1
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Wang X, Ma S, Bai Y, Wu X, Ji F, Jia L. AQP4-DARPin1: A Chimeric Antigen Based on Scaffold Protein DARPin for Efficient Detection of AQP4-IgG in NMOSD. Biochemistry 2024; 63:855-864. [PMID: 38498694 DOI: 10.1021/acs.biochem.3c00688] [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: 03/20/2024]
Abstract
AQP4-IgG is an autoantibody associated with neuromyelitis optica spectroscopic disorder (NMOSD), a central nervous system inflammatory disease that requires early diagnosis and treatment. We designed two fusion proteins, AQP4-DARPin1 and AQP4-DARPin2, comprising the complete antigenic epitopes of aquaporin-4 (AQP4) and the constant region of the scaffold protein DARPin. These fusion proteins were expressed and purified from Escherichia coli and coated on microplates to develop an efficient method for detecting AQP4-IgG. Molecular dynamics simulation revealed that the fusion of AQP4 extracellular epitopes with DARPin did not alter the main structure of DARPin. The purified AQP4-DARPins bound recombinant antibody rAb-53 (AQP4-IgG) with affinities of 135 and 285 nM, respectively. Enzyme-linked immunosorbent assay (ELISA) and immunoprecipitation demonstrated that AQP4-DARPin1 specifically recognized AQP4-IgG in the NMOSD patient serum. AQP4-DARPin1 as a coated antigen showed higher ELISA signal and end point dilution ratio than full-length AQP4. Our AQP4-DARPin1-coated AQP4-IgG ELISA had 100% specificity and 90% sensitivity. These results indicate that AQP4-DARPin1, compared to existing detection strategies that use full-length or extracellular loop peptides of AQP4, provides a new and more effective approach to the ELISA detection of NMOSD.
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Affiliation(s)
- Xiaofei Wang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Shubei Ma
- Department of Neurology, Dalian Municipal Central Hospital, Dalian 116000, P. R. China
| | - Ying Bai
- Department of Neurology, Dalian University Affiliated Xinhua Hospital, Dalian 116021, P. R. China
| | - Xinyang Wu
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China
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2
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Kolesnik VV, Nurtdinov RF, Oloruntimehin ES, Karabelsky AV, Malogolovkin AS. Optimization strategies and advances in the research and development of AAV-based gene therapy to deliver large transgenes. Clin Transl Med 2024; 14:e1607. [PMID: 38488469 PMCID: PMC10941601 DOI: 10.1002/ctm2.1607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 03/18/2024] Open
Abstract
Adeno-associated virus (AAV)-based therapies are recognized as one of the most potent next-generation treatments for inherited and genetic diseases. However, several biological and technological aspects of AAV vectors remain a critical issue for their widespread clinical application. Among them, the limited capacity of the AAV genome significantly hinders the development of AAV-based gene therapy. In this context, genetically modified transgenes compatible with AAV are opening up new opportunities for unlimited gene therapies for many genetic disorders. Recent advances in de novo protein design and remodelling are paving the way for new, more efficient and targeted gene therapeutics. Using computational and genetic tools, AAV expression cassette and transgenic DNA can be split, miniaturized, shuffled or created from scratch to mediate efficient gene transfer into targeted cells. In this review, we highlight recent advances in AAV-based gene therapy with a focus on its use in translational research. We summarize recent research and development in gene therapy, with an emphasis on large transgenes (>4.8 kb) and optimizing strategies applied by biomedical companies in the research pipeline. We critically discuss the prospects for AAV-based treatment and some emerging challenges. We anticipate that the continued development of novel computational tools will lead to rapid advances in basic gene therapy research and translational studies.
