1
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Fonseca G, Poltavsky I, Tkatchenko A. Force Field Analysis Software and Tools (FFAST): Assessing Machine Learning Force Fields under the Microscope. J Chem Theory Comput 2023; 19:8706-8717. [PMID: 38011895 PMCID: PMC10720330 DOI: 10.1021/acs.jctc.3c00985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023]
Abstract
As the sophistication of machine learning force fields (MLFF) increases to match the complexity of extended molecules and materials, so does the need for tools to properly analyze and assess the practical performance of MLFFs. To go beyond average error metrics and into a complete picture of a model's applicability and limitations, we developed FFAST (force field analysis software and tools): a cross-platform software package designed to gain detailed insights into a model's performance and limitations, complete with an easy-to-use graphical user interface. The software allows the user to gauge the performance of any molecular force field,─such as popular state-of-the-art MLFF models, ─ on various popular data set types, providing general prediction error overviews, outlier detection mechanisms, atom-projected errors, and more. It has a 3D visualizer to find and picture problematic configurations, atoms, or clusters in a large data set. In this paper, the example of the MACE and NequIP models is used on two data sets of interest [stachyose and docosahexaenoic acid (DHA)]─to illustrate the use cases of the software. With this, it was found that carbons and oxygens involved in or near glycosidic bonds inside the stachyose molecule present increased prediction errors. In addition, prediction errors on DHA rise as the molecule folds, especially for the carboxylic group at the edge of the molecule. We emphasize the need for a systematic assessment of MLFF models for ensuring their successful application to the study of dynamics of molecules and materials.
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Affiliation(s)
- Gregory Fonseca
- Department of Physics and Materials
Science, University of Luxembourg, Luxembourg City L-1511, Luxembourg
| | - Igor Poltavsky
- Department of Physics and Materials
Science, University of Luxembourg, Luxembourg City L-1511, Luxembourg
| | - Alexandre Tkatchenko
- Department of Physics and Materials
Science, University of Luxembourg, Luxembourg City L-1511, Luxembourg
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2
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Mansbach R, Patel LA, Watson NA, Kubicek-Sutherland JZ, Gnanakaran S. Inferring Pathways of Oxidative Folding from Prefolding Free Energy Landscapes of Disulfide-Rich Toxins. J Phys Chem B 2023; 127:1689-1703. [PMID: 36791259 PMCID: PMC9987446 DOI: 10.1021/acs.jpcb.2c07124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/07/2022] [Indexed: 02/17/2023]
Abstract
Short, cysteine-rich peptides can exist in stable or metastable structural ensembles due to the number of possible patterns of formation of their disulfide bonds. One interesting subset of this peptide group is the conotoxins, which are produced by aquatic snails in the family Conidae. The μ conotoxins, which are antagonists and blockers of the voltage-gated sodium channel, exist in a folding spectrum: on one end of the spectrum are more hirudin-like folders, which form disulfide bonds and then reshuffle them, leading to an ensemble of kinetically trapped isomers, and on the other end are more BPTI-like folders, which form the native disulfide bonds one by one in a particular order, leading to a preponderance of conformations existing in a single stable state. In this Article, we employ the composite diffusion map approach to study the unified free energy surface of prefolding μ-conotoxin equilibrium. We identify the two most important nonlinear collective modes of the unified folding landscape and demonstrate that in the absence of their disulfides, the conotoxins can be thought of as largely disordered polymers. A small increase in the number of hydrophobic residues in the protein shifts the free energy landscape toward hydrophobically collapsed coil conformations responsible for cysteine proximity in hirudin-like folders, compared to semiextended coil conformations with more distal cysteines in BPTI-like folders. Overall, this work sheds important light on the folding processes and free energy landscapes of cysteine-rich peptides and demonstrates the extent to which sequence and length contribute to these landscapes.
