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Grønning AGB, Kacprowski T, Schéele C. MultiPep: a hierarchical deep learning approach for multi-label classification of peptide bioactivities. Biol Methods Protoc 2021; 6:bpab021. [PMID: 34909478 PMCID: PMC8665375 DOI: 10.1093/biomethods/bpab021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/28/2021] [Accepted: 11/17/2021] [Indexed: 11/14/2022] Open
Abstract
Peptide-based therapeutics are here to stay and will prosper in the future. A key step in identifying novel peptide-drugs is the determination of their bioactivities. Recent advances in peptidomics screening approaches hold promise as a strategy for identifying novel drug targets. However, these screenings typically generate an immense number of peptides and tools for ranking these peptides prior to planning functional studies are warranted. Whereas a couple of tools in the literature predict multiple classes, these are constructed using multiple binary classifiers. We here aimed to use an innovative deep learning approach to generate an improved peptide bioactivity classifier with capacity of distinguishing between multiple classes. We present MultiPep: a deep learning multi-label classifier that assigns peptides to zero or more of 20 bioactivity classes. We train and test MultiPep on data from several publically available databases. The same data are used for a hierarchical clustering, whose dendrogram shapes the architecture of MultiPep. We test a new loss function that combines a customized version of Matthews correlation coefficient with binary cross entropy (BCE), and show that this is better than using class-weighted BCE as loss function. Further, we show that MultiPep surpasses state-of-the-art peptide bioactivity classifiers and that it predicts known and novel bioactivities of FDA-approved therapeutic peptides. In conclusion, we present innovative machine learning techniques used to produce a peptide prediction tool to aid peptide-based therapy development and hypothesis generation.
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Affiliation(s)
- Alexander G B Grønning
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics, TU Braunschweig and Hannover Medical School, 38106 Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), 38106 Braunschweig, Germany
| | - Camilla Schéele
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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Immunopotentiator thymosin alpha-1 attenuates inflammatory pain by modulating the Wnt3a/β-catenin pathway in spinal cord. Neuroreport 2020; 31:69-75. [PMID: 31764244 DOI: 10.1097/wnr.0000000000001370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The mechanism of inflammatory pain involves the central nervous system (CNS) and the immune system. It is reported that immunopotentiator thymosin alpha-1 (Tα1) can reduce inflammation, protect neurons and strengthen the immune function. However, the roles of Tα1 in inflammatory pain still remain unclear. In this study, we found Tα1 can attenuate the complete Freund's adjuvant (CFA)-induced mechanical allodynia and heat hyperalgesia. Meanwhile, it reduced the upregulation of CFA-induced inflammatory mediators (interferon (IFN)-γ, tumor necrosis factor-α and brain-derived neurotrophic factor). In addition, we found the Wnt3a/β-catenin pathway was activated in spinal cord after the injection of CFA, paralleling with pain hypersensitivity. However, Tα1 reversed this status. In summary, Tα1 could attenuate inflammatory pain by modulating the Wnt3a/β-catenin pathway. It might be related to the downregulation of inflammatory mediators.
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Xu Y, Jiang Y, Wang L, Huang J, Wen J, Lv H, Wu X, Wan C, Yu C, Zhang W, Zhao J, Zhou Y, Chen Y. Thymosin Alpha-1 Inhibits Complete Freund's Adjuvant-Induced Pain and Production of Microglia-Mediated Pro-inflammatory Cytokines in Spinal Cord. Neurosci Bull 2019; 35:637-648. [PMID: 30790216 DOI: 10.1007/s12264-019-00346-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/13/2018] [Indexed: 01/06/2023] Open
Abstract
Activation of inflammatory responses regulates the transmission of pain pathways through an integrated network in the peripheral and central nervous systems. The immunopotentiator thymosin alpha-1 (Tα1) has recently been reported to have anti-inflammatory and neuroprotective functions in rodents. However, how Tα1 affects inflammatory pain remains unclear. In the present study, intraperitoneal injection of Tα1 attenuated complete Freund's adjuvant (CFA)-induced pain hypersensitivity, and decreased the up-regulation of pro-inflammatory cytokines (TNF-α, IL-1β, and IL-6) in inflamed skin and the spinal cord. We found that CFA-induced peripheral inflammation evoked strong microglial activation, but the effect was reversed by Tα1. Notably, Tα1 reversed the CFA-induced up-regulation of vesicular glutamate transporter (VGLUT) and down-regulated the vesicular γ-aminobutyric acid transporter (VGAT) in the spinal cord. Taken together, these results suggest that Tα1 plays a therapeutic role in inflammatory pain and in the modulation of microglia-induced pro-inflammatory cytokine production in addition to mediation of VGLUT and VGAT expression in the spinal cord.
