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Florentino BR, Parmezan Bonidia R, Sanches NH, da Rocha UN, de Carvalho AC. BioPrediction-RPI: Democratizing the prediction of interaction between non-coding RNA and protein with end-to-end machine learning. Comput Struct Biotechnol J 2024; 23:2267-2276. [PMID: 38827228 PMCID: PMC11140557 DOI: 10.1016/j.csbj.2024.05.031] [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: 03/14/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/04/2024] Open
Abstract
Machine Learning (ML) algorithms have been important tools for the extraction of useful knowledge from biological sequences, particularly in healthcare, agriculture, and the environment. However, the categorical and unstructured nature of these sequences requiring usually additional feature engineering steps, before an ML algorithm can be efficiently applied. The addition of these steps to the ML algorithm creates a processing pipeline, known as end-to-end ML. Despite the excellent results obtained by applying end-to-end ML to biotechnology problems, the performance obtained depends on the expertise of the user in the components of the pipeline. In this work, we propose an end-to-end ML-based framework called BioPrediction-RPI, which can identify implicit interactions between sequences, such as pairs of non-coding RNA and proteins, without the need for specialized expertise in end-to-end ML. This framework applies feature engineering to represent each sequence by structural and topological features. These features are divided into feature groups and used to train partial models, whose partial decisions are combined into a final decision, which, provides insights to the user by giving an interpretability report. In our experiments, the developed framework was competitive when compared with various expert-created models. We assessed BioPrediction-RPI with 12 datasets when it presented equal or better performance than all tools in 40% to 100% of cases, depending on the experiment. Finally, BioPrediction-RPI can fine-tune models based on new data and perform at the same level as ML experts, democratizing end-to-end ML and increasing its access to those working in biological sciences.
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Affiliation(s)
- Bruno Rafael Florentino
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, 13566-590, São Paulo, Brazil
| | - Robson Parmezan Bonidia
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, 13566-590, São Paulo, Brazil
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, 86300-000, Paraná, Brazil
| | - Natan Henrique Sanches
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, 13566-590, São Paulo, Brazil
| | - Ulisses N. da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ GmbH, Leipzig, Saxony, Germany
| | - André C.P.L.F. de Carvalho
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, 13566-590, São Paulo, Brazil
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Nelson DR, Mystikou A, Jaiswal A, Rad-Menendez C, Preston MJ, De Boever F, El Assal DC, Daakour S, Lomas MW, Twizere JC, Green DH, Ratcliff WC, Salehi-Ashtiani K. Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity. MOLECULAR PLANT 2024; 17:747-771. [PMID: 38614077 DOI: 10.1016/j.molp.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/31/2024] [Accepted: 03/08/2024] [Indexed: 04/15/2024]
Abstract
Macroalgae are multicellular, aquatic autotrophs that play vital roles in global climate maintenance and have diverse applications in biotechnology and eco-engineering, which are directly linked to their multicellularity phenotypes. However, their genomic diversity and the evolutionary mechanisms underlying multicellularity in these organisms remain uncharacterized. In this study, we sequenced 110 macroalgal genomes from diverse climates and phyla, and identified key genomic features that distinguish them from their microalgal relatives. Genes for cell adhesion, extracellular matrix formation, cell polarity, transport, and cell differentiation distinguish macroalgae from microalgae across all three major phyla, constituting conserved and unique gene sets supporting multicellular processes. Adhesome genes show phylum- and climate-specific expansions that may facilitate niche adaptation. Collectively, our study reveals genetic determinants of convergent and divergent evolutionary trajectories that have shaped morphological diversity in macroalgae and provides genome-wide frameworks to understand photosynthetic multicellular evolution in aquatic environments.
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Affiliation(s)
- David R Nelson
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Alexandra Mystikou
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE; Biotechnology Research Center, Technology Innovation Institute, PO Box 9639, Masdar City, Abu Dhabi, UAE.
| | - Ashish Jaiswal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Cecilia Rad-Menendez
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - Michael J Preston
- National Center for Marine Algae and Microbiota, Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Frederik De Boever
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - Diana C El Assal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Michael W Lomas
- National Center for Marine Algae and Microbiota, Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Jean-Claude Twizere
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
| | - David H Green
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kourosh Salehi-Ashtiani
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE.
