1
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Schmitz M, Ballestin JB, Liang J, Tomas F, Freist L, Voigt K, Di Ventura B, Öztürk MA. Int&in: A machine learning-based web server for active split site identification in inteins. Protein Sci 2024; 33:e4985. [PMID: 38717278 PMCID: PMC11078102 DOI: 10.1002/pro.4985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/06/2024] [Accepted: 03/24/2024] [Indexed: 05/12/2024]
Abstract
Inteins are proteins that excise themselves out of host proteins and ligate the flanking polypeptides in an auto-catalytic process called protein splicing. In nature, inteins are either contiguous or split. In the case of split inteins, the two fragments must first form a complex for the splicing to occur. Contiguous inteins have previously been artificially split in two fragments because split inteins allow for distinct applications than contiguous ones. Even naturally split inteins have been split at unnatural split sites to obtain fragments with reduced affinity for one another, which are useful to create conditional inteins or to study protein-protein interactions. So far, split sites in inteins have been heuristically identified. We developed Int&in, a web server freely available for academic research (https://intein.biologie.uni-freiburg.de) that runs a machine learning model using logistic regression to predict active and inactive split sites in inteins with high accuracy. The model was trained on a dataset of 126 split sites generated using the gp41-1, Npu DnaE and CL inteins and validated using 97 split sites extracted from the literature. Despite the limited data size, the model, which uses various protein structural features, as well as sequence conservation information, achieves an accuracy of 0.79 and 0.78 for the training and testing sets, respectively. We envision Int&in will facilitate the engineering of novel split inteins for applications in synthetic and cell biology.
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Affiliation(s)
- Mirko Schmitz
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
- 4HF Biotec GmbHFreiburgGermany
| | - Jara Ballestin Ballestin
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
- Bioprocess Innovation Unit, ViraTherapeutics GmbHRumAustria
| | - Junsheng Liang
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
| | - Franziska Tomas
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Leon Freist
- Institute of Biology III, University of FreiburgFreiburgGermany
| | - Karsten Voigt
- Institute of Biology III, University of FreiburgFreiburgGermany
| | - Barbara Di Ventura
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
| | - Mehmet Ali Öztürk
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
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2
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O'Shea JM, Goutou A, Brydon J, Sethna CR, Wood CW, Greiss S. Generation of Photocaged Nanobodies for Intracellular Applications in an Animal Using Genetic Code Expansion and Computationally Guided Protein Engineering. Chembiochem 2022; 23:e202200321. [PMID: 35731601 PMCID: PMC9542635 DOI: 10.1002/cbic.202200321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 11/12/2022]
Abstract
Nanobodies are becoming increasingly popular as tools for manipulating and visualising proteins in vivo. The ability to control nanobody/antigen interactions using light could provide precise spatiotemporal control over protein function. We develop a general approach to engineer photo-activatable nanobodies using photocaged amino acids that are introduced into the target binding interface by genetic code expansion. Guided by computational alanine scanning and molecular dynamics simulations, we tune nanobody/target binding affinity to eliminate binding before uncaging. Upon photo-activation using 365 nm light, binding is restored. We use this approach to generate improved photocaged variants of two anti-GFP nanobodies that function robustly when directly expressed in a complex intracellular environment together with their antigen. We apply them to control subcellular protein localisation in the nematode worm Caenorhabditis elegans. Our approach applies predictions derived from computational modelling directly in a living animal and demonstrates the importance of accounting for in vivo effects on protein-protein interactions.
