1
|
Madden SK, Brennan A, Mason JM. A library-derived peptide inhibitor of the BZLF1 transcription factor. J Pept Sci 2024; 30:e3557. [PMID: 38041527 DOI: 10.1002/psc.3557] [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: 04/19/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023]
Abstract
Transcription factor dysregulation is associated with many diseases, including cancer. Peptide-based molecules are increasingly recognised as important modulators of difficult intracellular protein-protein interaction targets, with peptide library screening consequently proven to be a viable strategy in developing inhibitors against a wide range of transcription factors (TFs). However, current strategies simply select the highest affinity of binding to a target TF rather than the ability to inhibit TF function. Here, we utilise our Transcription Block Survival (TBS) screening platform to enable high-throughput identification of peptides that inhibit TFs from binding to cognate DNA sites, hence inhibiting functionality. In this study, we explore whether the TBS can be expanded to derive a potent and functional peptide inhibitor of the BZLF1 transcription factor. The library-derived peptide, AcidicW, is shown to form a more stable dimer with BZLF1 than the BZLF1 homodimer, with a thermal denaturation temperature exceeding 80°C. AcidicW can also functionally inhibit the BZLF1:TRE DNA interaction with high potency and an IC50 of 612 nM.
Collapse
Affiliation(s)
- Sarah K Madden
- Department of Life Sciences, University of Bath, Bath, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Andrew Brennan
- Department of Life Sciences, University of Bath, Bath, UK
| | - Jody M Mason
- Department of Life Sciences, University of Bath, Bath, UK
| |
Collapse
|
2
|
Imai M, Colas K, Suga H. Protein Grafting Techniques: From Peptide Epitopes to Lasso-Grafted Neobiologics. Chempluschem 2024:e202400152. [PMID: 38693599 DOI: 10.1002/cplu.202400152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/03/2024]
Abstract
Protein engineering techniques have vastly expanded their domain of impact, notably following the success of antibodies. Likewise, smaller peptide therapeutics have carved an increasingly significant niche for themselves in the pharmaceutical landscape. The concept of grafting such peptides onto larger protein scaffolds, thus harvesting the advantages of both, has given rise to a variety of protein engineering strategies that are reviewed herein. We also describe our own "Lasso-Grafting" approach, which combines traditional grafting concepts with mRNA display to streamline the production of multiple grafted drug candidates for virtually any target.
Collapse
Affiliation(s)
- Mikio Imai
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kilian Colas
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| |
Collapse
|
3
|
Liu PY, Li G, Lin CB, Wu JJ, Jiang S, Huang FH, Wan X. Modulating DHA-Producing Schizochytrium sp. toward Astaxanthin Biosynthesis via a Seamless Genome Editing System. ACS Synth Biol 2022; 11:4171-4183. [PMID: 36454215 DOI: 10.1021/acssynbio.2c00490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Schizochytrium sp. is commercially used for the production of docosahexaenoic acid (DHA). Some strains of Schizochytrium sp. are also known to produce low amounts of carotenoids, including astaxanthin and β-carotene. In order to enhance the production of astaxanthin in Schizochytrium sp., we established a seamless genome editing system with a dual selection marker for rapid screening of positive transformants. By using this system, we strengthened the endogenous mevalonate pathway, enhanced the supply of geranylgeranyl diphosphate and β-carotene, upregulated endogenous β-carotene hydroxylase, and introduced the algal astaxanthin pathway. The highest astaxanthin production in the engineered Schizochytrium sp. was achieved at 8.1 mg/L (307.1 μg/g dry cell weight) under shake-flask conditions, which was 2.6-fold higher than that in the start strain. Meanwhile, the percentage of DHA to total fatty acids was not obviously affected. We then eliminated the dual selection marker by using the Cre-loxP recombination system, and the engineered strain was ready for iterative editing. The developed system could be applied to seamlessly engineer DHA-producing Schizochytrium sp. toward astaxanthin and other value-added terpenoids, which broadens the application of this strain.