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Affiliation(s)
- Valeria V. Kolesnik
- Martsinovsky Institute of Medical ParasitologyTropical and Vector‐Borne Diseases, Sechenov UniversityMoscowRussia
| | - Ruslan F. Nurtdinov
- Martsinovsky Institute of Medical ParasitologyTropical and Vector‐Borne Diseases, Sechenov UniversityMoscowRussia
| | - Ezekiel Sola Oloruntimehin
- Martsinovsky Institute of Medical ParasitologyTropical and Vector‐Borne Diseases, Sechenov UniversityMoscowRussia
| | | | - Alexander S. Malogolovkin
- Martsinovsky Institute of Medical ParasitologyTropical and Vector‐Borne Diseases, Sechenov UniversityMoscowRussia
- Center for Translational MedicineSirius University of Science and TechnologySochiRussia
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3
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Paurević M, Šrajer Gajdošik M, Ribić R. Mannose Ligands for Mannose Receptor Targeting. Int J Mol Sci 2024; 25:1370. [PMID: 38338648 PMCID: PMC10855088 DOI: 10.3390/ijms25031370] [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: 12/14/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
The mannose receptor (MR, CD 206) is an endocytic receptor primarily expressed by macrophages and dendritic cells, which plays a critical role in both endocytosis and antigen processing and presentation. MR carbohydrate recognition domains (CRDs) exhibit a high binding affinity for branched and linear oligosaccharides. Furthermore, multivalent mannose presentation on the various templates like peptides, proteins, polymers, micelles, and dendrimers was proven to be a valuable approach for the selective and efficient delivery of various therapeutically active agents to MR. This review provides a detailed account of the most relevant and recent aspects of the synthesis and application of mannosylated bioactive formulations for MR-mediated delivery in treatments of cancer and other infectious diseases. It further highlights recent findings related to the necessary structural features of the mannose-containing ligands for successful binding to the MR.
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Affiliation(s)
- Marija Paurević
- Department of Chemistry, Josip Juraj Strossmayer University of Osijek, Cara Hadrijana 8/A, HR-31000 Osijek, Croatia; (M.P.); (M.Š.G.)
| | - Martina Šrajer Gajdošik
- Department of Chemistry, Josip Juraj Strossmayer University of Osijek, Cara Hadrijana 8/A, HR-31000 Osijek, Croatia; (M.P.); (M.Š.G.)
| | - Rosana Ribić
- Department of Nursing, University Center Varaždin, University North, Jurja Križanića 31b, HR-42000 Varaždin, Croatia
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4
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Ohnuma K, Yamashita A, Yasui N. Investigating the Effect of Substituting a Single Cysteine Residue on the Thermal Stability of an Engineered Sweet Protein, Single-Chain Monellin. Protein J 2023; 42:698-708. [PMID: 37737932 PMCID: PMC10590300 DOI: 10.1007/s10930-023-10154-0] [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] [Accepted: 09/02/2023] [Indexed: 09/23/2023]
Abstract
Single-chain monellin (SCM) is an engineered protein that links the two chains of monellin, a naturally sweet-tasting protein. This protein is an attractive candidate for use as a sugar replacement in food and beverages and has numerous other applications. Therefore, generating SCM mutants with improved stability is an active area of research to broaden the range of its potential applications. In this study, we focused on the Cys41 residue of SCM, which is a single cysteine residue present at a structurally important position. This residue is often substituted with Ser. However, this substitution may destabilize SCM because Cys41 is buried in the hydrophobic core of the protein. Therefore, we designed mutants that substituted Ala, Val, and Leu for this residue, namely C41A, C41V, and C41L. We characterized these three mutants, SCM C41S, and wild type (WT). Differential scanning fluorimetric analysis revealed that substituting Cys41 with Ala or Val increased the thermal stability of SCM, while substitution with Ser or Leu decreased its stability. Determination of the crystal structures of SCM C41A and C41V mutants revealed that the overall structures and main chain structures around the 41st residue of both mutants were almost identical to the WT. On the other hand, the orientations of the amino acid side chains near the 41st residue differed among the SCM variants. Taken together, our results indicate that substituting Cys41 with Ala or Val increases the stability of SCM and provide insight into the structural basis of this improvement.