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Affiliation(s)
| | - Lara A. Patel
- OpenEye
Scientific Research, Santa Fe, New Mexico 87508, United States
| | - Natalya A. Watson
- Physics
Department, University of Concordia, Montreal, QC H4B 1R6, Canada
| | | | - S. Gnanakaran
- Physical
Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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3
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Nguyen LTT, Craik DJ, Kaas Q. Bibliometric Review of the Literature on Cone Snail Peptide Toxins from 2000 to 2022. Mar Drugs 2023; 21:md21030154. [PMID: 36976203 PMCID: PMC10058278 DOI: 10.3390/md21030154] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/18/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
The venom of marine cone snails is mainly composed of peptide toxins called conopeptides, among which conotoxins represent those that are disulfide-rich. Publications on conopeptides frequently state that conopeptides attract considerable interest for their potent and selective activity, but there has been no analysis yet that formally quantifies the popularity of the field. We fill this gap here by providing a bibliometric analysis of the literature on cone snail toxins from 2000 to 2022. Our analysis of 3028 research articles and 393 reviews revealed that research in the conopeptide field is indeed prolific, with an average of 130 research articles per year. The data show that the research is typically carried out collaboratively and worldwide, and that discoveries are truly a community-based effort. An analysis of the keywords provided with each article revealed research trends, their evolution over the studied period, and important milestones. The most employed keywords are related to pharmacology and medicinal chemistry. In 2004, the trend in keywords changed, with the pivotal event of that year being the approval by the FDA of the first peptide toxin drug, ziconotide, a conopeptide, for the treatment of intractable pain. The corresponding research article is among the top ten most cited articles in the conopeptide literature. From the time of that article, medicinal chemistry aiming at engineering conopeptides to treat neuropathic pain ramped up, as seen by an increased focus on topological modifications (e.g., cyclization), electrophysiology, and structural biology.
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Affiliation(s)
- Linh T. T. Nguyen
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J. Craik
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Quentin Kaas
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence:
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4
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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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5
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Gao B, Huang Y, Peng C, Lin B, Liao Y, Bian C, Yang J, Shi Q. High-Throughput Prediction and Design of Novel Conopeptides for Biomedical Research and Development. BIODESIGN RESEARCH 2022; 2022:9895270. [PMID: 37850131 PMCID: PMC10521759 DOI: 10.34133/2022/9895270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/23/2022] [Indexed: 10/19/2023] Open
Abstract
Cone snail venoms have been considered a valuable treasure for international scientists and businessmen, mainly due to their pharmacological applications in development of marine drugs for treatment of various human diseases. To date, around 800 Conus species are recorded, and each of them produces over 1,000 venom peptides (termed as conopeptides or conotoxins). This reflects the high diversity and complexity of cone snails, although most of their venoms are still uncharacterized. Advanced multiomics (such as genomics, transcriptomics, and proteomics) approaches have been recently developed to mine diverse Conus venom samples, with the main aim to predict and identify potentially interesting conopeptides in an efficient way. Some bioinformatics techniques have been applied to predict and design novel conopeptide sequences, related targets, and their binding modes. This review provides an overview of current knowledge on the high diversity of conopeptides and multiomics advances in high-throughput prediction of novel conopeptide sequences, as well as molecular modeling and design of potential drugs based on the predicted or validated interactions between these toxins and their molecular targets.