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Su H, Yan Q, Du W, Hu E, Yang Z, Zhang W, Li Y, Tang T, Zhao S, Wang Y. Calycosin ameliorates osteoarthritis by regulating the imbalance between chondrocyte synthesis and catabolism. BMC Complement Med Ther 2024; 24:48. [PMID: 38254101 PMCID: PMC10804771 DOI: 10.1186/s12906-023-04314-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
Osteoarthritis (OA) is a severe chronic inflammatory disease. As the main active component of Astragalus mongholicus Bunge, a classic traditional ethnic herb, calycosin exhibits anti-inflammatory action and its mechanism of exact targets for OA have yet to be determined. In this study, we established an anterior cruciate ligament transection (ACLT) mouse model. Mice were randomized to sham, OA, and calycosin groups. Cartilage synthesis markers type II collagen (Col-2) and SRY-Box Transcription Factor 9 (Sox-9) increased significantly after calycosin gavage. While cartilage matrix degradation index cyclooxygenase-2 (COX-2), phosphor-epidermal growth factor receptor (p-EGFR), and matrix metalloproteinase-9 (MMP9) expression were decreased. With the help of network pharmacology and molecular docking, these results were confirmed in chondrocyte ADTC5 cells. Our results indicated that the calycosin treatment significantly improved cartilage damage, this was probably attributed to reversing the imbalance between chondrocyte synthesis and catabolism.
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Affiliation(s)
- Hong Su
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China
| | - Qiuju Yan
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China
| | - Wei Du
- Department of Orthopedics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan Province, China
- Department of Rehabilitation Medicine, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan Province, China
| | - En Hu
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China
| | - Zhaoyu Yang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China
| | - Wei Zhang
- The College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Yusheng Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China
- Department of Orthopedics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan Province, China
| | - Tao Tang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China
| | - Shushan Zhao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China.
- Department of Orthopedics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan Province, China.
| | - Yang Wang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China.
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Bitencourt-Ferreira G, Villarreal MA, Quiroga R, Biziukova N, Poroikov V, Tarasova O, de Azevedo Junior WF. Exploring Scoring Function Space: Developing Computational Models for Drug Discovery. Curr Med Chem 2024; 31:2361-2377. [PMID: 36944627 DOI: 10.2174/0929867330666230321103731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/15/2022] [Accepted: 12/29/2022] [Indexed: 03/23/2023]
Abstract
BACKGROUND The idea of scoring function space established a systems-level approach to address the development of models to predict the affinity of drug molecules by those interested in drug discovery. OBJECTIVE Our goal here is to review the concept of scoring function space and how to explore it to develop machine learning models to address protein-ligand binding affinity. METHODS We searched the articles available in PubMed related to the scoring function space. We also utilized crystallographic structures found in the protein data bank (PDB) to represent the protein space. RESULTS The application of systems-level approaches to address receptor-drug interactions allows us to have a holistic view of the process of drug discovery. The scoring function space adds flexibility to the process since it makes it possible to see drug discovery as a relationship involving mathematical spaces. CONCLUSION The application of the concept of scoring function space has provided us with an integrated view of drug discovery methods. This concept is useful during drug discovery, where we see the process as a computational search of the scoring function space to find an adequate model to predict receptor-drug binding affinity.
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Affiliation(s)
| | - Marcos A Villarreal
- CONICET-Departamento de Matemática y Física, Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Rodrigo Quiroga
- CONICET-Departamento de Matemática y Física, Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Nadezhda Biziukova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow, 119121, Russia
| | - Vladimir Poroikov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow, 119121, Russia
| | - Olga Tarasova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow, 119121, Russia
| | - Walter F de Azevedo Junior
- Pontifical Catholic University of Rio Grande do Sul - PUCRS, Porto Alegre-RS, Brazil
- Specialization Program in Bioinformatics, The Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681 Porto Alegre / RS 90619-900, Brazil
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Cen LP, Ng TK, Ji J, Lin JW, Yao Y, Yang R, Dong G, Cao Y, Chen C, Yao SQ, Wang WY, Huang Z, Qiu K, Pang CP, Liu Q, Zhang M. Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases. Database (Oxford) 2023; 2023:baad083. [PMID: 38109881 PMCID: PMC10727695 DOI: 10.1093/database/baad083] [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: 10/29/2022] [Revised: 07/17/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
The aim of the study is to establish an online database for predicting protein structures altered in ocular diseases by Alphafold2 and RoseTTAFold algorithms. Totally, 726 genes of multiple ocular diseases were collected for protein structure prediction. Both Alphafold2 and RoseTTAFold algorithms were built locally using the open-source codebases. A dataset with 48 protein structures from Protein Data Bank (PDB) was adopted for algorithm set-up validation. A website was built to match ocular genes with the corresponding predicted tertiary protein structures for each amino acid sequence. The predicted local distance difference test-Cα (pLDDT) and template modeling (TM) scores of the validation protein structure and the selected ocular genes were evaluated. Molecular dynamics and molecular docking simulations were performed to demonstrate the applications of the predicted structures. For the validation dataset, 70.8% of the predicted protein structures showed pLDDT greater than 90. Compared to the PDB structures, 100% of the AlphaFold2-predicted structures and 97.9% of the RoseTTAFold-predicted structure showed TM score greater than 0.5. Totally, 1329 amino acid sequences of 430 ocular disease-related genes have been predicted, of which 75.9% showed pLDDT greater than 70 for the wildtype sequences and 76.1% for the variant sequences. Small molecule docking and molecular dynamics simulations revealed that the predicted protein structures with higher confidence scores showed similar molecular characteristics with the structures from PDB. We have developed an ocular protein structure database (EyeProdb) for ocular disease, which is released for the public and will facilitate the biological investigations and structure-based drug development for ocular diseases. Database URL: http://eyeprodb.jsiec.org.
