tufts University Medford MA 02155 USA
| | - Lynne-Marie Postovit
- Department of Experimental Oncology, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Ratmir Derda
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
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41
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Hong H, Zou Q, Liu Y, Wang S, Shen G, Yan X. Supramolecular Nanodrugs Based on Covalent Assembly of Therapeutic Peptides toward In Vitro Synergistic Anticancer Therapy. ChemMedChem 2021; 16:2381-2385. [PMID: 33908190 DOI: 10.1002/cmdc.202100236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Indexed: 01/07/2023]
Abstract
Therapeutic peptides have attracted significant attention in clinical applications due to their advantages in biological origination and good biocompatibility. However, the therapeutic performance of peptides is usually hindered by their short half-lives in blood and inferior activity. Herein, supramolecular nanodrugs of therapeutic peptides are constructed by covalent assembly of chemotherapeutic peptides through genipin cross-linking. The resulting nanodrugs have intense absorbance in the near-infrared region and high photothermal conversion efficiencies, leading to the possibility of photothermal therapy. The combination of photothermal therapy and chemotherapy using the nanodrugs shows synergistic therapeutic effects on cancer cells. Hence, covalent assembly not only maintains the chemotherapeutic activities of the peptides but also triggers supramolecular photothermal effects, demonstrating that the covalent assembly of therapeutic peptides through genipin cross-linking is an efficient approach in constructing supramolecular nanodrugs toward synergistic anticancer therapy.
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Affiliation(s)
- Huadong Hong
- Anhui Provincial Engineering Research Center for Polysaccharide Drugs Institute of Synthesis and Application of Medical Materials Department of Pharmacy, Wannan Medical College Jinghu, Wuhu, 241001, Anhui, China
| | - Qianli Zou
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.,Center of Advanced Pharmaceuticals and Medical Materials School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Yamei Liu
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Shaozhen Wang
- Anhui Provincial Engineering Research Center for Polysaccharide Drugs Institute of Synthesis and Application of Medical Materials Department of Pharmacy, Wannan Medical College Jinghu, Wuhu, 241001, Anhui, China
| | - Guizhi Shen
- Nanjing IPE Institute of Green Manufacturing Industry, Nanjing, 211135, China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
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42
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Gleeson JP, Fein KC, Whitehead KA. Oral delivery of peptide therapeutics in infants: Challenges and opportunities. Adv Drug Deliv Rev 2021; 173:112-124. [PMID: 33774115 PMCID: PMC8178217 DOI: 10.1016/j.addr.2021.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/09/2021] [Accepted: 03/18/2021] [Indexed: 12/14/2022]
Abstract
The vast majority of drugs are not designed or developed for pediatric and infant populations. Peptide drugs, which have become increasingly relevant in the past several decades, are no exception. Unfortunately, nearly all of the 60+ approved peptide drugs are formulated for injection, a particularly unfriendly mode of administration for infants. Although three peptide drugs were recently approved for oral formulations, this major advance in peptide drug delivery is available only for adults. In this review, we consider the current challenges and opportunities for the oral formulation of peptide therapeutics, specifically for infant populations. We describe the strategies that enable oral protein delivery and the potential impact of infant physiology on those strategies. We also detail the limited but encouraging progress towards 1) adapting conventional drug development and delivery approaches to infants and 2) designing novel infant-centric formulations. Together, these efforts underscore the feasibility of oral peptide delivery in infants and provide motivation to increase attention paid to this underserved area of drug delivery and formulation.
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Affiliation(s)
- John P Gleeson
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Katherine C Fein
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Kathryn A Whitehead
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, United States; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, United States.
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43
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Development and approval of rybelsus (oral semaglutide): ushering in a new era in peptide delivery. Drug Deliv Transl Res 2021; 12:1-6. [PMID: 34024013 DOI: 10.1007/s13346-021-01000-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
Achieving efficacious systemic levels of orally administered peptides is incredibly challenging due to the significant barriers to their bioavailability-their stability in the gastrointestinal tract and challenge of transepithelial transit, and variable pharmacokinetics. Even so, as the generally preferred route of administration, significant research effort in academic and industrial settings has focused on enabling the systemic absorption of orally delivered peptides. Despite several decades of research, few have ever reached the market. The recent approval of Rybelsus® (oral semaglutide) by the FDA [1], the EMA [2], and the Pmda [3] represents a significant landmark in the delivery of therapeutic peptides and is the culmination of more than 30 years research and development of the drug delivery technology enabling the product-Emisphere's Eligen™ technology-and an outstanding commitment to scientific, technical, and clinical innovation by Novo Nordisk. Following years of fundamental and applied research, an innovative clinical strategy led to the aptly named PIONEER clinical programme. This included ten Phase 3 clinical trials that demonstrated the tablet formulation to be as effective as the already approved injectable form of the drug, and more effective than competitor products in terms of its blood glucose lowering effects and weight loss. Not only is this a potentially life changing medicine for diabetic patients, it holds tremendous commercial potential for Novo Nordisk, with some analysts predicting the product to reach $5 billion in peak revenues [3]. In this "Inspirational Note," we summarize some of the public domain work that led to the achievement of this significant milestone and provide commentary on its potential future impact.
