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Shoombuatong W, Homdee N, Schaduangrat N, Chumnanpuen P. Leveraging a meta-learning approach to advance the accuracy of Na v blocking peptides prediction. Sci Rep 2024; 14:4463. [PMID: 38396246 PMCID: PMC10891130 DOI: 10.1038/s41598-024-55160-z] [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: 12/28/2023] [Accepted: 02/21/2024] [Indexed: 02/25/2024] Open
Abstract
The voltage-gated sodium (Nav) channel is a crucial molecular component responsible for initiating and propagating action potentials. While the α subunit, forming the channel pore, plays a central role in this function, the complete physiological function of Nav channels relies on crucial interactions between the α subunit and auxiliary proteins, known as protein-protein interactions (PPI). Nav blocking peptides (NaBPs) have been recognized as a promising and alternative therapeutic agent for pain and itch. Although traditional experimental methods can precisely determine the effect and activity of NaBPs, they remain time-consuming and costly. Hence, machine learning (ML)-based methods that are capable of accurately contributing in silico prediction of NaBPs are highly desirable. In this study, we develop an innovative meta-learning-based NaBP prediction method (MetaNaBP). MetaNaBP generates new feature representations by employing a wide range of sequence-based feature descriptors that cover multiple perspectives, in combination with powerful ML algorithms. Then, these feature representations were optimized to identify informative features using a two-step feature selection method. Finally, the selected informative features were applied to develop the final meta-predictor. To the best of our knowledge, MetaNaBP is the first meta-predictor for NaBP prediction. Experimental results demonstrated that MetaNaBP achieved an accuracy of 0.948 and a Matthews correlation coefficient of 0.898 over the independent test dataset, which were 5.79% and 11.76% higher than the existing method. In addition, the discriminative power of our feature representations surpassed that of conventional feature descriptors over both the training and independent test datasets. We anticipate that MetaNaBP will be exploited for the large-scale prediction and analysis of NaBPs to narrow down the potential NaBPs.
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Affiliation(s)
- Watshara Shoombuatong
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand.
| | - Nutta Homdee
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Nalini Schaduangrat
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Pramote Chumnanpuen
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
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2
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Jian X, Wu Y, Mei Z, Zhu X, Zhangsun D, Luo S. Synthesis of the Most Potent Isomer of μ-Conotoxin KIIIA Using Different Strategies. Molecules 2023; 28:molecules28083377. [PMID: 37110612 PMCID: PMC10143212 DOI: 10.3390/molecules28083377] [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: 03/15/2023] [Revised: 03/30/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
In the chemical synthesis of conotoxins with multiple disulfide bonds, the oxidative folding process can result in diverse disulfide bond connectivities, which presents a challenge for determining the natural disulfide bond connectivities and leads to significant structural differences in the synthesized toxins. Here, we focus on KIIIA, a μ-conotoxin that has high potency in inhibiting Nav1.2 and Nav1.4. The non-natural connectivity pattern (C1-C9, C2-C15, C4-C16) of KIIIA exhibits the highest activity. In this study, we report an optimized Fmoc solid-phase synthesis of KIIIA using various strategies. Our results indicate that free random oxidation is the simplest method for peptides containing triple disulfide bonds, resulting in high yields and a simplified process. Alternatively, the semi-selective strategy utilizing Trt/Acm groups can also produce the ideal isomer, albeit with a lower yield. Furthermore, we performed distributed oxidation using three different protecting groups, optimizing their positions and cleavage order. Our results showed that prioritizing the cleavage of the Mob group over Acm may result in disulfide bond scrambling and the formation of new isomers. We also tested the activity of synthesized isomers on Nav1.4. These findings provide valuable guidance for the synthesis of multi-disulfide-bonded peptides in future studies.
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Affiliation(s)
- Xunxun Jian
- School of Medicine, Guangxi University, Nanning 530004, China
| | - Yong Wu
- School of Medicine, Guangxi University, Nanning 530004, China
| | - Zaoli Mei
- School of Medicine, Guangxi University, Nanning 530004, China
| | - Xiaopeng Zhu
- School of Medicine, Guangxi University, Nanning 530004, China
| | - Dongting Zhangsun
- School of Medicine, Guangxi University, Nanning 530004, China
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
| | - Sulan Luo
- School of Medicine, Guangxi University, Nanning 530004, China
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
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3
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Fiorotti HB, Figueiredo SG, Campos FV, Pimenta DC. Cone snail species off the Brazilian coast and their venoms: a review and update. J Venom Anim Toxins Incl Trop Dis 2023; 29:e20220052. [PMID: 36756364 PMCID: PMC9897318 DOI: 10.1590/1678-9199-jvatitd-2022-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/14/2022] [Indexed: 01/31/2023] Open
Abstract
The genus Conus includes over 900 species of marine invertebrates known as cone snails, whose venoms are among the most powerful described so far. This potency is mainly due to the concerted action of hundreds of small bioactive peptides named conopeptides, which target different ion channels and membrane receptors and thus interfere with crucial physiological processes. By swiftly harpooning and injecting their prey and predators with such deadly cocktails, the slow-moving cone snails guarantee their survival in the harsh, competitive marine environment. Each cone snail species produces a unique venom, as the mature sequences of conopeptides from the venoms of different species share very little identity. This biochemical diversity, added to the numerous species and conopeptides contained in their venoms, results in an immense biotechnological and therapeutic potential, still largely unexplored. That is especially true regarding the bioprospection of the venoms of cone snail species found off the Brazilian coast - a region widely known for its biodiversity. Of the 31 species described in this region so far, only four - Conus cancellatus, Conus regius, Conus villepinii, and Conus ermineus - have had their venoms partially characterized, and, although many bioactive molecules have been identified, only a few have been actually isolated and studied. In addition to providing an overview on all the cone snail species found off the Brazilian coast to date, this review compiles the information on the structural and pharmacological features of conopeptides and other molecules identified in the venoms of the four aforementioned species, paving the way for future studies.