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Affiliation(s)
- Jack M. O'Shea
- Centre for Discovery Brain SciencesUniversity of Edinburgh, Hugh Robson Building George SquareEdinburghEH8 9XDUK
| | - Angeliki Goutou
- Centre for Discovery Brain SciencesUniversity of Edinburgh, Hugh Robson Building George SquareEdinburghEH8 9XDUK
| | - Jack Brydon
- MRC Institute of Genetics & Molecular MedicineUniversity of Edinburgh, Western General Hospital Crewe Road SouthEdinburghEH4 2XRUK
| | - Cyrus R. Sethna
- Centre for Discovery Brain SciencesUniversity of Edinburgh, Hugh Robson Building George SquareEdinburghEH8 9XDUK
| | - Christopher W. Wood
- Institute of Quantitative Biology, Biochemistry and BiotechnologyUniversity of Edinburgh, Roger Land Building King's BuildingsEdinburghEH9 3JQUK
| | - Sebastian Greiss
- Centre for Discovery Brain SciencesUniversity of Edinburgh, Hugh Robson Building George SquareEdinburghEH8 9XDUK
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3
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Li Z, Li W, Wang Y, Chen Z, Nakanishi H, Xu X, Gao XD. Establishment of a Novel Cell Surface Display Platform Based on Natural "Chitosan Beads" of Yeast Spores. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7479-7489. [PMID: 35678723 DOI: 10.1021/acs.jafc.2c01983] [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: 06/15/2023]
Abstract
Cell surface display technology, which expresses and anchors proteins on the surface of microbial cells, has broad application prospects in many fields, such as protein library screening, biocatalysis, and biosensor development. However, traditional cell surface display systems have disadvantages: the molecular weight of phage display proteins cannot be too large; bacterial display lacks the post-translational modification process for eukaryotic proteins; yeast display is prone to excessive protein glycosylation and misfolding of multisubunit proteins; and the compatibility of Bacillus subtilis spore display needs to be further improved. Therefore, it is extremely valuable to develop an efficient surface display platform with strong universality and stress resistance properties. Although yeast surface display systems have been extensively investigated, the establishment of a surface display platform using yeast spores has rarely been reported. In this study, a novel cell surface display platform based on natural "chitosan beads" of yeast spores was developed. The target protein in fusion with the chitosan affinity protein (CAP) exhibited strong binding capability with "chitosan beads" of yeast spores in vitro and in vivo. Moreover, this protein display system showed highly preferable enzymatic properties and stability. As an example, the displayed LXYL-P1-2-CAP demonstrated high thermostability and reusability (60% of the initial activity after seven cycles of reuse), high storage stability (75% of original activity after 8 weeks), and excellent tolerance to a concentration up to 75% (v/v) organic reagents. To prove the practicability of this surface display system, the semisynthesis of paclitaxel intermediate was demonstrated and its highest conversion rate was 92% using 0.25 mM substrate. This study provides a novel and useful platform for the surface display of proteins, especially for multimeric macromolecular proteins of eukaryotic origin.
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Affiliation(s)
- Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Wanjie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Yasen Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zhou Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Xiangyang Xu
- Zaozhuang Jienuo Enzyme Co., Ltd., Zaozhuang 277100, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
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4
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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: 15] [Impact Index Per Article: 7.5] [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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5
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Preparation of Bacterial Cell-Surface Displayed Semisynthetic Cyclic Peptides. Methods Mol Biol 2021. [PMID: 34596850 DOI: 10.1007/978-1-0716-1689-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Semisynthetic cyclic peptides bearing both non-proteinogenic and genetically encoded amino acids are excellent ligands for peptide-based drug discovery. While semisynthesis expands the chemical space, genetic encoding allows access to a large library via randomization at the nucleic acid level. Selection of novel binders of such macrocyclic ligands requires linking their genotype to phenotype. In this chapter, we report a bacterial cell-surface display system to present cyclic peptides composed of synthetic and genetically encoded fragments. The synthetic fragment along with the split intein partner and an aminooxy moiety is ligated and cyclized with the recombinant backbone containing an unnatural amino acid by protein trans-splicing and intramolecular oxime ligation, respectively. A pH-shift protocol was applied to accelerate on surface cyclization. This method will enable generation of semisynthetic cyclic peptide libraries and their selection by fluorescence-activated cell sorting.