Collapse
Affiliation(s)
- Peng-Yang Liu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Gang Li
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Chu-Bin Lin
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jun-Jie Wu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Shan Jiang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Feng-Hong Huang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China.,Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.,Key Laboratory of Oilseeds processing, Ministry of Agriculture, Wuhan 430062, China
| | - Xia Wan
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China.,Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.,Key Laboratory of Oilseeds processing, Ministry of Agriculture, Wuhan 430062, China
| |
Collapse
|
4
|
Chang MP, Huang W, Mai DJ. Monomer‐scale design of functional protein polymers using consensus repeat sequences. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210506] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Marina P. Chang
- Department of Materials Science and Engineering Stanford University Stanford California USA
| | - Winnie Huang
- Department of Chemical Engineering Stanford University Stanford California USA
| | - Danielle J. Mai
- Department of Chemical Engineering Stanford University Stanford California USA
| |
Collapse
|
5
|
Yin H, Huang YH, Best SA, Sutherland KD, Craik DJ, Wang CK. An Integrated Molecular Grafting Approach for the Design of Keap1-Targeted Peptide Inhibitors. ACS Chem Biol 2021; 16:1276-1287. [PMID: 34152716 DOI: 10.1021/acschembio.1c00388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Inhibiting the Nrf2:Keap1 interaction to trigger cytoprotective gene expression is a promising treatment strategy for oxidative stress-related diseases. A short linear motif from Nrf2 has the potential to directly inhibit this protein-protein interaction, but poor stability and limited cellular uptake impede its therapeutic development. To address these limitations, we utilized an integrated molecular grafting strategy to re-engineer the Nrf2 motif. We combined the motif with an engineered non-native disulfide bond and a cell-penetrating peptide onto a single multifunctionalizable and ultrastable molecular scaffold, namely, the cyclotide MCoTI-II, resulting in the grafted peptide MCNr-2c. The engineered disulfide bond enhanced the conformational rigidity of the motif, resulting in a nanomolar affinity of MCNr-2c for Keap1. The cell-penetrating peptide led to an improved cellular uptake and increased ability to enhance the intracellular expression of two well-described Nrf2-target genes NQO1 and TALDO1. Furthermore, the stability of the scaffold was inherited by the grafted peptide, which became resistant to proteolysis in serum. Overall, we have provided proof-of-concept for a strategy that enables the encapsulation of multiple desired and complementary activities into a single molecular entity to design a Keap1-targeted inhibitor. We propose that this integrated approach could have broad utility for the design of peptide drug leads that require multiple functions and/or biopharmaceutical properties to elicit a therapeutic activity.
Collapse
Affiliation(s)
- Huawu Yin
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sarah A. Best
- ACRF Cancer Biology and Stem Cells Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Kate D. Sutherland
- ACRF Cancer Biology and Stem Cells Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| |
Collapse
|
6
|
Mihara E, Watanabe S, Bashiruddin NK, Nakamura N, Matoba K, Sano Y, Maini R, Yin Y, Sakai K, Arimori T, Matsumoto K, Suga H, Takagi J. Lasso-grafting of macrocyclic peptide pharmacophores yields multi-functional proteins. Nat Commun 2021; 12:1543. [PMID: 33750839 PMCID: PMC7943567 DOI: 10.1038/s41467-021-21875-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/17/2021] [Indexed: 12/27/2022] Open
Abstract
Protein engineering has great potential for devising multifunctional recombinant proteins to serve as next-generation protein therapeutics, but it often requires drastic modifications of the parental protein scaffolds e.g., additional domains at the N/C-terminus or replacement of a domain by another. A discovery platform system, called RaPID (Random non-standard Peptides Integrated Discovery) system, has enabled rapid discovery of small de novo macrocyclic peptides that bind a target protein with high binding specificity and affinity. Capitalizing on the optimized binding properties of the RaPID-derived peptides, here we show that RaPID-derived pharmacophore sequences can be readily implanted into surface-exposed loops on recombinant proteins and maintain both the parental peptide binding function(s) and the host protein function. We refer to this protein engineering method as lasso-grafting and demonstrate that it can endow specific binding capacity toward various receptors into a diverse set of scaffolds that includes IgG, serum albumin, and even capsid proteins of adeno-associated virus, enabling us to rapidly formulate and produce bi-, tri-, and even tetra-specific binder molecules.
