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Wang L, Zeng Z, Xue Z, Wang Y. DeepNeuropePred: A robust and universal tool to predict cleavage sites from neuropeptide precursors by protein language model. Comput Struct Biotechnol J 2024; 23:309-315. [PMID: 38179071 PMCID: PMC10764246 DOI: 10.1016/j.csbj.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 01/06/2024] Open
Abstract
Neuropeptides play critical roles in many biological processes such as growth, learning, memory, metabolism, and neuronal differentiation. A few approaches have been reported for predicting neuropeptides that are cleaved from precursor protein sequences. However, these models for cleavage site prediction of precursors were developed using a limited number of neuropeptide precursor datasets and simple precursors representation models. In addition, a universal method for predicting neuropeptide cleavage sites that can be applied to all species is still lacking. In this paper, we proposed a novel deep learning method called DeepNeuropePred, using a combination of pre-trained language model and Convolutional Neural Networks for feature extraction and predicting the neuropeptide cleavage sites from precursors. To demonstrate the model's effectiveness and robustness, we evaluated the performance of DeepNeuropePred and four models from the NeuroPred server in the independent dataset and our model achieved the highest AUC score (0.916), which are 6.9%, 7.8%, 8.8%, and 10.9% higher than Mammalian (0.857), insects (0.850), Mollusc (0.842) and Motif (0.826), respectively. For the convenience of researchers, we provide a web server (http://isyslab.info/NeuroPepV2/deepNeuropePred.jsp).
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Affiliation(s)
- Lei Wang
- Institute of Medical Artificial Intelligence, Binzhou Medical University, Yantai, Shandong 264003, China
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zilu Zeng
- Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, China
| | - Zhidong Xue
- Institute of Medical Artificial Intelligence, Binzhou Medical University, Yantai, Shandong 264003, China
- School of Software Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yan Wang
- Institute of Medical Artificial Intelligence, Binzhou Medical University, Yantai, Shandong 264003, China
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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2
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Chen Q, Xu N, Zhao C, He Y, Kam SHT, Wu X, Huang P, Yang M, Wong CTT, Radis-Baptista G, Tang B, Fan G, Gong G, Lee SMY. A new invertebrate NPY-like polypeptide, ZoaNPY, from the Zoanthus sociatus, as a novel ligand of human NPY Y2 receptor rescues vascular insufficiency via PLC/PKC and Src- FAK-dependent signaling pathways. Pharmacol Res 2024; 203:107173. [PMID: 38580186 DOI: 10.1016/j.phrs.2024.107173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/23/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Our recent multi-omics studies have revealed rich sources of novel bioactive proteins and polypeptides from marine organisms including cnidarians. In the present study, we initially conducted a transcriptomic analysis to review the composition profile of polypeptides from Zoanthus sociatus. Then, a newly discovered NPY-like polypeptide-ZoaNPY was selected for further in silico structural, binding and virtually pharmacological studies. To evaluate the pro-angiogenic effects of ZoaNPY, we employed an in vitro HUVECs model and an in vivo zebrafish model. Our results indicate that ZoaNPY, at 1-100 pmol, enhances cell survival, migration and tube formation in the endothelial cells. Besides, treatment with ZoaNPY could restore a chemically-induced vascular insufficiency in zebrafish embryos. Western blot results demonstrated the application of ZoaNPY could increase the phosphorylation of proteins related to angiogenesis signaling including PKC, PLC, FAK, Src, Akt, mTOR, MEK, and ERK1/2. Furthermore, through molecular docking and surface plasmon resonance (SPR) verification, ZoaNPY was shown to directly and physically interact with NPY Y2 receptor. In view of this, all evidence showed that the pro-angiogenic effects of ZoaNPY involve the activation of NPY Y2 receptor, thereby activating the Akt/mTOR, PLC/PKC, ERK/MEK and Src- FAK-dependent signaling pathways. Furthermore, in an excision wound model, the treatment with ZoaNPY was shown to accelerate the wound healing process in mice. Our findings provide new insights into the discovery and development of novel pro-angiogenic drugs derived from NPY-like polypeptides in the future.