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Affiliation(s)
| | - Tsz Kin Ng
- Joint Shantou International Eye Centre of Shantou University and The Chinese University of Hong Kong, North Dongxia Road (Guangxia New Town), Shantou, Guangdong 515041, China
- Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong 515041, China
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, 147K Argyle Street, KLN, Hong Kong
| | - Jie Ji
- Network & Information Centre, Shantou University, 243 Daxue Road, Shantou, Guangdong 515063, China
| | - Jian-Wei Lin
- Joint Shantou International Eye Centre of Shantou University and The Chinese University of Hong Kong, North Dongxia Road (Guangxia New Town), Shantou, Guangdong 515041, China
| | - Yao Yao
- Joint Shantou International Eye Centre of Shantou University and The Chinese University of Hong Kong, North Dongxia Road (Guangxia New Town), Shantou, Guangdong 515041, China
- Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong 515041, China
| | - Rucui Yang
- Joint Shantou International Eye Centre of Shantou University and The Chinese University of Hong Kong, North Dongxia Road (Guangxia New Town), Shantou, Guangdong 515041, China
- Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong 515041, China
| | - Geng Dong
- Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong 515041, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong 515041, China
| | - Yingjie Cao
- Joint Shantou International Eye Centre of Shantou University and The Chinese University of Hong Kong, North Dongxia Road (Guangxia New Town), Shantou, Guangdong 515041, China
| | - Chongbo Chen
- Joint Shantou International Eye Centre of Shantou University and The Chinese University of Hong Kong, North Dongxia Road (Guangxia New Town), Shantou, Guangdong 515041, China
| | - Shi-Qi Yao
- Joint Shantou International Eye Centre of Shantou University and The Chinese University of Hong Kong, North Dongxia Road (Guangxia New Town), Shantou, Guangdong 515041, China
- Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong 515041, China
| | - Wen-Ying Wang
- Joint Shantou International Eye Centre of Shantou University and The Chinese University of Hong Kong, North Dongxia Road (Guangxia New Town), Shantou, Guangdong 515041, China
- Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong 515041, China
| | - Zijing Huang
- Joint Shantou International Eye Centre of Shantou University and The Chinese University of Hong Kong, North Dongxia Road (Guangxia New Town), Shantou, Guangdong 515041, China
| | - Kunliang Qiu
- Joint Shantou International Eye Centre of Shantou University and The Chinese University of Hong Kong, North Dongxia Road (Guangxia New Town), Shantou, Guangdong 515041, China
| | - Chi Pui Pang
- Joint Shantou International Eye Centre of Shantou University and The Chinese University of Hong Kong, North Dongxia Road (Guangxia New Town), Shantou, Guangdong 515041, China
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, 147K Argyle Street, KLN, Hong Kong
| | - Qingping Liu
- Joint Shantou International Eye Centre of Shantou University and The Chinese University of Hong Kong, North Dongxia Road (Guangxia New Town), Shantou, Guangdong 515041, China
- Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong 515041, China
| | - Mingzhi Zhang
- Joint Shantou International Eye Centre of Shantou University and The Chinese University of Hong Kong, North Dongxia Road (Guangxia New Town), Shantou, Guangdong 515041, China
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Kunnakkattu IR, Choudhary P, Pravda L, Nadzirin N, Smart OS, Yuan Q, Anyango S, Nair S, Varadi M, Velankar S. PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank. J Cheminform 2023; 15:117. [PMID: 38042830 PMCID: PMC10693035 DOI: 10.1186/s13321-023-00786-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
While the Protein Data Bank (PDB) contains a wealth of structural information on ligands bound to macromolecules, their analysis can be challenging due to the large amount and diversity of data. Here, we present PDBe CCDUtils, a versatile toolkit for processing and analysing small molecules from the PDB in PDBx/mmCIF format. PDBe CCDUtils provides streamlined access to all the metadata for small molecules in the PDB and offers a set of convenient methods to compute various properties using RDKit, such as 2D depictions, 3D conformers, physicochemical properties, scaffolds, common fragments, and cross-references to small molecule databases using UniChem. The toolkit also provides methods for identifying all the covalently attached chemical components in a macromolecular structure and calculating similarity among small molecules. By providing a broad range of functionality, PDBe CCDUtils caters to the needs of researchers in cheminformatics, structural biology, bioinformatics and computational chemistry.