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Affiliation(s)
- Kyosuke Ohnuma
- School of Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Atsuko Yamashita
- School of Pharmaceutical Sciences, Okayama University, Okayama, Japan
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
| | - Norihisa Yasui
- School of Pharmaceutical Sciences, Okayama University, Okayama, Japan.
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
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5
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Gaudreault F, Baardsnes J, Martynova Y, Dachon A, Hogues H, Corbeil CR, Purisima EO, Arbour M, Sulea T. Exploring rigid-backbone protein docking in biologics discovery: a test using the DARPin scaffold. Front Mol Biosci 2023; 10:1253689. [PMID: 37692063 PMCID: PMC10484509 DOI: 10.3389/fmolb.2023.1253689] [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: 07/05/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023] Open
Abstract
Accurate protein-protein docking remains challenging, especially for artificial biologics not coevolved naturally against their protein targets, like antibodies and other engineered scaffolds. We previously developed ProPOSE, an exhaustive docker with full atomistic details, which delivers cutting-edge performance by allowing side-chain rearrangements upon docking. However, extensive protein backbone flexibility limits its practical applicability as indicated by unbound docking tests. To explore the usefulness of ProPOSE on systems with limited backbone flexibility, here we tested the engineered scaffold DARPin, which is characterized by its relatively rigid protein backbone. A prospective screening campaign was undertaken, in which sequence-diversified DARPins were docked and ranked against a directed epitope on the target protein BCL-W. In this proof-of-concept study, only a relatively small set of 2,213 diverse DARPin interfaces were selected for docking from the huge theoretical library from mutating 18 amino-acid positions. A computational selection protocol was then applied for enrichment of binders based on normalized computed binding scores and frequency of binding modes against the predefined epitope. The top-ranked 18 designed DARPin interfaces were selected for experimental validation. Three designs exhibited binding affinities to BCL-W in the nanomolar range comparable to control interfaces adopted from known DARPin binders. This result is encouraging for future screening and engineering campaigns of DARPins and possibly other similarly rigid scaffolds against targeted protein epitopes. Method limitations are discussed and directions for future refinements are proposed.
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Affiliation(s)
- Francis Gaudreault
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Yuliya Martynova
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Aurore Dachon
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Hervé Hogues
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Christopher R. Corbeil
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Enrico O. Purisima
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Mélanie Arbour
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
- Institute of Parasitology, McGill University, Montreal, QC, Canada
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6
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Gupta A, Lu C, Wang F, Chou T, Shan S. An ankyrin repeat chaperone targets toxic oligomers during amyloidogenesis. Protein Sci 2023; 32:e4728. [PMID: 37433015 PMCID: PMC10367600 DOI: 10.1002/pro.4728] [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: 02/15/2023] [Revised: 05/18/2023] [Accepted: 07/10/2023] [Indexed: 07/13/2023]
Abstract
Numerous age-linked diseases are rooted in protein misfolding; this has motivated the development of small molecules and therapeutic antibodies that target the aggregation of disease-linked proteins. Here we explore another approach: molecular chaperones with engineerable protein scaffolds such as the ankyrin repeat domain (ARD). We tested the ability of cpSRP43, a small, robust, ATP- and cofactor-independent plant chaperone built from an ARD, to antagonize disease-linked protein aggregation. cpSRP43 delays the aggregation of multiple proteins including the amyloid beta peptide (Aβ) associated with Alzheimer's disease and α-synuclein associated with Parkinson's disease. Kinetic modeling and biochemical analyses show that cpSRP43 targets early oligomers during Aβ aggregation, preventing their transition to a self-propagating nucleus on the fibril surface. Accordingly, cpSRP43 rescued neuronal cells from the toxicity of extracellular Aβ42 aggregates. The substrate-binding domain of cpSRP43, composed primarily of the ARD, is necessary and sufficient to prevent Aβ42 aggregation and protect cells against Aβ42 toxicity. This work provides an example in which an ARD chaperone non-native to mammalian cells harbors anti-amyloidal activity, which may be exploited for bioengineering.