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Khursheed A, Jain V, Rasool A, Rather MA, Malik NA, Shalla AH. Molecular scaffolds from mother nature as possible lead compounds in drug design and discovery against coronaviruses: A landscape analysis of published literature and molecular docking studies. Microb Pathog 2021; 157:104933. [PMID: 33984466 PMCID: PMC8110334 DOI: 10.1016/j.micpath.2021.104933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/13/2021] [Accepted: 04/28/2021] [Indexed: 12/23/2022]
Abstract
The recent outbreak of viral infection and its transmission has highlighted the importance of its slowdown for the safeguard of public health, globally. The identification of novel drugs and efficient therapies against these infectious viruses is need of the hour. The eruption of COVID-19 is caused by a novel acute respiratory syndrome virus SARS-CoV-2 which has taken the whole world by storm as it has transformed into a global pandemic. This lethal syndrome is a global health threat to general public which has already affected millions of people. Despite the development of some potential vaccines and repurposed drugs by some Pharma companies, this health emergency needs more attention due to the less efficacy of these vaccines coupled with the emergence of novel and resistant strains of SARS-CoV-2. Due to enormous structural diversity and biological applications, natural products are considered as a wonderful source of drugs for such diseases. Natural product based drugs constitute a substantial proportion of the pharmaceutical market particularly in the therapeutic areas of infectious diseases and oncology. The naturally occurring bioactive antiviral phytochemicals including alkaloids, flavonoids and peptides have been subjected to virtual screening against COVID-19. Since there is no specific medicine available for the treatment of Covid-19, designing new drugs using in silico methods plays an all important role to find that magic bullet which can target this lethal virus. The in silico method is not only quick but economical also when compared to the other conventional methods which are hit and trial methods. Based on this in silico approach, various natural products have been recently identified which might have a potential to inhibit COVID-19 outbreak. These natural products have been shown by these docking studies to interact with the spike protein of the novel coronavirus. This spike protein has been shown to bind to a transmembrane protein called Angiotensin converting enzyme 2 (ACE2), this protein acts as a receptor for the viral spike protein. This comprehensive review article anticipates providing a summary of the authentic and peer reviewed published literature about the potential of natural metabolites that can be developed into possible lead compounds against this new threat of Covid-19. Main focus of the article will be to highlight natural sources of potential anti-coronavirus molecules, mechanism of action, docking studies and the target proteins as well as their toxicity profiles. This review article intends to provide a starting point for the research endeavors that are needed for the design and development of drugs based on pure natural products, their synthetic or semi-synthetic derivatives and standardized plant extracts. This review article will be highly helpful for scientists who are working or intend to work on antiviral drugs from natural sources.
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Affiliation(s)
- Aadil Khursheed
- Department of Chemistry, Madhyanchal Professional University, Ratibad, Bhopal, 462044, Madhya Pradesh, India
| | - Vikrant Jain
- Department of Chemistry, Madhyanchal Professional University, Ratibad, Bhopal, 462044, Madhya Pradesh, India
| | - Ajaz Rasool
- Department of Zoology, University of Kashmir, Srinagar, 190006, India
| | - Manzoor A Rather
- Department of Chemistry, Islamic University of Science and Technology, Awanti Pora, 192122, Jammu and Kashmir, India.
| | - Nisar Ahmad Malik
- Department of Chemistry, Islamic University of Science and Technology, Awanti Pora, 192122, Jammu and Kashmir, India
| | - Aabid Hussain Shalla
- Department of Chemistry, Islamic University of Science and Technology, Awanti Pora, 192122, Jammu and Kashmir, India
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7
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Iskandar SE, Haberman VA, Bowers AA. Expanding the Chemical Diversity of Genetically Encoded Libraries. ACS COMBINATORIAL SCIENCE 2020; 22:712-733. [PMID: 33167616 PMCID: PMC8284915 DOI: 10.1021/acscombsci.0c00179] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The power of ribosomes has increasingly been harnessed for the synthesis and selection of molecular libraries. Technologies, such as phage display, yeast display, and mRNA display, effectively couple genotype to phenotype for the molecular evolution of high affinity epitopes for many therapeutic targets. Genetic code expansion is central to the success of these technologies, allowing researchers to surpass the intrinsic capabilities of the ribosome and access new, genetically encoded materials for these selections. Here, we review techniques for the chemical expansion of genetically encoded libraries, their abilities and limits, and opportunities for further development. Importantly, we also discuss methods and metrics used to assess the efficiency of modification and library diversity with these new techniques.