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Affiliation(s)
- Bingmiao Gao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, Hainan 570102, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China
- BGI-Marine Research Institute for Biomedical Technology, Shenzhen Huahong Marine Biomedicine Co. Ltd., Shenzhen, Guangdong 518119, China
| | - Bo Lin
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical University, Haikou, Hainan 570102, China
| | - Yanling Liao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, Hainan 570102, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China
| | - Jiaan Yang
- Research and Development Department, Micro Pharmtech Ltd., Wuhan, Hubei 430075, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China
- BGI-Marine Research Institute for Biomedical Technology, Shenzhen Huahong Marine Biomedicine Co. Ltd., Shenzhen, Guangdong 518119, China
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6
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Shen S, Wang W, Chen Z, Zhang H, Yang Y, Wang X, Fu P, Han B. Absolute Structure Determination and Kv1.5 Ion Channel Inhibition Activities of New Debromoaplysiatoxin Analogues. Mar Drugs 2021; 19:630. [PMID: 34822501 PMCID: PMC8622842 DOI: 10.3390/md19110630] [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: 09/16/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 12/04/2022] Open
Abstract
Potassium channel Kv1.5 has been considered a key target for new treatments of atrial tachyarrhythmias, with few side effects. Four new debromoaplysiatoxin analogues with a 6/6/12 fused ring system were isolated from marine cyanobacterium Lyngbya sp. Their planar structures were elucidated by HRESIMS, 1D and 2D NMR. The absolute configuration of oscillatoxin J (1) was determined by single-crystal X-ray diffraction, and the absolute configurations of oscillatoxin K (2), oscillatoxin L (3) and oscillatoxin M (4) were confirmed on the basis of GIAO NMR shift calculation followed by DP4 analysis. The current study confirmed the absolute configuration of the pivotal chiral positions (7S, 9S, 10S, 11R, 12S, 15S, 29R and 30R) at traditional ATXs with 6/12/6 tricyclic ring system. Compound 1, 2 and 4 exhibited blocking activities against Kv1.5 with IC50 values of 2.61 ± 0.91 µM, 3.86 ± 1.03 µM and 3.79 ± 1.01 µM, respectively. However, compound 3 exhibited a minimum effect on Kv1.5 at 10 µM. Furthermore, all of these new debromoaplysiatoxin analogs displayed no apparent activity in a brine shrimp toxicity assay.
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Affiliation(s)
- Sicheng Shen
- Department of Development Technology of Marine Resources, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (S.S.); (Z.C.); (H.Z.); (Y.Y.)
| | - Weiping Wang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (W.W.); (X.W.)
| | - Zijun Chen
- Department of Development Technology of Marine Resources, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (S.S.); (Z.C.); (H.Z.); (Y.Y.)
| | - Huihui Zhang
- Department of Development Technology of Marine Resources, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (S.S.); (Z.C.); (H.Z.); (Y.Y.)
| | - Yuchun Yang
- Department of Development Technology of Marine Resources, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (S.S.); (Z.C.); (H.Z.); (Y.Y.)
| | - Xiaoliang Wang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (W.W.); (X.W.)
| | - Peng Fu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Bingnan Han
- Department of Development Technology of Marine Resources, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (S.S.); (Z.C.); (H.Z.); (Y.Y.)
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7
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8
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Zhao L, Barber LM, Hung A. Structural and dynamical effects of targeted mutations on μO-Conotoxin MfVIA: Molecular simulation studies. J Mol Graph Model 2020; 102:107777. [PMID: 33130390 DOI: 10.1016/j.jmgm.2020.107777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/25/2020] [Accepted: 10/12/2020] [Indexed: 12/19/2022]
Abstract
Conotoxins are a group of cysteine-rich, neurotoxic peptides isolated from the venom of marine cone snails. MfVIA is a member of the μO-conotoxin family, and acts as an inhibitor of subtype 1.8 voltage-gated sodium ion channels (NaV1.8). The unique selectivity of MfVIA as an inhibitor of NaV1.8 makes it an ideal peptide for elucidation of the physiological functions of this voltage-gated ion channel. Previous experimental studies of point mutations of MfVIA showed that the double mutant [E5K,E8K] exhibited greater activity at NaV1.8 relative to the wild-type toxin. The present study employs molecular dynamics (MD) simulations to examine the effects of various mutations at these key residues (E5 and E8) on the structure and dynamics of MfVIA. Five double mutants were studied, in which the positions 5 and 8 residues were mutated to amino acids with a range of different physicochemical properties, namely [E5A,E8A], [E5D,E8D], [E5F,E8F], [E5K,E8K], and [E5R,E8R]. Except for [E5D,E8D], all of the mutants tend to show decreased contacts at the N-terminus owing to the loss of the R1-E5 salt bridge relative to that of the wild-type, which subsequently lead to greater exposure and flexibility of the N-terminus for most of the mutant peptides studied, potentially rendering them more able to interact with other species, including NaV1.8. Molecular docking studies of the peptides to NaV1.8 via different binding mechanisms suggest that the [E5R, E8R] mutant may be especially worthy of further investigation owing to its predicted binding mode, which differs markedly from those of the other peptides in this study.