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Affiliation(s)
- Ibrahim Roshan Kunnakkattu
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Preeti Choudhary
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Lukas Pravda
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Nurul Nadzirin
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Oliver S Smart
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Qi Yuan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stephen Anyango
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sreenath Nair
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Mihaly Varadi
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Chinyama HA, Wei L, Mokgautsi N, Lawal B, Wu ATH, Huang HS. Identification of CDK1, PBK, and CHEK1 as an Oncogenic Signature in Glioblastoma: A Bioinformatics Approach to Repurpose Dapagliflozin as a Therapeutic Agent. Int J Mol Sci 2023; 24:16396. [PMID: 38003585 PMCID: PMC10671581 DOI: 10.3390/ijms242216396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/27/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Glioblastoma multiforme (GBM) is the most aggressive and lethal primary brain tumor whose median survival is less than 15 months. The current treatment regimen comprising surgical resectioning, chemotherapy with Temozolomide (TMZ), and adjuvant radiotherapy does not achieve total patient cure. Stem cells' presence and GBM tumor heterogeneity increase their resistance to TMZ, hence the poor overall survival of patients. A dysregulated cell cycle in glioblastoma enhances the rapid progression of GBM by evading senescence or apoptosis through an over-expression of cyclin-dependent kinases and other protein kinases that are the cell cycle's main regulatory proteins. Herein, we identified and validated the biomarker and predictive properties of a chemoradio-resistant oncogenic signature in GBM comprising CDK1, PBK, and CHEK1 through our comprehensive in silico analysis. We found that CDK1/PBK/CHEK1 overexpression drives the cell cycle, subsequently promoting GBM tumor progression. In addition, our Kaplan-Meier survival estimates validated the poor patient survival associated with an overexpression of these genes in GBM. We used in silico molecular docking to analyze and validate our objective to repurpose Dapagliflozin against CDK1/PBK/CHEK1. Our results showed that Dapagliflozin forms putative conventional hydrogen bonds with CDK1, PBK, and CHEK1 and arrests the cell cycle with the lowest energies as Abemaciclib.
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Affiliation(s)
- Harold A. Chinyama
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Li Wei
- Department of Neurosurgery, Wan Fang Hospital, Taipei Medical University, No.111, Sec. 3, Xinglong Rd., Taipei 11696, Taiwan;
- Taipei Neuroscience Institute, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Injury Prevention and Control, College of Public Health, Taipei Medical University, Taipei 11031, Taiwan
| | - Ntlotlang Mokgautsi
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan;
- Graduate Institute for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Bashir Lawal
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232, USA;
| | - Alexander T. H. Wu
- PhD Program of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Clinical Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 11490, Taiwan
| | - Hsu-Shan Huang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan;
- Graduate Institute for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- School of Pharmacy, National Defense Medical Center, Taipei 11490, Taiwan
- PhD Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
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8
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Mukherjee S, Patra R, Behzadi P, Masotti A, Paolini A, Sarshar M. Toll-like receptor-guided therapeutic intervention of human cancers: molecular and immunological perspectives. Front Immunol 2023; 14:1244345. [PMID: 37822929 PMCID: PMC10562563 DOI: 10.3389/fimmu.2023.1244345] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/07/2023] [Indexed: 10/13/2023] Open
Abstract
Toll-like receptors (TLRs) serve as the body's first line of defense, recognizing both pathogen-expressed molecules and host-derived molecules released from damaged or dying cells. The wide distribution of different cell types, ranging from epithelial to immune cells, highlights the crucial roles of TLRs in linking innate and adaptive immunity. Upon stimulation, TLRs binding mediates the expression of several adapter proteins and downstream kinases, that lead to the induction of several other signaling molecules such as key pro-inflammatory mediators. Indeed, extraordinary progress in immunobiological research has suggested that TLRs could represent promising targets for the therapeutic intervention of inflammation-associated diseases, autoimmune diseases, microbial infections as well as human cancers. So far, for the prevention and possible treatment of inflammatory diseases, various TLR antagonists/inhibitors have shown to be efficacious at several stages from pre-clinical evaluation to clinical trials. Therefore, the fascinating role of TLRs in modulating the human immune responses at innate as well as adaptive levels directed the scientists to opt for these immune sensor proteins as suitable targets for developing chemotherapeutics and immunotherapeutics against cancer. Hitherto, several TLR-targeting small molecules (e.g., Pam3CSK4, Poly (I:C), Poly (A:U)), chemical compounds, phytocompounds (e.g., Curcumin), peptides, and antibodies have been found to confer protection against several types of cancers. However, administration of inappropriate doses of such TLR-modulating therapeutics or a wrong infusion administration is reported to induce detrimental outcomes. This review summarizes the current findings on the molecular and structural biology of TLRs and gives an overview of the potency and promises of TLR-directed therapeutic strategies against cancers by discussing the findings from established and pipeline discoveries.