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Affiliation(s)
- Helena B. Fiorotti
- Laboratory of Biochemistry and Biophysics, Butantan Institute, São
Paulo, SP, Brazil.,Graduate Program in Biochemistry, Laboratory of Protein Chemistry
(LQP), Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Suely G. Figueiredo
- Graduate Program in Biochemistry, Laboratory of Protein Chemistry
(LQP), Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Fabiana V. Campos
- Laboratory of Biochemistry and Biophysics, Butantan Institute, São
Paulo, SP, Brazil.,Graduate Program in Biochemistry, Laboratory of Protein Chemistry
(LQP), Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Daniel C. Pimenta
- Laboratory of Biochemistry and Biophysics, Butantan Institute, São
Paulo, SP, Brazil.,Correspondence:
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4
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Discovery and characterization of the novel conotoxin Lv1d from Conus lividus that presents analgesic activity. Toxicon 2021; 194:70-78. [PMID: 33610632 DOI: 10.1016/j.toxicon.2021.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/08/2020] [Accepted: 02/15/2021] [Indexed: 12/21/2022]
Abstract
Cone snails are predatory gastropod mollusks that are distributed in all tropical marine environments and contain small peptides (conotoxins) in their venom to capture prey. However, the biochemical and molecular aspects of conotoxins remain poorly understood. In this article, a novel α4/7-conotoxin, Lv1d, was obtained from the venom duct cDNA library of the worm-hunting Conus lividus collected from the South China Sea. The cDNA of Lv1c encodes a 65 residue conopeptide precursor, which consists of a 21 residue signal peptide, a 27 residue Pro region, and 17 residues of mature peptide. The mature peptide Lv1d was chemically synthesized according to the sequence GCCSDPPCRHKHQDLCG. It was found that 10 μM Lv1d can completely inhibit frog sciatic nerve-gastrocnemius muscle contractility within 60 min. Moreover, 100 μg/kg Lv1d showed good analgesic effects in mouse hot plate model and formalin test. Patch clamp experiments showed that 5 μM Lv1d can inhibit the cholinergic microexcitatory postsynaptic currents (mEPSCs) requency and amplitude of projection neurons in Drosophila. In conclusion, the synthesis of Lv1d and its biological and physiological data might contribute to the development of this peptide as a novel potential drug for therapeutic applications. This finding also expands the knowledge of the targeting mechanism of the α4/7-subfamily conotoxins.
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5
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Morales Duque H, Campos Dias S, Franco OL. Structural and Functional Analyses of Cone Snail Toxins. Mar Drugs 2019; 17:md17060370. [PMID: 31234371 PMCID: PMC6628382 DOI: 10.3390/md17060370] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/16/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022] Open
Abstract
Cone snails are marine gastropod mollusks with one of the most powerful venoms in nature. The toxins, named conotoxins, must act quickly on the cone snails´ prey due to the fact that snails are extremely slow, reducing their hunting capability. Therefore, the characteristics of conotoxins have become the object of investigation, and as a result medicines have been developed or are in the trialing process. Conotoxins interact with transmembrane proteins, showing specificity and potency. They target ion channels and ionotropic receptors with greater regularity, and when interaction occurs, there is immediate physiological decompensation. In this review we aimed to evaluate the structural features of conotoxins and the relationship with their target types.
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Affiliation(s)
- Harry Morales Duque
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF 70.790-160, Brazil.
| | - Simoni Campos Dias
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF 70.790-160, Brazil.
| | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF 70.790-160, Brazil.
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande-MS 79.117-900, Brazil.