Collapse
Affiliation(s)
- Emiko Mihara
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Satoshi Watanabe
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Nasir K Bashiruddin
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nozomi Nakamura
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kyoko Matoba
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Yumi Sano
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Rumit Maini
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yizhen Yin
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Katsuya Sakai
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Takao Arimori
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kunio Matsumoto
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan.
| |
Collapse
|
7
|
Madden SK, Itzhaki LS. Exploring the binding of rationally engineered tandem-repeat proteins to E3 ubiquitin ligase Keap1. Protein Eng Des Sel 2021; 34:gzab027. [PMID: 34882773 PMCID: PMC8660007 DOI: 10.1093/protein/gzab027] [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: 04/15/2021] [Revised: 09/06/2021] [Accepted: 10/04/2021] [Indexed: 11/12/2022] Open
Abstract
The process of displaying functional peptides by 'grafting' them onto loops of a stable protein scaffold can be used to impart binding affinity for a target, but it can be difficult to predict the affinity of the grafted peptide and the effect of grafting on scaffold stability. In this study, we show that a series of peptides that bind to the E3 ubiquitin ligase Keap1 can be grafted into the inter-repeat loop of a consensus-designed tetratricopeptide repeat (CTPR) protein resulting in proteins with high stability. We found that these CTPR-grafted peptides had similar affinities to their free peptide counterparts and achieved a low nanomolar range. This result is likely due to a good structural match between the inter-repeat loop of the CTPR and the Keap1-binding peptide. The grafting process led to the discovery of a new Keap1-binding peptide, Ac-LDPETGELL-NH2, with low nanomolar affinity for Keap1, highlighting the potential of the repeat-protein class for application in peptide display.
Collapse
Affiliation(s)
- Sarah K Madden
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
| |
Collapse
|
8
|
Diamante A, Chaturbedy PK, Rowling PJE, Kumita JR, Eapen RS, McLaughlin SH, de la Roche M, Perez-Riba A, Itzhaki LS. Engineering mono- and multi-valent inhibitors on a modular scaffold. Chem Sci 2021; 12:880-895. [PMID: 33623657 PMCID: PMC7885266 DOI: 10.1039/d0sc03175e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
Here we exploit the simple, ultra-stable, modular architecture of consensus-designed tetratricopeptide repeat proteins (CTPRs) to create a platform capable of displaying both single as well as multiple functions and with diverse programmable geometrical arrangements by grafting non-helical short linear binding motifs (SLiMs) onto the loops between adjacent repeats. As proof of concept, we built synthetic CTPRs to bind and inhibit the human tankyrase proteins (hTNKS), which play a key role in Wnt signaling and are upregulated in cancer. A series of mono-valent and multi-valent hTNKS binders was assembled. To fully exploit the modular scaffold and to further diversify the multi-valent geometry, we engineered the binding modules with two different formats, one monomeric and the other trimeric. We show that the designed proteins are stable, correctly folded and capable of binding to and inhibiting the cellular activity of hTNKS leading to downregulation of the Wnt pathway. Multivalency in both the CTPR protein arrays and the hTNKS target results in the formation of large macromolecular assemblies, which can be visualized both in vitro and in the cell. When delivered into the cell by nanoparticle encapsulation, the multivalent CTPR proteins displayed exceptional activity. They are able to inhibit Wnt signaling where small molecule inhibitors have failed to date. Our results point to the tremendous potential of the CTPR platform to exploit a range of SLiMs and assemble synthetic binding molecules with built-in multivalent capabilities and precise, pre-programmed geometries.