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Affiliation(s)
- Suprabhat Mukherjee
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
| | - Ritwik Patra
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
| | - Payam Behzadi
- Department of Microbiology, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
| | - Alessandro Paolini
- Research Laboratories, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
| | - Meysam Sarshar
- Research Laboratories, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
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9
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Kuang Y, Shen W, Ma X, Wang Z, Xu R, Rao Q, Yang S. In silico identification of natural compounds against SARS-CoV-2 main protease from Chinese herbal medicines. Future Sci OA 2023; 9:FSO873. [PMID: 37485448 PMCID: PMC10357396 DOI: 10.2144/fsoa-2023-0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/30/2023] [Indexed: 07/25/2023] Open
Abstract
Aims To determine natural compounds with inhibitory effects toward SARS-CoV-2 Mpro from Chinese herbal medicines. Materials & methods ∼1200 natural compounds from 19 Chinese herbal medicines were collected. Computational methods including molecular docking, drug-likeness assessment, molecular dynamics simulation and molecular mechanics Poisson-Boltzmann surface area analysis were combined to obtain potent inhibitors against SARS-CoV-2 Mpro. Results Top 20 compounds mainly originated from Ranunculus ternatus and Picrasma quassioides exhibited low binding free energies which below -9.0 kcal/mol. Compounds Japonicone G and Picrasidine T were obtained with favorable drug-likeness. Moreover, the complex of Japonicone G and Mpro had prominent stability. Conclusion Natural compound Japonicone G is highly promising as a potent inhibitor against SARS-CoV-2 for further study.
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Affiliation(s)
- Yi Kuang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China
| | - Wenjing Shen
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China
| | - Xiaodong Ma
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China
| | - Ziwei Wang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China
| | - Rui Xu
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China
| | - Qingqing Rao
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China
| | - Shengxiang Yang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China
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10
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Wang L, Li P, Zhou Y, Gu R, Lu G, Zhang C. Magnoflorine Ameliorates Collagen-Induced Arthritis by Suppressing the Inflammation Response via the NF-κB/MAPK Signaling Pathways. J Inflamm Res 2023; 16:2271-2296. [PMID: 37265745 PMCID: PMC10231344 DOI: 10.2147/jir.s406298] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/18/2023] [Indexed: 06/03/2023] Open
Abstract
Objective Magnoflorine (Mag) has been reported to have anxiolytics, anti-cancer, and anti-inflammatory properties. In this study, we aim to investigate the effects of Mag on the rheumatoid arthritis (RA) and explore the underlying mechanism using a collagen-induced arthritis (CIA) mouse model and a lipopolysaccharide (LPS)-stimulated macrophage inflammation model. Methods The in vivo effects of Mag on CIA were studied by inducing CIA in a mouse model using DBA/1J mice followed by treatment with vehicle, methotrexate (MTX, 1 mg/kg/d), and Mag (5 mg/kg/d, 10 mg/kg/d, and 20 mg/kg/d), and the in vitro effects of Mag on macrophages were examined by stimulation of RAW264.7 cells line and peritoneal macrophages (PMs) by LPS in the presence of different concentrations of Mag. Network pharmacology and molecular docking was then performed to predict the the binding ability between Mag and its targets. Inflammatory mediators were assayed by quantitative real-time PCR and enzyme linked immunosorbent assay (ELISA). Signaling pathway changes were subsequently determined by Western blotting and immunohistochemistry (IHC). Results In vivo experiments demonstrated that Mag decreased arthritis severity scores, joints destruction, and macrophages infiltration into the synovial tissues of the CIA mice. Network pharmacology analysis revealed that Mag interacted with TNF-α, IL-6, IL-1β, and MCP-1. Consistent with this, analysis of the serum, synovial tissue of the CIA mice, and the supernatant of the cultured RAW264.7 cells and PMs showed that Mag suppressed the expression of TNF-α, IL-6, IL-1β, MCP-1, iNOS, and IFN-β. Furthermore, Mag attenuated the phosphorylation of p65, IκBα, ERK, JNK, and p38 MAPKs in the synovial tissues of the CIA mice and LPS-stimulated RAW 264.7 cells. Conclusion Mag may exert anti-arthritic and anti-inflammatory effects by inhibiting the activation of NF-κB and MAPK signaling pathways.