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Affiliation(s)
- Arpit Gupta
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Chuqi Lu
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Feng Wang
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Tsui‐Fen Chou
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Shu‐ou Shan
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
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7
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Gabriele F, Palerma M, Ippoliti R, Angelucci F, Pitari G, Ardini M. Recent Advances on Affibody- and DARPin-Conjugated Nanomaterials in Cancer Therapy. Int J Mol Sci 2023; 24:ijms24108680. [PMID: 37240041 DOI: 10.3390/ijms24108680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Affibodies and designed ankyrin repeat proteins (DARPins) are synthetic proteins originally derived from the Staphylococcus aureus virulence factor protein A and the human ankyrin repeat proteins, respectively. The use of these molecules in healthcare has been recently proposed as they are endowed with biochemical and biophysical features heavily demanded to target and fight diseases, as they have a strong binding affinity, solubility, small size, multiple functionalization sites, biocompatibility, and are easy to produce; furthermore, impressive chemical and thermal stability can be achieved. especially when using affibodies. In this sense, several examples reporting on affibodies and DARPins conjugated to nanomaterials have been published, demonstrating their suitability and feasibility in nanomedicine for cancer therapy. This minireview provides a survey of the most recent studies describing affibody- and DARPin-conjugated zero-dimensional nanomaterials, including inorganic, organic, and biological nanoparticles, nanorods, quantum dots, liposomes, and protein- and DNA-based assemblies for targeted cancer therapy in vitro and in vivo.
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Affiliation(s)
- Federica Gabriele
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Marta Palerma
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Rodolfo Ippoliti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Francesco Angelucci
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Giuseppina Pitari
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Matteo Ardini
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
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8
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Gerber HP, Presta LG. TCR mimic compounds for pHLA targeting with high potency modalities in oncology. Front Oncol 2022; 12:1027548. [PMID: 36338746 PMCID: PMC9635445 DOI: 10.3389/fonc.2022.1027548] [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: 08/25/2022] [Accepted: 09/29/2022] [Indexed: 12/02/2022] Open
Abstract
pHLA complexes represent the largest class of cell surface markers on cancer cells, making them attractive for targeted cancer therapies. Adoptive cell therapies expressing TCRs that recognize tumor specific pHLAs take advantage of the unique selectivity and avidity of TCR: pHLA interactions. More recently, additional protein binding domains binding to pHLAs, known as TCR mimics (TCRm), were developed for tumor targeting of high potency therapeutic modalities, including bispecifics, ADCs, CAR T and -NK cells. TCRm compounds take advantage of the exquisite tumor specificity of certain pHLA targets, including cell lineage commitment markers and cancer testis antigens (CTAs). To achieve meaningful anti-tumor responses, it is critical that TCRm compounds integrate both, high target binding affinities and a high degree of target specificity. In this review, we describe the most advanced approaches to achieve both criteria, including affinity- and specificity engineering of TCRs, antibodies and alternative protein scaffolds. We also discuss the status of current TCRm based therapeutics developed in the clinic, key challenges, and emerging trends to improve treatment options for cancer patients treated with TCRm based therapeutics in Oncology.
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9
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Walser M, Mayor J, Rothenberger S. Designed Ankyrin Repeat Proteins: A New Class of Viral Entry Inhibitors. Viruses 2022; 14:2242. [PMID: 36298797 PMCID: PMC9611651 DOI: 10.3390/v14102242] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 08/08/2023] Open
Abstract
Designed ankyrin repeat proteins (DARPins) are engineered proteins comprising consensus designed ankyrin repeats as scaffold. Tightly packed repeats form a continuous hydrophobic core and a large groove-like solvent-accessible surface that creates a binding surface. DARPin domains recognizing a target of interest with high specificity and affinity can be generated using a synthetic combinatorial library and in vitro selection methods. They can be linked together in a single molecule to build multispecific and multifunctional proteins without affecting expression or function. The modular architecture of DARPins offers unprecedented possibilities of design and opens avenues for innovative antiviral strategies.