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Affiliation(s)
- Sabrina E Iskandar
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Victoria A Haberman
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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8
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Morse JS, Lalonde T, Xu S, Liu WR. Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019-nCoV. Chembiochem 2020; 21:730-738. [PMID: 32022370 PMCID: PMC7162020 DOI: 10.1002/cbic.202000047] [Citation(s) in RCA: 495] [Impact Index Per Article: 123.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Indexed: 11/08/2022]
Abstract
With the current trajectory of the 2019-nCoV outbreak unknown, public health and medicinal measures will both be needed to contain spreading of the virus and to optimize patient outcomes. Although little is known about the virus, an examination of the genome sequence shows strong homology with its better-studied cousin, SARS-CoV. The spike protein used for host cell infection shows key nonsynonymous mutations that might hamper the efficacy of previously developed therapeutics but remains a viable target for the development of biologics and macrocyclic peptides. Other key drug targets, including RNA-dependent RNA polymerase and coronavirus main proteinase (3CLpro), share a strikingly high (>95 %) homology to SARS-CoV. Herein, we suggest four potential drug candidates (an ACE2-based peptide, remdesivir, 3CLpro-1 and a novel vinylsulfone protease inhibitor) that could be used to treat patients suffering with the 2019-nCoV. We also summarize previous efforts into drugging these targets and hope to help in the development of broad-spectrum anti-coronaviral agents for future epidemics.
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Affiliation(s)
- Jared S. Morse
- The Texas A&M Drug Discovery LaboratoryDepartment of ChemistryTexas A&M UniversityCollege StationTX77843USA
| | - Tyler Lalonde
- The Texas A&M Drug Discovery LaboratoryDepartment of ChemistryTexas A&M UniversityCollege StationTX77843USA
| | - Shiqing Xu
- The Texas A&M Drug Discovery LaboratoryDepartment of ChemistryTexas A&M UniversityCollege StationTX77843USA
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery LaboratoryDepartment of ChemistryTexas A&M UniversityCollege StationTX77843USA
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9
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Morse JS, Lalonde T, Xu S, Liu W. Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019-nCoV. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020. [PMID: 32511285 DOI: 10.26434/chemrxiv.11728983.v1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
With the current trajectory of the 2019-nCoV outbreak unknown, public health and medicinal measures will both be needed to contain spreading of the virus and to optimize patient outcomes. While little is known about the virus, an examination of the genome sequence shows strong homology with its more well-studied cousin, SARS-CoV. The spike protein used for host cell infection shows key nonsynonymous mutations which may hamper efficacy of previously developed therapeutics but remains a viable target for the development of biologics and macrocyclic peptides. Other key drug targets, including RdRp and 3CLpro, share a strikingly high (>95%) homology to SARS-CoV. Herein, we suggest 4 potential drug candidates (an ACE2-based peptide, remdesivir, 3CLpro-1 and a novel vinylsulfone protease inhibitor) that can be used to treat patients suffering with the 2019-nCoV. We also summarize previous efforts into drugging these targets and hope to help in the development of broad spectrum anti-coronaviral agents for future epidemics.
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10
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Morse JS, Lalonde T, Xu S, Liu WR. Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019-nCoV. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:11728983. [PMID: 32511285 PMCID: PMC7251965 DOI: 10.26434/chemrxiv.11728983] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Revised: 01/27/2020] [Indexed: 01/06/2023]
Abstract
With the current trajectory of the 2019-nCoV outbreak unknown, public health and medicinal measures will both be needed to contain spreading of the virus and to optimize patient outcomes. While little is known about the virus, an examination of the genome sequence shows strong homology with its more well-studied cousin, SARS-CoV. The spike protein used for host cell infection shows key nonsynonymous mutations which may hamper efficacy of previously developed therapeutics but remains a viable target for the development of biologics and macrocyclic peptides. Other key drug targets, including RdRp and 3CLpro, share a strikingly high (>95%) homology to SARS-CoV. Herein, we suggest 4 potential drug candidates (an ACE2-based peptide, remdesivir, 3CLpro-1 and a novel vinylsulfone protease inhibitor) that can be used to treat patients suffering with the 2019-nCoV. We also summarize previous efforts into drugging these targets and hope to help in the development of broad spectrum anti-coronaviral agents for future epidemics.