Collapse
Affiliation(s)
- Aurora Diamante
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Piyush K Chaturbedy
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Pamela J E Rowling
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Janet R Kumita
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Rohan S Eapen
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Stephen H McLaughlin
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge Biomedical Campus , Cambridge , CB2 0QH , UK
| | - Marc de la Roche
- Department of Biochemistry , University of Cambridge , Tennis Court Road , Cambridge CB2 1GA , UK
| | - Albert Perez-Riba
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Laura S Itzhaki
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| |
Collapse
|
9
|
Ripka JF, Perez-Riba A, Chaturbedy PK, Itzhaki LS. Testing the length limit of loop grafting in a helical repeat protein. Curr Res Struct Biol 2020; 3:30-40. [PMID: 34235484 PMCID: PMC8244534 DOI: 10.1016/j.crstbi.2020.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/13/2020] [Accepted: 12/02/2020] [Indexed: 11/19/2022] Open
Abstract
Alpha-helical repeat proteins such as consensus-designed tetratricopeptide repeats (CTPRs) are exceptionally stable molecules that are able to tolerate destabilizing sequence alterations and are therefore becoming increasingly valued as a modular platform for biotechnology and biotherapeutic applications. A simple approach to functionalize the CTPR scaffold that we are pioneering is the insertion of short linear motifs (SLiMs) into the loops between adjacent repeats. Here, we test the limits of the scaffold by inserting 17 highly diverse amino acid sequences of up to 58 amino acids in length into a two-repeat protein and examine the impact on protein folding, stability and solubility. The sequences include three SLiMs that bind oncoproteins and eleven naturally occurring linker sequences all predicted to be intrinsically disordered but with conformational preferences ranging from compact globules to expanded coils. We show that the loop-grafted proteins retain the native CTPR structure and are thermally stable with melting temperatures above 60 °C, despite the longest loop sequence being almost the same size as the CTPR scaffold itself (68 amino acids). Although the main determinant of the effect of stability was found to be loop length and was relatively insensitive to amino acid composition, the relationship between protein solubility and the loop sequences was more complex, with the presence of negatively charged amino acids enhancing the solubility. Our findings will help us to fully realize the potential of the repeat-protein scaffold, allowing a rational design approach to create artificial modular proteins with customized functional capabilities.
Collapse
Key Words
- CD, circular dichroism
- CTPRs, consensus-designed tetratricopeptide repeats
- FCR, fraction of charged residues
- IDPs, intrinsically disordered proteins
- IDRs, intrinsically disordered regions
- Intrinsically disordered protein
- Intrinsically disordered region
- NCPR, net charge per residue
- PBIP1, polo-box interacting protein 1
- Peptide grafting
- SLiMs, short linear motifs
- TBP, tankyrase-binding peptides
- Tandem-repeat protein
- Tetratricopeptide repeat
- ves, effective solvation volume
Collapse
Affiliation(s)
- Juliane F. Ripka
- Department of Pharmacology University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | | | - Piyush K. Chaturbedy
- Department of Pharmacology University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Laura S. Itzhaki
- Department of Pharmacology University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| |
Collapse
|
10
|
Madden SK, Itzhaki LS. Structural and mechanistic insights into the Keap1-Nrf2 system as a route to drug discovery. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140405. [PMID: 32120017 DOI: 10.1016/j.bbapap.2020.140405] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 02/11/2020] [Accepted: 02/26/2020] [Indexed: 01/13/2023]
Abstract
The proteins Keap1 and Nrf2 together act as a cytoprotective mechanism that enables cells to overcome electrophilic and oxidative stress. Research has shown that manipulating this system by modulating the Keap1-Nrf2 interaction either through inhibition at the binding interface or via the covalent modification of Keap1 could provide a powerful therapeutic strategy for a range of diseases. However, despite intensive investigation of the system and significant progress in the development of inhibitory small molecules, there is still much to learn about the pathways associated with the Keap1-Nrf2 system and the structural details underpinning its mechanism of action. In this review, we discuss how a deeper understanding could prove revolutionary in the development of new inhibitors and activators as well as guiding how to best harness Keap1 for targeted protein degradation.
Collapse
Affiliation(s)
- Sarah K Madden
- Department of Pharmacology, University of Cambridge, Tennis Court Road, CB2 1PD, United Kingdom
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, CB2 1PD, United Kingdom.
| |
Collapse
|