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44
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Stevens CA, Bachtiger F, Kong XD, Abriata LA, Sosso GC, Gibson MI, Klok HA. A minimalistic cyclic ice-binding peptide from phage display. Nat Commun 2021; 12:2675. [PMID: 33976148 PMCID: PMC8113477 DOI: 10.1038/s41467-021-22883-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 04/01/2021] [Indexed: 11/09/2022] Open
Abstract
Developing molecules that emulate the properties of naturally occurring ice-binding proteins (IBPs) is a daunting challenge. Rather than relying on the (limited) existing structure-property relationships that have been established for IBPs, here we report the use of phage display for the identification of short peptide mimics of IBPs. To this end, an ice-affinity selection protocol is developed, which enables the selection of a cyclic ice-binding peptide containing just 14 amino acids. Mutational analysis identifies three residues, Asp8, Thr10 and Thr14, which are found to be essential for ice binding. Molecular dynamics simulations reveal that the side chain of Thr10 hydrophobically binds to ice revealing a potential mechanism. To demonstrate the biotechnological potential of this peptide, it is expressed as a fusion ('Ice-Tag') with mCherry and used to purify proteins directly from cell lysate.
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Affiliation(s)
- Corey A Stevens
- Laboratoire des Polymères, Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Fabienne Bachtiger
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK
| | - Xu-Dong Kong
- Laboratory of Therapeutic Proteins and Peptides, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Luciano A Abriata
- Protein Production and Structure Core Facility and Laboratory for Biomolecular Modeling, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gabriele C Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK
| | - Matthew I Gibson
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK.,Warwick Medical School, University of Warwick, Coventry, UK
| | - Harm-Anton Klok
- Laboratoire des Polymères, Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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45
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Carle V, Wu Y, Mukherjee R, Kong XD, Rogg C, Laurent Q, Cecere E, Villequey C, Konakalla MS, Maric T, Lamers C, Díaz-Perlas C, Butler K, Goto J, Stegmayr B, Heinis C. Development of Selective FXIa Inhibitors Based on Cyclic Peptides and Their Application for Safe Anticoagulation. J Med Chem 2021; 64:6802-6813. [PMID: 33974422 DOI: 10.1021/acs.jmedchem.1c00056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Coagulation factor XI (FXI) has emerged as a promising target for the development of safer anticoagulation drugs that limit the risk of severe and life-threatening bleeding. Herein, we report the first cyclic peptide-based FXI inhibitor that selectively and potently inhibits activated FXI (FXIa) in human and animal blood. The cyclic peptide inhibitor (Ki = 2.8 ± 0.5 nM) achieved anticoagulation effects that are comparable to that of the gold standard heparin applied at a therapeutic dose (0.3-0.7 IU/mL in plasma) but with a substantially broader estimated therapeutic range. We extended the plasma half-life of the peptide via PEGylation and demonstrated effective FXIa inhibition over extended periods in vivo. We validated the anticoagulant effects of the PEGylated inhibitor in an ex vivo hemodialysis model with human blood. Our work shows that FXI can be selectively targeted with peptides and provides a promising candidate for the development of a safe anticoagulation therapy.
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Affiliation(s)
- Vanessa Carle
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Yuteng Wu
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Rakesh Mukherjee
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Xu-Dong Kong
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Chloé Rogg
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Quentin Laurent
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Enza Cecere
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Camille Villequey
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Madhuree S Konakalla
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Tamara Maric
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Christina Lamers
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Cristina Díaz-Perlas
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Kaycie Butler
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Junko Goto
- Department of Public Health and Clinical Medicine, University of Umeå, SE-901 87 Umeå, Sweden
| | - Bernd Stegmayr
- Department of Public Health and Clinical Medicine, University of Umeå, SE-901 87 Umeå, Sweden
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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Ekanayake AI, Sobze L, Kelich P, Youk J, Bennett NJ, Mukherjee R, Bhardwaj A, Wuest F, Vukovic L, Derda R. Genetically Encoded Fragment-Based Discovery from Phage-Displayed Macrocyclic Libraries with Genetically Encoded Unnatural Pharmacophores. J Am Chem Soc 2021; 143:5497-5507. [PMID: 33784084 DOI: 10.1021/jacs.1c01186] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genetically encoded macrocyclic peptide libraries with unnatural pharmacophores are valuable sources for the discovery of ligands for many targets of interest. Traditionally, generation of such libraries employs "early stage" incorporation of unnatural building blocks into the chemically or translationally produced macrocycles. Here, we describe a divergent late-stage approach to such libraries starting from readily available starting material: genetically encoded libraries of peptides. A diketone linchpin 1,5-dichloropentane-2,4-dione converts peptide libraries displayed on phage to 1,3-diketone bearing macrocyclic peptides (DKMP): shelf-stable precursors for Knorr pyrazole synthesis. Ligation of diverse hydrazine derivatives onto DKMP libraries displayed on phage that carries silent DNA-barcodes yields macrocyclic libraries in which the amino acid sequence and the pharmacophore are encoded by DNA. Selection of this library against carbonic anhydrase enriched macrocycles with benzenesulfonamide pharmacophore and nanomolar Kd. The methodology described in this manuscript can graft diverse pharmacophores into many existing genetically encoded phage libraries and significantly increase the value of such libraries in molecular discoveries.
