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Menzies SK, Arinto-Garcia R, Amorim FG, Cardoso IA, Abada C, Crasset T, Durbesson F, Edge RJ, El-Kazzi P, Hall S, Redureau D, Stenner R, Boldrini-França J, Sun H, Roldão A, Alves PM, Harrison RA, Vincentelli R, Berger I, Quinton L, Casewell NR, Schaffitzel C. ADDovenom: Thermostable Protein-Based ADDomer Nanoparticles as New Therapeutics for Snakebite Envenoming. Toxins (Basel) 2023; 15:673. [PMID: 38133177 PMCID: PMC10747859 DOI: 10.3390/toxins15120673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Snakebite envenoming can be a life-threatening medical emergency that requires prompt medical intervention to neutralise the effects of venom toxins. Each year up to 138,000 people die from snakebites and threefold more victims suffer life-altering disabilities. The current treatment of snakebite relies solely on antivenom-polyclonal antibodies isolated from the plasma of hyperimmunised animals-which is associated with numerous deficiencies. The ADDovenom project seeks to deliver a novel snakebite therapy, through the use of an innovative protein-based scaffold as a next-generation antivenom. The ADDomer is a megadalton-sized, thermostable synthetic nanoparticle derived from the adenovirus penton base protein; it has 60 high-avidity binding sites to neutralise venom toxins. Here, we outline our experimental strategies to achieve this goal using state-of-the-art protein engineering, expression technology and mass spectrometry, as well as in vitro and in vivo venom neutralisation assays. We anticipate that the approaches described here will produce antivenom with unparalleled efficacy, safety and affordability.
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Affiliation(s)
- Stefanie K. Menzies
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Raquel Arinto-Garcia
- iBET, Instituto de Biologia Experimental e Technológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Fernanda Gobbi Amorim
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Iara Aimê Cardoso
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Camille Abada
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Thomas Crasset
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Fabien Durbesson
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Rebecca J. Edge
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Priscila El-Kazzi
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Sophie Hall
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Damien Redureau
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Richard Stenner
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Johara Boldrini-França
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Huan Sun
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - António Roldão
- iBET, Instituto de Biologia Experimental e Technológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Paula M. Alves
- iBET, Instituto de Biologia Experimental e Technológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Robert A. Harrison
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Imre Berger
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Nicholas R. Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Christiane Schaffitzel
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
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2
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Spolaore B, Fernández J, Lomonte B, Massimino ML, Tonello F. Enzymatic labelling of snake venom phospholipase A 2 toxins. Toxicon 2019; 170:99-107. [PMID: 31563525 DOI: 10.1016/j.toxicon.2019.09.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/02/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022]
Abstract
Almost all animal venoms contain secretory phospholipases A2 (PLA2s), 14 kDa disulfide-rich enzymes that hydrolyze membrane phospholipids at the sn-2 position, releasing lysophospholipids and fatty acids. These proteins, depending on their sequence, show a wide variety of biochemical, toxic and pharmacological effects and deserve to be studied for their numerous possible applications, and to improve antivenom drugs. The cellular localization and activity of a protein can be studied by conjugating it with a tag. In this work, we applied an enzymatic labelling method, using Streptomyces mobaraense transglutaminase, on three snake venom PLA2s: a recombinant neuro- and myotoxic group I PLA2 from Notechis scutatus scutatus, and two myotoxic group II PLA2s from Bothrops asper - one of them a natural catalytically inactive variant. We demonstrate that TGase can be used to produce active mono- or bi-derivatives of these three PLA2s modified at specific Lys residues, and that all three of these proteins, conjugated with fluorescent peptides, are internalized in primary myotubes.
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Affiliation(s)
- Barbara Spolaore
- Dipartimento di Scienze del Farmaco, Università di Padova, Via F. Marzolo, 5, 35131, Padova, Italy.
| | - Julián Fernández
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, 11501, Costa Rica
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, 11501, Costa Rica
| | | | - Fiorella Tonello
- Istituto di Neuroscienze, CNR, Viale G. Colombo, 3, 35121, Padova, Italy.
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3
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Blaha-Nelson D, Krüger DM, Szeler K, Ben-David M, Kamerlin SCL. Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1. J Am Chem Soc 2017; 139:1155-1167. [PMID: 28026940 PMCID: PMC5269640 DOI: 10.1021/jacs.6b10801] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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Serum
paraoxonase 1 (PON1) is a native lactonase capable of promiscuously
hydrolyzing a broad range of substrates, including organophosphates,
esters, and carbonates. Structurally, PON1 is a six-bladed β-propeller
with a flexible loop (residues 70–81) covering the active site.