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Affiliation(s)
- Marcel Walser
- Molecular Partners AG, Wagistrasse 14, 8952 Zurich-Schlieren, Switzerland
| | - Jennifer Mayor
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
| | - Sylvia Rothenberger
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
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10
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Costa CFS, Barbosa AJM, Dias AMGC, Roque ACA. Native, engineered and de novo designed ligands targeting the SARS-CoV-2 spike protein. Biotechnol Adv 2022; 59:107986. [PMID: 35598822 PMCID: PMC9119173 DOI: 10.1016/j.biotechadv.2022.107986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 04/29/2022] [Accepted: 05/16/2022] [Indexed: 01/27/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the deadly coronavirus disease 2019 (Covid-19) and is a concerning hazard to public health. This virus infects cells by establishing a contact between its spike protein (S-protein) and host human angiotensin-converting enzyme 2 (hACE2) receptor, subsequently initiating viral fusion. The inhibition of the interaction between the S-protein and hACE2 has immediately drawn attention amongst the scientific community, and the S-protein was considered the prime target to design vaccines and to develop affinity ligands for diagnostics and therapy. Several S-protein binders have been reported at a fast pace, ranging from antibodies isolated from immunised patients to de novo designed ligands, with some binders already yielding promising in vivo results in protecting against SARS-CoV-2. Natural, engineered and designed affinity ligands targeting the S-protein are herein summarised, focusing on molecular recognition aspects, whilst identifying preferred hot spots for ligand binding. This review serves as inspiration for the improvement of already existing ligands or for the design of new affinity ligands towards SARS-CoV-2 proteins. Lessons learnt from the Covid-19 pandemic are also important to consolidate tools and processes in protein engineering to enable the fast discovery, production and delivery of diagnostic, prophylactic, and therapeutic solutions in future pandemics.
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Affiliation(s)
- Carlos F S Costa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Arménio J M Barbosa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Margarida G C Dias
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Cecília A Roque
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
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11
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Nguyen THD, Chapman S, Kashio M, Saito C, Strom T, Yasui M, Tominaga M. Single amino acids set apparent temperature thresholds for heat-evoked activation of mosquito transient receptor potential channel TRPA1. J Biol Chem 2022; 298:102271. [PMID: 35850302 PMCID: PMC9396403 DOI: 10.1016/j.jbc.2022.102271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 10/27/2022] Open
Abstract
Animals detect heat using thermosensitive transient receptor potential (TRP) channels. In insects, these include TRPA1, which in mosquitoes is crucial for noxious heat avoidance and thus is an appealing pest control target. However, the molecular basis for heat-evoked activation has not been fully elucidated, impeding both studies of the molecular evolution of temperature sensitivity and rational design of inhibitors. In TRPA1 and other thermosensitive TRPs, the N-terminal cytoplasmic ankyrin repeat (AR) domain has been suggested to participate in heat-evoked activation, but the lack of a structure containing the full AR domain has hindered our mechanistic understanding of its role. Here, we focused on elucidating the structural basis of apparent temperature threshold determination by taking advantage of two closely related mosquito TRPA1s from Aedes aegypti and Culex pipiens pallens with 86.9% protein sequence identity but a 10 °C difference in apparent temperature threshold. We identified two positions in the N-terminal cytoplasmic AR domain of these proteins, E417 (A. aegypti)/Q414 (C. pipiens) and R459 (A. aegypti )/Q456 (C. pipiens), at which a single exchange of amino acid identity was sufficient to change apparent thresholds by 5-7 °C. We further found that the role of these positions is conserved in TRPA1 of a third related species, Anopheles stephensi. Our results suggest a structural basis for temperature threshold determination, as well as for the evolutionary adaptation of mosquito TRPA1 to the wide range of climates inhabited by mosquitoes.