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Affiliation(s)
- Qian Chen
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, 999078, Macao
| | - Nan Xu
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, 999078, Macao
| | - Chen Zhao
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, 999078, Macao
| | - Yulin He
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom 999077, Hong Kong, SAR China
| | - Sandy Hio Tong Kam
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, 999078, Macao
| | - Xue Wu
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, 999078, Macao
| | - Pan Huang
- Kunming Institute of Zoology, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Min Yang
- Kunming Institute of Zoology, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Clarence Tsun Ting Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, 999077, Hong Kong, SAR China
| | | | - Benqin Tang
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom 999077, Hong Kong, SAR China; Research Centre for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom 999077, Hong Kong, SAR China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Guiyi Gong
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, 999078, Macao; Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom 999077, Hong Kong, SAR China; Research Centre for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom 999077, Hong Kong, SAR China.
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, 999078, Macao; Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom 999077, Hong Kong, SAR China; Research Centre for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom 999077, Hong Kong, SAR China.
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3
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Perisic M, Woolcock K, Hering A, Mendel H, Muttenthaler M. Oxytocin and vasopressin signaling in health and disease. Trends Biochem Sci 2024; 49:361-377. [PMID: 38418338 DOI: 10.1016/j.tibs.2024.01.010] [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: 09/21/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 03/01/2024]
Abstract
Neurohypophysial peptides are ancient and evolutionarily highly conserved neuropeptides that regulate many crucial physiological functions in vertebrates and invertebrates. The human neurohypophysial oxytocin/vasopressin (OT/VP) signaling system with its four receptors has become an attractive drug target for a variety of diseases, including cancer, pain, cardiovascular indications, and neurological disorders. Despite its promise, drug development faces hurdles, including signaling complexity, selectivity and off-target concerns, translational interspecies differences, and inefficient drug delivery. In this review we dive into the complexity of the OT/VP signaling system in health and disease, provide an overview of relevant pharmacological probes, and discuss the latest trends in therapeutic lead discovery and drug development.
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Affiliation(s)
- Monika Perisic
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; Vienna Doctoral School in Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Katrina Woolcock
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Anke Hering
- Institute for Molecular Bioscience, The University of Queensland, 4072 Brisbane, Australia
| | - Helen Mendel
- Institute for Molecular Bioscience, The University of Queensland, 4072 Brisbane, Australia
| | - Markus Muttenthaler
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; Institute for Molecular Bioscience, The University of Queensland, 4072 Brisbane, Australia.
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4
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Wang M, Wang L, Xu W, Chu Z, Wang H, Lu J, Xue Z, Wang Y. NeuroPep 2.0: An Updated Database Dedicated to Neuropeptide and Its Receptor Annotations. J Mol Biol 2024; 436:168416. [PMID: 38143020 DOI: 10.1016/j.jmb.2023.168416] [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: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
Neuropeptides not only work through nervous system but some of them also work peripherally to regulate numerous physiological processes. They are important in regulation of numerous physiological processes including growth, reproduction, social behavior, inflammation, fluid homeostasis, cardiovascular function, and energy homeostasis. The various roles of neuropeptides make them promising candidates for prospective therapeutics of different diseases. Currently, NeuroPep has been updated to version 2.0, it now holds 11,417 unique neuropeptide entries, which is nearly double of the first version of NeuroPep. When available, we collected information about the receptor for each neuropeptide entry and predicted the 3D structures of those neuropeptides without known experimental structure using AlphaFold2 or APPTEST according to the peptide sequence length. In addition, DeepNeuropePred and NeuroPred-PLM, two neuropeptide prediction tools developed by us recently, were also integrated into NeuroPep 2.0 to help to facilitate the identification of new neuropeptides. NeuroPep 2.0 is freely accessible at https://isyslab.info/NeuroPepV2/.
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Affiliation(s)
- Mingxia Wang
- Institute of Medical Artificial Intelligence, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Lei Wang
- School of Software Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Wei Xu
- Institute of Medical Artificial Intelligence, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Ziqiang Chu
- School of Software Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Hengzhi Wang
- School of Software Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jingxiang Lu
- Institute of Medical Artificial Intelligence, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Zhidong Xue
- Institute of Medical Artificial Intelligence, Binzhou Medical University, Yantai, Shandong 264003, China; School of Software Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yan Wang
- Institute of Medical Artificial Intelligence, Binzhou Medical University, Yantai, Shandong 264003, China; School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
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5
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Mishra G, Townsend KL. Sensory nerve and neuropeptide diversity in adipose tissues. Mol Cells 2024; 47:100030. [PMID: 38364960 PMCID: PMC10960112 DOI: 10.1016/j.mocell.2024.100030] [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: 01/19/2024] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Both brown and white adipose tissues (BAT/WAT) are innervated by the peripheral nervous system, including efferent sympathetic nerves that communicate from the brain/central nervous system out to the tissue, and afferent sensory nerves that communicate from the tissue back to the brain and locally release neuropeptides to the tissue upon stimulation. This bidirectional neural communication is important for energy balance and metabolic control, as well as maintaining adipose tissue health through processes like browning (development of metabolically healthy brown adipocytes in WAT), thermogenesis, lipolysis, and adipogenesis. Decades of sensory nerve denervation studies have demonstrated the particular importance of adipose sensory nerves for brown adipose tissue and WAT functions, but far less is known about the tissue's sensory innervation compared to the better-studied sympathetic nerves and their neurotransmitter norepinephrine. In this review, we cover what is known and not yet known about sensory nerve activities in adipose, focusing on their effector neuropeptide actions in the tissue.