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Affiliation(s)
- Lina Zhao
- School of Science, RMIT University, Melbourne, VIC, 3001, Australia
| | - Lisa M Barber
- School of Science, RMIT University, Melbourne, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, RMIT University, Melbourne, VIC, 3001, Australia.
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9
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Imhof D, Roy D, Albericio F. Editorial: Chemical Design and Biomedical Applications of Disulfide-rich Peptides: Challenges and Opportunities. Front Chem 2020; 8:586377. [PMID: 33195084 PMCID: PMC7645163 DOI: 10.3389/fchem.2020.586377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/12/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, Bonn, Germany
- *Correspondence: Diana Imhof
| | - Durba Roy
- Department of Chemistry, Birla Institute of Technology and Science-Pilani, Hyderabad, India
- Durba Roy
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
- Institute for Advanced Chemistry of Catalonia, Instituto de Quimica Avanzada de Catalunya–Consejo Superior de Investigaciones Cientificas (IQAC-CSIC), Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Department of Organic Chemistry, University of Barcelona, Barcelona, Spain
- Fernando Albericio
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10
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Gallo A, Boni R, Tosti E. Neurobiological activity of conotoxins via sodium channel modulation. Toxicon 2020; 187:47-56. [PMID: 32877656 DOI: 10.1016/j.toxicon.2020.08.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/20/2020] [Accepted: 08/22/2020] [Indexed: 01/02/2023]
Abstract
Conotoxins (CnTX) are bioactive peptides produced by marine molluscs belonging to Conus genus. The biochemical structure of these venomous peptides is characterized by a low number of amino acids linked with disulfide bonds formed by a high degree of post-translational modifications and glycosylation steps which increase the diversity and rate of evolution of these molecules. CnTX different isoforms are known to target ion channels and, in particular, voltage-gated sodium (Na+) channels (Nav channels). These are transmembrane proteins fundamental in excitable cells for generating the depolarization of plasma membrane potential known as action potential which propagates electrical signals in muscles and nerves for physiological functions. Disorders in Nav channel activity have been shown to induce neurological pathologies and pain states. Here, we describe the current knowledge of CnTX isoform modulation of the Nav channel activity, the mechanism of action and the potential therapeutic use of these toxins in counteracting neurological dysfunctions.
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Affiliation(s)
- Alessandra Gallo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Raffele Boni
- Department of Sciences, University of Basilicata, 85100, Potenza, Italy.
| | - Elisabetta Tosti
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
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11
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Mansbach RA, Chakraborty S, Travers T, Gnanakaran S. Graph-Directed Approach for Downselecting Toxins for Experimental Structure Determination. Mar Drugs 2020; 18:E256. [PMID: 32422972 PMCID: PMC7281422 DOI: 10.3390/md18050256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/24/2020] [Accepted: 05/09/2020] [Indexed: 11/29/2022] Open
Abstract
Conotoxins are short, cysteine-rich peptides of great interest as novel therapeutic leads and of great concern as lethal biological agents due to their high affinity and specificity for various receptors involved in neuromuscular transmission. Currently, of the approximately 6000 known conotoxin sequences, only about 3% have associated structural characterization, which leads to a bottleneck in rapid high-throughput screening (HTS) for identification of potential leads or threats. In this work, we combine a graph-based approach with homology modeling to expand the library of conotoxin structures and to identify those conotoxin sequences that are of the greatest value for experimental structural characterization. The latter would allow for the rapid expansion of the known structural space for generating high quality template-based models. Our approach generalizes to other evolutionarily-related, short, cysteine-rich venoms of interest. Overall, we present and validate an approach for venom structure modeling and experimental guidance and employ it to produce a 290%-larger library of approximate conotoxin structures for HTS. We also provide a set of ranked conotoxin sequences for experimental structure determination to further expand this library.