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Affiliation(s)
- Yunlong Xu
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Yanjun Jiang
- College of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Lin Wang
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Jiahua Huang
- The First Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Junmao Wen
- Graduate College, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Hang Lv
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xiaoli Wu
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Chaofan Wan
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Chuanxin Yu
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Wenjie Zhang
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Jiaying Zhao
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Yinqi Zhou
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Yongjun Chen
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
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Maltman DJ, Brand S, Belau E, Paape R, Suckau D, Przyborski SA. Top-down label-free LC-MALDI analysis of the peptidome during neural progenitor cell differentiation reveals complexity in cytoskeletal protein dynamics and identifies progenitor cell markers. Proteomics 2011; 11:3992-4006. [DOI: 10.1002/pmic.201100024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Revised: 05/26/2011] [Accepted: 06/10/2011] [Indexed: 12/19/2022]
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Siemion IZ, Kluczyk A, Cebrat M. The peptide molecular links between the central nervous and the immune systems. Amino Acids 2005; 29:161-76. [PMID: 16059661 DOI: 10.1007/s00726-005-0231-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Accepted: 06/17/2005] [Indexed: 12/24/2022]
Abstract
The central nervous system (CNS) and the immune system were for many years considered as two autonomous systems. Now, the reciprocal connections between them are generally recognized and very well documented. The links are realized mainly by various immuno- and neuropeptides. In the review the influence of the following immunopeptides on CNS is presented: tuftsin, thymulin, thymopoietin and thymopentin, thymosins, and thymic humoral factor. On the other side, the activity in the immune system of such neuropeptides as substance P, neurotensin, some neurokinins, enkephalins, and endorphins is discussed.
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Affiliation(s)
- I Z Siemion
- Faculty of Chemistry, University of Wrocław, Wrocław, Poland.
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Yang S, Liu ZW, Zhou WX, Zhang YX. Thymosin alpha-1 modulates excitatory synaptic transmission in cultured hippocampal neurons in rats. Neurosci Lett 2003; 350:81-4. [PMID: 12972158 DOI: 10.1016/s0304-3940(03)00862-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Thymosin alpha-1 (Talpha1) not only possesses immunoregulatory properties in periphery but also is expressed in the central nervous system (CNS) and affects the function of the CNS. To further elucidate the role of Talpha1 in the CNS, the whole-cell recording technique was used to observe the effect of Talpha1 on the spontaneous excitatory synaptic transmission in cultured rat hippocampal neurons. The results showed that acute treatment with Talpha1 significantly enhanced the frequency of AMPA-mediated spontaneous excitatory postsynaptic current (sEPSC) at the concentrations of 1 and 10 microg/ml and also enhanced the frequency of AMPA-mediated miniature excitatory postsynaptic current (mEPSC) at 10 microg/ml. However, the amplitude of both sEPSC and mEPSC were not changed by Talpha1. Those results suggested that Talpha1 involves in the regulation of excitatory synaptic transmission in hippocampal neurons, which contribute to its neurophysiological function in the CNS.
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Affiliation(s)
- Sheng Yang
- DBeijing Institute of Pharmacology and Toxicology, 27 Tai-Ping Road, Haidian District, Beijing 100850, China
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