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Affiliation(s)
- Gargi Mishra
- Department of Neurological Surgery, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Kristy L Townsend
- Department of Neurological Surgery, College of Medicine, The Ohio State University, Columbus, OH, USA.
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Chen S, Li Q, Zhao J, Bin Y, Zheng C. NeuroPred-CLQ: incorporating deep temporal convolutional networks and multi-head attention mechanism to predict neuropeptides. Brief Bioinform 2022; 23:6672901. [DOI: 10.1093/bib/bbac319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/27/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Neuropeptides (NPs) are a particular class of informative substances in the immune system and physiological regulation. They play a crucial role in regulating physiological functions in various biological growth and developmental stages. In addition, NPs are crucial for developing new drugs for the treatment of neurological diseases. With the development of molecular biology techniques, some data-driven tools have emerged to predict NPs. However, it is necessary to improve the predictive performance of these tools for NPs. In this study, we developed a deep learning model (NeuroPred-CLQ) based on the temporal convolutional network (TCN) and multi-head attention mechanism to identify NPs effectively and translate the internal relationships of peptide sequences into numerical features by the Word2vec algorithm. The experimental results show that NeuroPred-CLQ learns data information effectively, achieving 93.6% accuracy and 98.8% AUC on the independent test set. The model has better performance in identifying NPs than the state-of-the-art predictors. Visualization of features using t-distribution random neighbor embedding shows that the NeuroPred-CLQ can clearly distinguish the positive NPs from the negative ones. We believe the NeuroPred-CLQ can facilitate drug development and clinical trial studies to treat neurological disorders.
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Affiliation(s)
- Shouzhi Chen
- School of Mathematics and System Science, Xinjiang University , Urumqi, China
| | - Qing Li
- School of Mathematics and System Science, Xinjiang University , Urumqi, China
| | - Jianping Zhao
- School of Mathematics and System Science, Xinjiang University , Urumqi, China
| | - Yannan Bin
- School of Computer Science and Technology, Anhui University , Hefei, China
| | - Chunhou Zheng
- School of Mathematics and System Science, Xinjiang University , Urumqi, China
- School of Computer Science and Technology, Anhui University , Hefei, China
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7
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De La Toba EA, Bell SE, Romanova EV, Sweedler JV. Mass Spectrometry Measurements of Neuropeptides: From Identification to Quantitation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2022; 15:83-106. [PMID: 35324254 DOI: 10.1146/annurev-anchem-061020-022048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Neuropeptides (NPs), a unique class of neuronal signaling molecules, participate in a variety of physiological processes and diseases. Quantitative measurements of NPs provide valuable information regarding how these molecules are differentially regulated in a multitude of neurological, metabolic, and mental disorders. Mass spectrometry (MS) has evolved to become a powerful technique for measuring trace levels of NPs in complex biological tissues and individual cells using both targeted and exploratory approaches. There are inherent challenges to measuring NPs, including their wide endogenous concentration range, transport and postmortem degradation, complex sample matrices, and statistical processing of MS data required for accurate NP quantitation. This review highlights techniques developed to address these challenges and presents an overview of quantitative MS-based measurement approaches for NPs, including the incorporation of separation methods for high-throughput analysis, MS imaging for spatial measurements, and methods for NP quantitation in single neurons.