This loop contains a functionally critical Tyr at position 71. We
have performed detailed experimental and computational analyses of
the role of selected Y71 variants in the active site stability and
catalytic activity in order to probe the role of Y71 in PON1’s
lactonase and organophosphatase activities. We demonstrate that the
impact of Y71 substitutions on PON1’s lactonase activity is
minimal, whereas the kcat for the paraoxonase
activity is negatively perturbed by up to 100-fold, suggesting greater
mutational robustness of the native activity. Additionally, while
these substitutions modulate PON1’s active site shape, volume,
and loop flexibility, their largest effect is in altering the solvent
accessibility of the active site by expanding the active site volume,
allowing additional water molecules to enter. This effect is markedly
more pronounced in the organophosphatase activity than the lactonase
activity. Finally, a detailed comparison of PON1 to other organophosphatases
demonstrates that either a similar “gating loop” or
a highly buried solvent-excluding active site is a common feature
of these enzymes. We therefore posit that modulating the active site
hydrophobicity is a key element in facilitating the evolution of organophosphatase
activity. This provides a concrete feature that can be utilized in
the rational design of next-generation organophosphate hydrolases
that are capable of selecting a specific reaction from a pool of viable
substrates.
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Affiliation(s)
- David Blaha-Nelson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , S-751 24 Uppsala, Sweden
| | - Dennis M Krüger
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , S-751 24 Uppsala, Sweden
| | - Klaudia Szeler
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , S-751 24 Uppsala, Sweden
| | - Moshe Ben-David
- Department of Biological Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , S-751 24 Uppsala, Sweden
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4
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Ben-David M, Sussman JL, Maxwell CI, Szeler K, Kamerlin SCL, Tawfik DS. Catalytic stimulation by restrained active-site floppiness--the case of high density lipoprotein-bound serum paraoxonase-1. J Mol Biol 2015; 427:1359-1374. [PMID: 25644661 DOI: 10.1016/j.jmb.2015.01.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 11/28/2022]
Abstract
Despite the abundance of membrane-associated enzymes, the mechanism by which membrane binding stabilizes these enzymes and stimulates their catalysis remains largely unknown. Serum paraoxonase-1 (PON1) is a lipophilic lactonase whose stability and enzymatic activity are dramatically stimulated when associated with high-density lipoprotein (HDL) particles. Our mutational and structural analyses, combined with empirical valence bond simulations, reveal a network of hydrogen bonds that connect HDL binding residues with Asn168--a key catalytic residue residing >15Å from the HDL contacting interface. This network ensures precise alignment of N168, which, in turn, ligates PON1's catalytic calcium and aligns the lactone substrate for catalysis. HDL binding restrains the overall motion of the active site and particularly of N168, thus reducing the catalytic activation energy barrier. We demonstrate herein that disturbance of this network, even at its most far-reaching periphery, undermines PON1's activity. Membrane binding thus immobilizes long-range interactions via second- and third-shell residues that reduce the active site's floppiness and pre-organize the catalytic residues. Although this network is critical for efficient catalysis, as demonstrated here, unraveling these long-rage interaction networks is challenging, let alone their implementation in artificial enzyme design.
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Affiliation(s)
- Moshe Ben-David
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joel L Sussman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Christopher I Maxwell
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, S-754 21 Uppsala, Sweden
| | - Klaudia Szeler
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, S-754 21 Uppsala, Sweden
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, S-754 21 Uppsala, Sweden.
| | - Dan S Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
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7
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Mariani ME, Villarreal MA, Cheung F, Leiva EPM, Madoery RR, Fidelio GD. In silico and in vitro characterization of phospholipase A₂ isoforms from soybean (Glycine max). Biochimie 2012; 94:2608-19. [PMID: 23281487 DOI: 10.1016/j.biochi.2012.07.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
At the present, no secreted phospholipase A₂ (sPLA₂) from soybean (Glycine max) was investigated in detail. In this work we identified five sequences of putative secreted sPLA₂ from soybean after a BLAST search in G. max database. Sequence analysis showed a conserved PA2c domain bearing the Ca²⁺ binding loop and the active site motif. All the five mature proteins contain 12 cysteine residues, which are commonly conserved in plant sPLA₂s. We propose a phylogenetic tree based on sequence alignment of reported plant sPLA₂s including the novel enzymes from G. max. According to PLA₂ superfamily, two of G. max sPLA₂s are grouped as XIA and the rest of sequences as XIB, on the basis of differences found in their molecular weights and deviating sequences especially in the N- and C-terminal regions of the isoenzymes. Furthermore, we report the cloning, expression and purification of one of the putative isoenzyme denoted as GmsPLA₂-XIA-1. We demonstrate that this mature sPLA₂ of 114 residues had PLA₂ activity on Triton:phospholipid mixed micelles and determine the kinetic parameters for this system. We generate a model based on the known crystal structure of sPLA₂ from rice (isoform II), giving first insights into the three-dimensional structure of folded GmsPLA₂-XIA-1. Besides describing the spatial arrangement of highly conserved pair HIS-49/ASP-50 and the Ca⁺² loop domains, we propose the putative amino acids involved in the interfacial recognition surface. Additionally, molecular dynamics simulations indicate that calcium ion, besides its key function in the catalytic cycle, plays an important role in the overall stability of GmsPLA₂-XIA-1 structure.
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Affiliation(s)
- María Elisa Mariani
- Centro de Investigaciones en Química Biológica de Córdoba, (CIQUIBIC, UNCeCONICET), Departamento de Química Biológica, Fac. de Cs. Químicas, Universidad Nacional de Córdoba, Haya de Torre y Medina Allende, Ciudad Universitaria, X5000HUA Córdoba, Argentina
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