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Affiliation(s)
- Jared S. Morse
- The Texas A&M Drug Discovery Laboratory, Department of
Chemistry, Texas A&M University, College Station, Texas 77843, United
States
| | - Tyler Lalonde
- The Texas A&M Drug Discovery Laboratory, Department of
Chemistry, Texas A&M University, College Station, Texas 77843, United
States
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory, Department of
Chemistry, Texas A&M University, College Station, Texas 77843, United
States
| | - Wenshe R. Liu
- The Texas A&M Drug Discovery Laboratory, Department of
Chemistry, Texas A&M University, College Station, Texas 77843, United
States
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11
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Jedlitzke B, Yilmaz Z, Dörner W, Mootz HD. Photobodies: Light-Activatable Single-Domain Antibody Fragments. Angew Chem Int Ed Engl 2020; 59:1506-1510. [PMID: 31755215 PMCID: PMC7004160 DOI: 10.1002/anie.201912286] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/19/2019] [Indexed: 12/16/2022]
Abstract
Photocaged antibody fragments, termed photobodies, have been developed that are impaired in their antigen-binding capacity and can be activated by irradiation with UV light (365 nm). This rational design concept builds on the selective photocaging of a single tyrosine in a nanobody (a single-domain antibody fragment). Tyrosine is a frequently occurring residue in central positions of the paratope region. o-Nitrobenzyl-protected tyrosine variants were incorporated into four nanobodies, including examples directed against EGFR and HER2, and photodeprotection restores the native sequence. An anti-GFP photobody exhibited an at least 10 000-fold impaired binding affinity before photodeprotection compared with the parent nanobody. A bispecific nanobody-photobody fusion protein was generated to trigger protein heterodimerization by light. Photoactivatable antibodies are expected to become versatile protein reagents and to enable novel approaches in diagnostic and therapeutic applications.
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Affiliation(s)
- Benedikt Jedlitzke
- Institute of BiochemistryDepartment of Chemistry and PharmacyUniversity of MuensterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Zahide Yilmaz
- Institute of BiochemistryDepartment of Chemistry and PharmacyUniversity of MuensterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Wolfgang Dörner
- Institute of BiochemistryDepartment of Chemistry and PharmacyUniversity of MuensterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Henning D. Mootz
- Institute of BiochemistryDepartment of Chemistry and PharmacyUniversity of MuensterWilhelm-Klemm-Str. 248149MünsterGermany
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12
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Jedlitzke B, Yilmaz Z, Dörner W, Mootz HD. Photobodies: Light‐Activatable Single‐Domain Antibody Fragments. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201912286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Benedikt Jedlitzke
- Institute of Biochemistry Department of Chemistry and Pharmacy University of Muenster Wilhelm-Klemm-Str. 2 48149 Münster Germany
| | - Zahide Yilmaz
- Institute of Biochemistry Department of Chemistry and Pharmacy University of Muenster Wilhelm-Klemm-Str. 2 48149 Münster Germany
| | - Wolfgang Dörner
- Institute of Biochemistry Department of Chemistry and Pharmacy University of Muenster Wilhelm-Klemm-Str. 2 48149 Münster Germany
| | - Henning D. Mootz
- Institute of Biochemistry Department of Chemistry and Pharmacy University of Muenster Wilhelm-Klemm-Str. 2 48149 Münster Germany
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13
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Wang XS, Chen PC, Hampton JT, Tharp JM, Reed CA, Das SK, Wang D, Hayatshahi HS, Shen Y, Liu J, Liu WR. A Genetically Encoded, Phage‐Displayed Cyclic‐Peptide Library. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - J. Trae Hampton
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Jeffery M. Tharp
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Catrina A. Reed
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Sukant K. Das
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Duen‐Shian Wang
- Department of Pharmaceutical Sciences UNT Health Science Center Fort Worth TX 76107 USA
| | - Hamed S. Hayatshahi
- Department of Pharmaceutical Sciences UNT Health Science Center Fort Worth TX 76107 USA
| | - Yang Shen
- Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843-3218 USA
| | - Jin Liu
- Department of Pharmaceutical Sciences UNT Health Science Center Fort Worth TX 76107 USA
| | - Wenshe Ray Liu
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
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14
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Wang XS, Chen PHC, Hampton JT, Tharp JM, Reed CA, Das SK, Wang DS, Hayatshahi HS, Shen Y, Liu J, Liu WR. A Genetically Encoded, Phage-Displayed Cyclic-Peptide Library. Angew Chem Int Ed Engl 2019; 58:15904-15909. [PMID: 31398275 PMCID: PMC6803038 DOI: 10.1002/anie.201908713] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 11/10/2022]
Abstract
Superior to linear peptides in biological activities, cyclic peptides are considered to have great potential as therapeutic agents. To identify cyclic-peptide ligands for therapeutic targets, phage-displayed peptide libraries in which cyclization is achieved by the covalent conjugation of cysteines have been widely used. To resolve drawbacks related to cysteine conjugation, we have invented a phage-display technique in which its displayed peptides are cyclized through a proximity-driven Michael addition reaction between a cysteine and an amber-codon-encoded Nϵ -acryloyl-lysine (AcrK). Using a randomized 6-mer library in which peptides were cyclized at two ends through a cysteine-AcrK linker, we demonstrated the successful selection of potent ligands for TEV protease and HDAC8. All selected cyclic peptide ligands showed 4- to 6-fold stronger affinity to their protein targets than their linear counterparts. We believe this approach will find broad applications in drug discovery.