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Affiliation(s)
- Eduardo A De La Toba
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Sara E Bell
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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8
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Kremsmayr T, Aljnabi A, Blanco-Canosa JB, Tran HNT, Emidio NB, Muttenthaler M. On the Utility of Chemical Strategies to Improve Peptide Gut Stability. J Med Chem 2022; 65:6191-6206. [PMID: 35420805 PMCID: PMC9059125 DOI: 10.1021/acs.jmedchem.2c00094] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Inherent susceptibility
of peptides to enzymatic degradation in
the gastrointestinal tract is a key bottleneck in oral peptide drug
development. Here, we present a systematic analysis of (i) the gut
stability of disulfide-rich peptide scaffolds, orally administered
peptide therapeutics, and well-known neuropeptides and (ii) medicinal
chemistry strategies to improve peptide gut stability. Among a broad
range of studied peptides, cyclotides were the only scaffold class
to resist gastrointestinal degradation, even when grafted with non-native
sequences. Backbone cyclization, a frequently applied strategy, failed
to improve stability in intestinal fluid, but several site-specific
alterations proved efficient. This work furthermore highlights the
importance of standardized gut stability test conditions and suggests
defined protocols to facilitate cross-study comparison. Together,
our results provide a comparative overview and framework for the chemical
engineering of gut-stable peptides, which should be valuable for the
development of orally administered peptide therapeutics and molecular
probes targeting receptors within the gastrointestinal tract.
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Affiliation(s)
- Thomas Kremsmayr
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, Vienna 1090, Austria
| | - Aws Aljnabi
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, Vienna 1090, Austria
| | - Juan B Blanco-Canosa
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, Barcelona 08034, Spain
| | - Hue N T Tran
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Nayara Braga Emidio
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Markus Muttenthaler
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, Vienna 1090, Austria.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
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Duraisamy K, Singh K, Kumar M, Lefranc B, Bonnafé E, Treilhou M, Leprince J, Chow BKC. P17 induces chemotaxis and differentiation of monocytes via MRGPRX2-mediated mast cell-line activation. J Allergy Clin Immunol 2022; 149:275-291. [PMID: 34111449 DOI: 10.1016/j.jaci.2021.04.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 03/29/2021] [Accepted: 04/23/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND P17, a peptide isolated from Tetramorium bicarinatum ant venom, is known to induce an alternative phenotype of human monocyte-derived macrophages via activation of an unknown G protein-coupled receptor (GPCR). OBJECTIVE We sought to investigate the mechanism of action and the immunomodulatory effects of P17 mediated through MRGPRX2 (Mas-related G protein-coupled receptor X2). METHODS To identify the GPCR for P17, we screened 314 GPCRs. Upon identification of MRGPRX2, a battery of in silico, in vitro, ex vivo, and in vivo assays along with the receptor mutation studies were performed. In particular, to investigate the immunomodulatory actions, we used β-hexosaminidase release assay, cytokine releases, quantification of mRNA expression, cell migration and differentiation assays, immunohistochemical labeling, hematoxylin and eosin, and immunofluorescence staining. RESULTS P17 activated MRGPRX2 in a dose-dependent manner in β-arrestin recruitment assay. In LAD2 cells, P17 induced calcium and β-hexosaminidase release. Quercetin- and short hairpin RNA-mediated knockdown of MRGPRX2 reduced P17-evoked β-hexosaminidase release. In silico and in vitro mutagenesis studies showed that residue Lys8 of P17 formed a cation-π interaction with the Phe172 of MRGPRX2 and [Ala8]P17 lost its activity partially. P17 activated LAD2 cells to recruit THP-1 and human monocytes in Transwell migration assay, whereas MRGPRX2-impaired LAD2 cells cannot. In addition, P17-treated LAD2 cells stimulated differentiation of THP-1 and human monocytes, as indicated by the enhanced expression of macrophage markers cluster of differentiation 11b and TNF-α by quantitative RT-PCR. Immunohistochemical and immunofluorescent staining suggested monocyte recruitment in mice ears injected with P17. CONCLUSIONS Our data provide novel structural information regarding the interaction of P17 with MRGPRX2 and intracellular pathways for its immunomodulatory action.