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Affiliation(s)
- Thi Hong Dung Nguyen
- Division of Cell Signaling, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan; Thermal Biology Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 444-8787, Okazaki, Japan
| | - Stella Chapman
- Division of Cell Signaling, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan; Thermal Biology Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 444-8787, Okazaki, Japan
| | - Makiko Kashio
- Division of Cell Signaling, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan; Thermal Biology Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 444-8787, Okazaki, Japan
| | - Claire Saito
- Division of Cell Signaling, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan; Thermal Biology Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 444-8787, Okazaki, Japan
| | - Tatjana Strom
- Division of Cell Signaling, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan; Thermal Biology Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 444-8787, Okazaki, Japan; Institute for Biology, Humboldt University of Berlin, 10115 Berlin, Germany
| | - Mio Yasui
- Division of Cell Signaling, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan; Thermal Biology Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 444-8787, Okazaki, Japan; Nagoya City University Medicine School, Nagoya 467-8601, Japan
| | - Makoto Tominaga
- Division of Cell Signaling, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan; Thermal Biology Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 444-8787, Okazaki, Japan.
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12
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Xing L, Xu X, Xu W, Liu Z, Shen X, Zhou J, Xu L, Pu J, Yang C, Huang Y, Lu L, Jiang S, Liu S. A Five−Helix−Based SARS−CoV−2 Fusion Inhibitor Targeting Heptad Repeat 2 Domain against SARS−CoV−2 and Its Variants of Concern. Viruses 2022; 14:v14030597. [PMID: 35337003 PMCID: PMC8955665 DOI: 10.3390/v14030597] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/06/2022] [Accepted: 03/10/2022] [Indexed: 01/27/2023] Open
Abstract
The prolonged duration of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic has resulted in the continuous emergence of variants of concern (VOC, e.g., Omicron) and variants of interest (VOI, e.g., Lambda). These variants have challenged the protective efficacy of current COVID-19 vaccines, thus calling for the development of novel therapeutics against SARS-CoV-2 and its VOCs. Here, we constructed a novel fusion inhibitor-based recombinant protein, denoted as 5-Helix, consisting of three heptad repeat 1 (HR1) and two heptad repeat 2 (HR2) fragments. The 5-Helix interacted with the HR2 domain of the viral S2 subunit, the most conserved region in spike (S) protein, to block homologous six-helix bundle (6-HB) formation between viral HR1 and HR2 domains and, hence, viral S-mediated cell–cell fusion. The 5-Helix potently inhibited infection by pseudotyped SARS-CoV-2 and its VOCs, including Delta and Omicron variants. The 5-Helix also inhibited infection by authentic SARS-CoV-2 wild-type (nCoV-SH01) strain and its Delta variant. Collectively, our findings suggest that 5-Helix can be further developed as either a therapeutic or prophylactic to treat and prevent infection by SARS-CoV-2 and its variants.
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Affiliation(s)
- Lixiao Xing
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (L.X.); (W.X.); (Z.L.); (X.S.); (J.Z.); (L.X.); (J.P.)
| | - Xinfeng Xu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; (X.X.); (C.Y.); (Y.H.)