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Affiliation(s)
- Xiaoshan Shayna Wang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Peng-Hsun Chase Chen
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - J Trae Hampton
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Jeffery M Tharp
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Catrina A Reed
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Sukant K Das
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Duen-Shian Wang
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Hamed S Hayatshahi
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843-3218, USA
| | - Jin Liu
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Wenshe Ray Liu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
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15
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A mesophilic cysteine-less split intein for protein trans-splicing applications under oxidizing conditions. Proc Natl Acad Sci U S A 2019; 116:22164-22172. [PMID: 31611397 DOI: 10.1073/pnas.1909825116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Split intein-mediated protein trans-splicing has found extensive applications in chemical biology, protein chemistry, and biotechnology. However, an enduring limitation of all well-established split inteins has been the requirement to carry out the reaction in a reducing environment due to the presence of 1 or 2 catalytic cysteines that need to be in a reduced state for splicing to occur. The concomitant exposure of the fused proteins to reducing agents severely limits the scope of protein trans-splicing by excluding proteins sensitive to reducing conditions, such as those containing critical disulfide bonds. Here we report the discovery, characterization, and engineering of a completely cysteine-less split intein (CL intein) that is capable of efficient trans-splicing at ambient temperatures, without a denaturation step, and in the absence of reducing agents. We demonstrate its utility for the site-specific chemical modification of nanobodies and an antibody Fc fragment by N- and C-terminal trans-splicing with short peptide tags (CysTag) that consist of only a few amino acids and have been prelabeled on a single cysteine using classical cysteine bioconjugation. We also synthesized the short N-terminal fragment of the atypically split CL intein by solid-phase peptide synthesis. Furthermore, using the CL intein in combination with a nanobody-epitope pair as a high-affinity mediator, we showed chemical labeling of the extracellular domain of a cell surface receptor on living mammalian cells with a short CysTag containing a synthetic fluorophore. The CL intein thus greatly expands the scope of applications for protein trans-splicing.
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16
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Bosma T, Rink R, Moosmeier MA, Moll GN. Genetically Encoded Libraries of Constrained Peptides. Chembiochem 2019; 20:1754-1758. [PMID: 30794341 DOI: 10.1002/cbic.201900031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Indexed: 02/01/2023]
Abstract
Many therapeutic peptides can still be improved with respect to target specificity, target affinity, resistance to peptidases/proteases, physical stability, and capacity to pass through membranes required for oral delivery. Several modifications can improve the peptides' properties, in particular those that impose (a) conformational constraint(s). Screening of constrained peptides and the identification of hits is greatly facilitated by the generation of genetically encoded libraries. Recent breakthrough bacterial, phage, and yeast display screening systems of ribosomally synthesized post-translationally constrained peptides, particularly those of lanthipeptides, are earning special attention. Here we provide an overview of display systems for constrained, genetically encoded peptides and indicate prospects of constrained peptide-displaying phage and bacterial systems as such in vivo.
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Affiliation(s)
- Tjibbe Bosma
- Lanthio Pharma, a MorphoSys AG Company, Rozenburglaan 13B, 9727 DL, Groningen, The Netherlands
| | - Rick Rink
- Lanthio Pharma, a MorphoSys AG Company, Rozenburglaan 13B, 9727 DL, Groningen, The Netherlands
| | | | - Gert N Moll
- Lanthio Pharma, a MorphoSys AG Company, Rozenburglaan 13B, 9727 DL, Groningen, The Netherlands.,Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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