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Affiliation(s)
- Rachael A. Mansbach
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (R.A.M.); (S.C.); (T.T.)
| | - Srirupa Chakraborty
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (R.A.M.); (S.C.); (T.T.)
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Timothy Travers
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (R.A.M.); (S.C.); (T.T.)
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - S. Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (R.A.M.); (S.C.); (T.T.)
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12
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Li X, Liu H, Gao C, Li Y, Jia D, Yang Y, Yang J, Wei Z, Jiang T, Yu R. ConoMode, a database for conopeptide binding modes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5880464. [PMID: 32754758 PMCID: PMC7402919 DOI: 10.1093/database/baaa058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/23/2020] [Accepted: 07/07/2020] [Indexed: 11/24/2022]
Abstract
ConoMode is a database for complex three-dimensional (3D) structures of conopeptides binding with their target proteins. Conopeptides, a large family of peptides from the venom of marine snails of the Conus genus, have exceptionally diverse sequences, and their high specificity to block ion channels makes them crucial as drug leads and tools for physiological studies. ConoMode is a specialized archive for the collection of 3D coordinate data for the conopeptides and their binding target proteins from published literature and the Protein Data Bank. These 3D structures can be determined using experimental methods such as X-ray crystallography and electron microscopy and computational methods including docking, homology modeling and molecular dynamics simulations. The binding modes for the conopeptides determined using computational modeling must be validated based on experimental data. The 3D coordinate data from ConoMode can be searched, visualized, downloaded and uploaded. Currently, ConoMode manages 19 conopeptide sequences (from 10 Conus species), 15 protein sequences and 37 3D structures. ConoMode utilizes a modern technical framework to provide a good user experience on mobile devices with touch interaction features. Furthermore, the database is fully optimized for unstructured data and flexible data models. Database URL: http://conomode.qnlm.ac/conomode/conomode/index
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Affiliation(s)
- Xiao Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Hao Liu
- Department of Computer Science and Technology, Ocean University of China, Qingdao 266100, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Chunxiao Gao
- Department of Computer Science and Technology, Ocean University of China, Qingdao 266100, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Yangyang Li
- Department of Computer Science and Technology, Ocean University of China, Qingdao 266100, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Dongning Jia
- Department of Computer Science and Technology, Ocean University of China, Qingdao 266100, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Yanbo Yang
- Department of Computer Science and Technology, Ocean University of China, Qingdao 266100, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Jinbo Yang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Zhiqiang Wei
- Department of Computer Science and Technology, Ocean University of China, Qingdao 266100, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Tao Jiang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
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13
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Jin AH, Muttenthaler M, Dutertre S, Himaya SWA, Kaas Q, Craik DJ, Lewis RJ, Alewood PF. Conotoxins: Chemistry and Biology. Chem Rev 2019; 119:11510-11549. [PMID: 31633928 DOI: 10.1021/acs.chemrev.9b00207] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The venom of the marine predatory cone snails (genus Conus) has evolved for prey capture and defense, providing the basis for survival and rapid diversification of the now estimated 750+ species. A typical Conus venom contains hundreds to thousands of bioactive peptides known as conotoxins. These mostly disulfide-rich and well-structured peptides act on a wide range of targets such as ion channels, G protein-coupled receptors, transporters, and enzymes. Conotoxins are of interest to neuroscientists as well as drug developers due to their exquisite potency and selectivity, not just against prey but also mammalian targets, thereby providing a rich source of molecular probes and therapeutic leads. The rise of integrated venomics has accelerated conotoxin discovery with now well over 10,000 conotoxin sequences published. However, their structural and pharmacological characterization lags considerably behind. In this review, we highlight the diversity of new conotoxins uncovered since 2014, their three-dimensional structures and folds, novel chemical approaches to their syntheses, and their value as pharmacological tools to unravel complex biology. Additionally, we discuss challenges and future directions for the field.