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Affiliation(s)
- Karthi Duraisamy
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Kailash Singh
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Mukesh Kumar
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Benjamin Lefranc
- INSERM U1239, PRIMACEN, IRIB, Normandy University, Rouen, France
| | - Elsa Bonnafé
- EA7417 BTSB, Université Fédérale Toulouse Midi-Pyrénées, INU Champollion, Albi, France
| | - Michel Treilhou
- EA7417 BTSB, Université Fédérale Toulouse Midi-Pyrénées, INU Champollion, Albi, France
| | - Jérôme Leprince
- INSERM U1239, PRIMACEN, IRIB, Normandy University, Rouen, France.
| | - Billy K C Chow
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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Jiang M, Zhao B, Luo S, Wang Q, Chu Y, Chen T, Mao X, Liu Y, Wang Y, Jiang X, Wei DQ, Xiong Y. NeuroPpred-Fuse: an interpretable stacking model for prediction of neuropeptides by fusing sequence information and feature selection methods. Brief Bioinform 2021; 22:6350884. [PMID: 34396388 DOI: 10.1093/bib/bbab310] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/01/2021] [Accepted: 07/18/2021] [Indexed: 12/13/2022] Open
Abstract
Neuropeptides acting as signaling molecules in the nervous system of various animals play crucial roles in a wide range of physiological functions and hormone regulation behaviors. Neuropeptides offer many opportunities for the discovery of new drugs and targets for the treatment of neurological diseases. In recent years, there have been several data-driven computational predictors of various types of bioactive peptides, but the relevant work about neuropeptides is little at present. In this work, we developed an interpretable stacking model, named NeuroPpred-Fuse, for the prediction of neuropeptides through fusing a variety of sequence-derived features and feature selection methods. Specifically, we used six types of sequence-derived features to encode the peptide sequences and then combined them. In the first layer, we ensembled three base classifiers and four feature selection algorithms, which select non-redundant important features complementarily. In the second layer, the output of the first layer was merged and fed into logistic regression (LR) classifier to train the model. Moreover, we analyzed the selected features and explained the feasibility of the selected features. Experimental results show that our model achieved 90.6% accuracy and 95.8% AUC on the independent test set, outperforming the state-of-the-art models. In addition, we exhibited the distribution of selected features by these tree models and compared the results on the training set to that on the test set. These results fully showed that our model has a certain generalization ability. Therefore, we expect that our model would provide important advances in the discovery of neuropeptides as new drugs for the treatment of neurological diseases.
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Affiliation(s)
- Mingming Jiang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bowen Zhao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shenggan Luo
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiankun Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanyi Chu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tianhang Chen
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xueying Mao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yatong Liu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanjing Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue Jiang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi Xiong
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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11
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Nihei KI, Peigneur S, Tytgat J, Lange AB, Konno K. Isolation and characterization of FMRFamide-like peptides in the venoms of solitary sphecid wasps. Peptides 2021; 142:170575. [PMID: 34023397 DOI: 10.1016/j.peptides.2021.170575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/14/2021] [Accepted: 05/10/2021] [Indexed: 12/21/2022]
Abstract
Purification of small peptide components in the venoms of the solitary sphecid wasps, Sphex argentatus argentatus and Isodontia harmandi, led to the isolation of several major peptides. Analysis of MS/MS spectra by MALDI-TOF/TOF revealed the sequence of a new peptide Sa112 (EDVDHVFLRF-NH2), which is structurally very similar to leucomyosupressin (pQDVDHVFLRF-NH2) and SchistoFLRFamide (PDVDHVFLRF-NH2), the FMRFamide-like peptides from cockroach and locust, respectively. Indeed, this new peptide, like SchistoFLRFamide, inhibited the frequency and amplitude of spontaneous contractions of the locust oviduct in a dose-dependent manner. A non-amidated peptide Sa12b (EDVDHVFLRF) was also isolated, but this peptide had no effect on spontaneous locust oviduct contraction. This is the first example of a FMRF-like peptide to be found in solitary wasp venom. Additionally, a truncated form of the myosuppressins, which has previously been synthesized and tested for biological activity, DVDHVFLRF-NH2 (Sh5b), was found for the first time as a natural product. Four other novel peptides were isolated and characterized as Sa81 (EDDLEDFNPTVS), Sa10 (EDDLEDFNPTIA), Sh41 (DDLSDFNPKV), and Sh42 (EDDLSDFNPKV). They are structurally related to each other, having a high content of acidic amino acids, but no structural similarity to any known peptides. Ion channel associated activities of Sh41 and Sh42 were tested, but did not show any activity for Na+, K+, Ca2+ channels.