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6
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Mansbach RA, Travers T, McMahon BH, Fair JM, Gnanakaran S. Snails In Silico: A Review of Computational Studies on the Conopeptides. Mar Drugs 2019; 17:E145. [PMID: 30832207 PMCID: PMC6471681 DOI: 10.3390/md17030145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 12/26/2022] Open
Abstract
Marine cone snails are carnivorous gastropods that use peptide toxins called conopeptides both as a defense mechanism and as a means to immobilize and kill their prey. These peptide toxins exhibit a large chemical diversity that enables exquisite specificity and potency for target receptor proteins. This diversity arises in terms of variations both in amino acid sequence and length, and in posttranslational modifications, particularly the formation of multiple disulfide linkages. Most of the functionally characterized conopeptides target ion channels of animal nervous systems, which has led to research on their therapeutic applications. Many facets of the underlying molecular mechanisms responsible for the specificity and virulence of conopeptides, however, remain poorly understood. In this review, we will explore the chemical diversity of conopeptides from a computational perspective. First, we discuss current approaches used for classifying conopeptides. Next, we review different computational strategies that have been applied to understanding and predicting their structure and function, from machine learning techniques for predictive classification to docking studies and molecular dynamics simulations for molecular-level understanding. We then review recent novel computational approaches for rapid high-throughput screening and chemical design of conopeptides for particular applications. We close with an assessment of the state of the field, emphasizing important questions for future lines of inquiry.
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Affiliation(s)
- Rachael A Mansbach
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Benjamin H McMahon
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Jeanne M Fair
- Biosecurity and Public Health Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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7
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Paul George AA, Heimer P, Maaß A, Hamaekers J, Hofmann-Apitius M, Biswas A, Imhof D. Insights into the Folding of Disulfide-Rich μ-Conotoxins. ACS OMEGA 2018; 3:12330-12340. [PMID: 30411002 PMCID: PMC6217517 DOI: 10.1021/acsomega.8b01465] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
The study of protein conformations using molecular dynamics (MD) simulations has been in place for decades. A major contribution to the structural stability and native conformation of a protein is made by the primary sequence and disulfide bonds formed during the folding process. Here, we investigated μ-conotoxins GIIIA, KIIIA, PIIIA, SIIIA, and SmIIIA as model peptides possessing three disulfide bonds. Their NMR structures were used for MD simulations in a novel approach studying the conformations between the folded and the unfolded states by systematically breaking the distinct disulfide bonds and monitoring the conformational stability of the peptides. As an outcome, the use of a combination of the existing knowledge and results from the simulations to classify the studied peptides within the extreme models of disulfide folding pathways, namely the bovine pancreatic trypsin inhibitor pathway and the hirudin pathway, is demonstrated. Recommendations for the design and synthesis of cysteine-rich peptides with a reduced number of disulfide bonds conclude the study.
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Affiliation(s)
- Ajay Abisheck Paul George
- Pharmaceutical
Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Pascal Heimer
- Pharmaceutical
Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Astrid Maaß
- Department
of Virtual Material Design and Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific
Computing, Schloss Birlinghoven, D-53754 Sankt Augustin, Germany
| | - Jan Hamaekers
- Department
of Virtual Material Design and Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific
Computing, Schloss Birlinghoven, D-53754 Sankt Augustin, Germany
| | - Martin Hofmann-Apitius
- Department
of Virtual Material Design and Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific
Computing, Schloss Birlinghoven, D-53754 Sankt Augustin, Germany
- Bonn-Aachen
International Center for Information Technology, University of Bonn, Endenicher Allee 19 C, D-53115 Bonn, Germany
| | - Arijit Biswas
- Institute
for Experimental Hematology, University
Hospital Bonn, Sigmund-Freud-Straße
25, D-53127 Bonn, Germany
| | - Diana Imhof
- Pharmaceutical
Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
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9
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Lau CHY, King GF, Mobli M. Molecular basis of the interaction between gating modifier spider toxins and the voltage sensor of voltage-gated ion channels. Sci Rep 2016; 6:34333. [PMID: 27677715 PMCID: PMC5039624 DOI: 10.1038/srep34333] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/12/2016] [Indexed: 01/02/2023] Open
Abstract
Voltage-sensor domains (VSDs) are modular transmembrane domains of voltage-gated ion channels that respond to changes in membrane potential by undergoing conformational changes that are coupled to gating of the ion-conducting pore. Most spider-venom peptides function as gating modifiers by binding to the VSDs of voltage-gated channels and trapping them in a closed or open state. To understand the molecular basis underlying this mode of action, we used nuclear magnetic resonance to delineate the atomic details of the interaction between the VSD of the voltage-gated potassium channel KvAP and the spider-venom peptide VSTx1. Our data reveal that the toxin interacts with residues in an aqueous cleft formed between the extracellular S1-S2 and S3-S4 loops of the VSD whilst maintaining lipid interactions in the gaps formed between the S1-S4 and S2-S3 helices. The resulting network of interactions increases the energetic barrier to the conformational changes required for channel gating, and we propose that this is the mechanism by which gating modifier toxins inhibit voltage-gated ion channels.
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Affiliation(s)
- Carus H Y Lau
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, QLD 4072, Australia
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