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (L.X.); (W.X.); (Z.L.); (X.S.); (J.Z.); (L.X.); (J.P.)
| | - Zezhong Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (L.X.); (W.X.); (Z.L.); (X.S.); (J.Z.); (L.X.); (J.P.)
| | - Xin Shen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (L.X.); (W.X.); (Z.L.); (X.S.); (J.Z.); (L.X.); (J.P.)
| | - Jie Zhou
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (L.X.); (W.X.); (Z.L.); (X.S.); (J.Z.); (L.X.); (J.P.)
| | - Ling Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (L.X.); (W.X.); (Z.L.); (X.S.); (J.Z.); (L.X.); (J.P.)
| | - Jing Pu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (L.X.); (W.X.); (Z.L.); (X.S.); (J.Z.); (L.X.); (J.P.)
| | - Chan Yang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; (X.X.); (C.Y.); (Y.H.)
| | - Yuan Huang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; (X.X.); (C.Y.); (Y.H.)
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (L.X.); (W.X.); (Z.L.); (X.S.); (J.Z.); (L.X.); (J.P.)
- Correspondence: (L.L.); (S.J.); (S.L.)
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (L.X.); (W.X.); (Z.L.); (X.S.); (J.Z.); (L.X.); (J.P.)
- Correspondence: (L.L.); (S.J.); (S.L.)
| | - Shuwen Liu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; (X.X.); (C.Y.); (Y.H.)
- Correspondence: (L.L.); (S.J.); (S.L.)
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13
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Gisdon FJ, Kynast JP, Ayyildiz M, Hine AV, Plückthun A, Höcker B. Modular peptide binders - development of a predictive technology as alternative for reagent antibodies. Biol Chem 2022; 403:535-543. [PMID: 35089661 DOI: 10.1515/hsz-2021-0384] [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] [Received: 09/30/2021] [Accepted: 01/11/2022] [Indexed: 11/15/2022]
Abstract
Current biomedical research and diagnostics critically depend on detection agents for specific recognition and quantification of protein molecules. Monoclonal antibodies have been used for this purpose over decades and facilitated numerous biological and biomedical investigations. Recently, however, it has become apparent that many commercial reagent antibodies lack specificity or do not recognize their target at all. Thus, synthetic alternatives are needed whose complex designs are facilitated by multidisciplinary approaches incorporating experimental protein engineering with computational modeling. Here, we review the status of such an engineering endeavor based on the modular armadillo repeat protein scaffold and discuss challenges in its implementation.
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Affiliation(s)
- Florian J Gisdon
- Department of Biochemistry, University of Bayreuth, D-95447 Bayreuth, Germany
| | - Josef P Kynast
- Department of Biochemistry, University of Bayreuth, D-95447 Bayreuth, Germany
| | - Merve Ayyildiz
- Department of Biochemistry, University of Bayreuth, D-95447 Bayreuth, Germany
| | - Anna V Hine
- College of Health and Life Sciences, Aston University, Birmingham B4 7ET, UK
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, D-95447 Bayreuth, Germany
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14
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Sequence and Structure-Based Analyses of Human Ankyrin Repeats. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27020423. [PMID: 35056738 PMCID: PMC8781854 DOI: 10.3390/molecules27020423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/27/2021] [Accepted: 01/04/2022] [Indexed: 11/24/2022]
Abstract
Ankyrin is one of the most abundant protein repeat families found across all forms of life. It is found in a variety of multi-domain and single domain proteins in humans with diverse number of repeating units. They are observed to occur in several functionally diverse proteins, such as transcriptional initiators, cell cycle regulators, cytoskeletal organizers, ion transporters, signal transducers, developmental regulators, and toxins, and, consequently, defects in ankyrin repeat proteins have been associated with a number of human diseases. In this study, we have classified the human ankyrin proteins into clusters based on the sequence similarity in their ankyrin repeat domains. We analyzed the amino acid compositional bias and consensus ankyrin motif sequence of the clusters to understand the diversity of the human ankyrin proteins. We carried out network-based structural analysis of human ankyrin proteins across different clusters and showed the association of conserved residues with topologically important residues identified by network centrality measures. The analysis of conserved and structurally important residues helps in understanding their role in structural stability and function of these proteins. In this paper, we also discuss the significance of these conserved residues in disease association across the human ankyrin protein clusters.
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