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Affiliation(s)
- Ken-Ichi Nihei
- Department of Applied Biological Chemistry, School of Agriculture, Utsunomiya University, Tochigi 321-0943, Japan
| | - Steve Peigneur
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg, O&N2, Herestraat 49, P.O. Box 922, B-3000 Leuven, Belgium
| | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg, O&N2, Herestraat 49, P.O. Box 922, B-3000 Leuven, Belgium
| | - Angela B Lange
- Department of Biology, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Katsuhiro Konno
- Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan.
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Abstract
Since the introduction of insulin almost a century ago, more than 80 peptide drugs have reached the market for a wide range of diseases, including diabetes, cancer, osteoporosis, multiple sclerosis, HIV infection and chronic pain. In this Perspective, we summarize key trends in peptide drug discovery and development, covering the early efforts focused on human hormones, elegant medicinal chemistry and rational design strategies, peptide drugs derived from nature, and major breakthroughs in molecular biology and peptide chemistry that continue to advance the field. We emphasize lessons from earlier approaches that are still relevant today as well as emerging strategies such as integrated venomics and peptide-display libraries that create new avenues for peptide drug discovery. We also discuss the pharmaceutical landscape in which peptide drugs could be particularly valuable and analyse the challenges that need to be addressed for them to reach their full potential.
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13
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Southey BR, Zhang P, Keever MR, Rymut HE, Johnson RW, Sweedler JV, Rodriguez-Zas SL. Effects of maternal immune activation in porcine transcript isoforms of neuropeptide and receptor genes. J Integr Neurosci 2021; 20:21-31. [PMID: 33834688 PMCID: PMC8103820 DOI: 10.31083/j.jin.2021.01.332] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/11/2020] [Accepted: 02/09/2021] [Indexed: 12/17/2022] Open
Abstract
The prolonged effects of maternal immune activation in response stressors during gestation on the offspring's molecular pathways after birth are beginning to be understood. An association between maternal immune activation and neurodevelopmental and behavior disorders such as autism and schizophrenia spectrum disorders has been detected in long-term gene dysregulation. The incidence of alternative splicing among neuropeptides and neuropeptide receptor genes, critical cell-cell signaling molecules, associated with behavior may compromise the replicability of reported maternal immune activation effects at the gene level. This study aims to advance the understanding of the effect of maternal immune activation on transcript isoforms of the neuropeptide system (including neuropeptide, receptor and connecting pathway genes) underlying behavior disorders later in life. Recognizing the wide range of bioactive peptides and functional receptors stemming from alternative splicing, we studied the effects of maternal immune activation at the transcript isoform level on the hippocampus and amygdala of three-week-old pigs exposed to maternal immune activation due to viral infection during gestation. In the hippocampus and amygdala, 29 and 9 transcript isoforms, respectively, had maternal immune activation effects (P-value < 0.01). We demonstrated that the study of the effect of maternal immune activation on neuropeptide systems at the isoform level is necessary to expose opposite effects among transcript isoforms from the same gene. Genes were maternal immune activation effects have also been associated with neurodevelopmental and behavior disorders. The characterization of maternal immune activation effects at the transcript isoform level advances the understanding of neurodevelopmental disorders and identifies precise therapeutic targets.
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Affiliation(s)
- Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA
| | - Pan Zhang
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA
| | - Marissa R Keever
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA
| | - Haley E Rymut
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA
| | - Rodney W Johnson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA
| | - Jonathan V Sweedler
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA
| | - Sandra L Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA.,Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA.,Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA
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14
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Turner A, Kaas Q, Craik DJ. Hormone-like conopeptides - new tools for pharmaceutical design. RSC Med Chem 2020; 11:1235-1251. [PMID: 34095838 PMCID: PMC8126879 DOI: 10.1039/d0md00173b] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/11/2020] [Indexed: 12/24/2022] Open
Abstract
Conopeptides are a diverse family of peptides found in the venoms of marine cone snails and are used in prey capture and host defence. Because of their potent activity on a range of mammalian targets they have attracted interest as leads in drug design. Until recently most focus had been on studying conopeptides having activity at ion channels and related neurological targets but, with recent discoveries that some conopeptides might play hormonal roles, a new area of conopeptide research has opened. In this article we first summarize the canonical pharmaceutical families of Conus venom peptides and then focus on new research relating to hormone-like conopeptides and their potential applications. Finally, we briefly examine methods of chemically stabilizing conopeptides to improve their pharmacological properties. A summary is presented of conopeptides in clinical trials and a call for future work on hormone-like conopeptides.
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Affiliation(s)
- Ashlin Turner
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland 4072 Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland 4072 Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland 4072 Australia
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