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Affiliation(s)
- Ai-Hua Jin
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Markus Muttenthaler
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia.,Institute of Biological Chemistry, Faculty of Chemistry , University of Vienna , 1090 Vienna , Austria
| | - Sebastien Dutertre
- Département des Acides Amines, Peptides et Protéines, Unité Mixte de Recherche 5247, Université Montpellier 2-Centre Nationale de la Recherche Scientifique , Institut des Biomolécules Max Mousseron , Place Eugène Bataillon , 34095 Montpellier Cedex 5 , France
| | - S W A Himaya
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Richard J Lewis
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Paul F Alewood
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
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Conotoxin Diversity in the Venom Gland Transcriptome of the Magician's Cone, Pionoconus magus. Mar Drugs 2019; 17:md17100553. [PMID: 31569823 PMCID: PMC6835573 DOI: 10.3390/md17100553] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022] Open
Abstract
The transcriptomes of the venom glands of two individuals of the magician’s cone, Pionoconus magus, from Okinawa (Japan) were sequenced, assembled, and annotated. In addition, RNA-seq raw reads available at the SRA database from one additional specimen of P. magus from the Philippines were also assembled and annotated. The total numbers of identified conotoxin precursors and hormones per specimen were 118, 112, and 93. The three individuals shared only five identical sequences whereas the two specimens from Okinawa had 30 sequences in common. The total number of distinct conotoxin precursors and hormones for P. magus was 275, and were assigned to 53 conotoxin precursor and hormone superfamilies, two of which were new based on their divergent signal region. The superfamilies that had the highest number of precursors were M (42), O1 (34), T (27), A (18), O2 (17), and F (13), accounting for 55% of the total diversity. The D superfamily, previously thought to be exclusive of vermivorous cones was found in P. magus and contained a highly divergent mature region. Similarly, the A superfamily alpha 4/3 was found in P. magus despite the fact that it was previously postulated to be almost exclusive of the genus Rhombiconus. Differential expression analyses of P. magus compared to Chelyconus ermineus, the only fish-hunting cone from the Atlantic Ocean revealed that M and A2 superfamilies appeared to be more expressed in the former whereas the O2 superfamily was more expressed in the latter.
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15
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Structure, Function, and Therapeutic Potential of Marine Bioactive Peptides. Mar Drugs 2019; 17:md17090505. [PMID: 31466341 PMCID: PMC6780686 DOI: 10.3390/md17090505] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 08/25/2019] [Accepted: 08/26/2019] [Indexed: 12/11/2022] Open
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16
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Transcriptomic Analysis of Marine Gastropod Hemifusus tuba Provides Novel Insights into Conotoxin Genes. Mar Drugs 2019; 17:md17080466. [PMID: 31405144 PMCID: PMC6722550 DOI: 10.3390/md17080466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/03/2019] [Accepted: 08/07/2019] [Indexed: 12/26/2022] Open
Abstract
The marine gastropod Hemifusus tuba is served as a luxury food in Asian countries and used in traditional Chinese medicine to treat lumbago and deafness. The lack of genomic data on H. tuba is a barrier to aquaculture development and functional characteristics of potential bioactive molecules are poorly understood. In the present study, we used high-throughput sequencing technologies to generate the first transcriptomic database of H. tuba. A total of 41 unique conopeptides were retrieved from 44 unigenes, containing 6-cysteine frameworks belonging to four superfamilies. Duplication of mature regions and alternative splicing were also found in some of the conopeptides, and the de novo assembly identified a total of 76,306 transcripts with an average length of 824.6 nt, of which including 75,620 (99.1%) were annotated. In addition, simple sequence repeats (SSRs) detection identified 14,000 unigenes containing 20,735 SSRs, among which, 23 polymorphic SSRs were screened. Thirteen of these markers could be amplified in Hemifusus ternatanus and seven in Rapana venosa. This study provides reports of conopeptide genes in Buccinidae for the first time as well as genomic resources for further drug development, gene discovery and population resource studies of this species.
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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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