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Affiliation(s)
- Arunika I Ekanayake
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Lena Sobze
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Payam Kelich
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Jihea Youk
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Nicholas J Bennett
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Raja Mukherjee
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Atul Bhardwaj
- Cross Cancer Institute, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Frank Wuest
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Cross Cancer Institute, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Lela Vukovic
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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Abstract
The COVID-19, an acute respiratory syndrome caused by SARS-CoV2 is a major catastrophic event of the twenty first century. Relentless efforts for the development of effective pharmaco-therapeutics are in progress but the respite is the development of effective vaccines. However, monotherapy might not always exhibit complete efficacy and may culminate in the rapid evolution of drug-resistant viral strains. Hence, simultaneous modulation of multiple druggable targets not only enhances therapeutic efficacy but also quell the prospects of mutant viruses. Currently, milk peptides have bloomed beyond just being a quintessential part of nutrition to prominent therapeutic implications in human health and diseases. Hence, we have focused on colostrum/milk peptides as they have already been acknowledged for their high potency, target specificity with significantly low or no side effects and bio-toleration. The results presented provide a conceptual strategy for the rational designing of prospective multitargeted peptide inhibitors for SARS-CoV2.
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Abstract
Since the introduction of insulin almost a century ago, more than 80 peptide drugs have reached the market for a wide range of diseases, including diabetes, cancer, osteoporosis, multiple sclerosis, HIV infection and chronic pain. In this Perspective, we summarize key trends in peptide drug discovery and development, covering the early efforts focused on human hormones, elegant medicinal chemistry and rational design strategies, peptide drugs derived from nature, and major breakthroughs in molecular biology and peptide chemistry that continue to advance the field. We emphasize lessons from earlier approaches that are still relevant today as well as emerging strategies such as integrated venomics and peptide-display libraries that create new avenues for peptide drug discovery. We also discuss the pharmaceutical landscape in which peptide drugs could be particularly valuable and analyse the challenges that need to be addressed for them to reach their full potential.
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Li Y, Ji W, Peng H, Zhao R, Zhang T, Lu Z, Yang J, Liu R, Zhang X. Charge-switchable zwitterionic polycarboxybetaine particle as an intestinal permeation enhancer for efficient oral insulin delivery. Am J Cancer Res 2021; 11:4452-4466. [PMID: 33754071 PMCID: PMC7977443 DOI: 10.7150/thno.54176] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/03/2021] [Indexed: 12/24/2022] Open
Abstract
Insulin, a peptide hormone, is one of the most common and effective antidiabetic drugs. Although oral administration is considered to be the most convenient and safe choice for patients, the oral bioavailability of insulin is very low due to the poor oral absorption into blood circulation. Intestinal epithelium is a major barrier for the oral absorption of insulin. Therefore, it is vital to develop intestinal permeation enhancer to increase the antidiabetic efficacy of insulin after oral administration. Methods: Charge-switchable zwitterionic polycarboxybetaine (PCB) was used to load insulin to form PCB/insulin (PCB/INS) particles through the electrostatic interaction between positively charged PCB in pH 5.0 and negatively charged insulin in 0.01 M NaOH. The opening effect of PCB/INS particles on intestinal epithelium was evaluated by detecting the changes of claudin-4 (CLDN4) protein and transepithelial electrical resistance (TEER) after incubation or removal. The mechanism was further elucidated based on the results of Western blot and fluorescence images. The PCB/INS particles were then used for type 1 diabetes mellitus therapy after oral administration. Results: PCB could load insulin with the loading efficiency above 86% at weight ratio of 8:1. PCB/INS particles achieved sustained release of insulin at pH 7.4 due to their charge-switchable ability. Surprisingly, PCB/INS particles induced the open of the tight junctions of intestinal epithelium in endocytosis-mediated lysosomal degradation pathway, which resulted in increased intestinal permeability of insulin. Additionally, the opening effect of PCB/INS particles was reversible, and the decreased expression of CLDN4 protein and TEER values were gradually recovered after particles removal. In streptozotocin-induced type 1 diabetic rats, oral administration of PCB/INS particles with diameter sub-200 nm, especially in capsules, significantly enhanced the bioavailability of insulin and achieved longer duration of hypoglycemic effect than the subcutaneously injected insulin. Importantly, there was no endotoxin and pathological change during treatment, indicating that PCB/INS particles were safe enough for in vivo application. Conclusion: These findings indicate that this system can provide a platform for oral insulin and other protein drugs delivery.
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50
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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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