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Affiliation(s)
- Lei Wang
- College of First Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Pengfei Li
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
| | - Yu Zhou
- College of First Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Renjun Gu
- School of Chinese Medicine & School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Ge Lu
- College of Acupuncture-Moxibustion and Tuina, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Chunbing Zhang
- College of First Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- State Key Laboratory of Ultrasound in Medicine and Engineering, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
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11
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Kuang Y, Ma X, Shen W, Rao Q, Yang S. Discovery of 3CLpro inhibitor of SARS-CoV-2 main protease. Future Sci OA 2023; 9:FSO853. [PMID: 37090493 PMCID: PMC10116374 DOI: 10.2144/fsoa-2023-0020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
Coronavirus main protease (3CLpro), a special cysteine protease in coronavirus family, is highly desirable in the life cycle of coronavirus. Here, molecular docking, ADMET pharmacokinetic profiles and molecular dynamics (MD) simulation were performed to develop specific 3CLpro inhibitor. The results showed that the 137 compounds originated from Chinese herbal have good binding affinity to 3CLpro. Among these, Cleomiscosin C, (+)-Norchelidonine, Protopine, Turkiyenine, Isochelidonine and Mallotucin A possessed prominent drug-likeness properties. Cleomiscosin C and Turkiyenine exhibited excellent pharmacokinetic profiles. Furthermore, the complex of Cleomiscosin C with SARS-CoV-2 main protease presented high stability. The findings in this work indicated that Cleomiscosin C is highly promising as a potential 3CLpro inhibitor, thus facilitating the development of effective drugs for COVID-19.
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Affiliation(s)
- Yi Kuang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Xiaodong Ma
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Wenjing Shen
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Qingqing Rao
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Shengxiang Yang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
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12
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Abstract
Artificial intelligence (AI) methods have been and are now being increasingly integrated in prediction software implemented in bioinformatics and its glycoscience branch known as glycoinformatics. AI techniques have evolved in the past decades, and their applications in glycoscience are not yet widespread. This limited use is partly explained by the peculiarities of glyco-data that are notoriously hard to produce and analyze. Nonetheless, as time goes, the accumulation of glycomics, glycoproteomics, and glycan-binding data has reached a point where even the most recent deep learning methods can provide predictors with good performance. We discuss the historical development of the application of various AI methods in the broader field of glycoinformatics. A particular focus is placed on shining a light on challenges in glyco-data handling, contextualized by lessons learnt from related disciplines. Ending on the discussion of state-of-the-art deep learning approaches in glycoinformatics, we also envision the future of glycoinformatics, including development that need to occur in order to truly unleash the capabilities of glycoscience in the systems biology era.
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Affiliation(s)
- Daniel Bojar
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 41390, Sweden
- Wallenberg
Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg 41390, Sweden
| | - Frederique Lisacek
- Proteome
Informatics Group, Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland
- Computer
Science Department & Section of Biology, University of Geneva, route de Drize 7, CH-1227, Geneva, Switzerland
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13
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Sagulkoo P, Chuntakaruk H, Rungrotmongkol T, Suratanee A, Plaimas K. Multi-Level Biological Network Analysis and Drug Repurposing Based on Leukocyte Transcriptomics in Severe COVID-19: In Silico Systems Biology to Precision Medicine. J Pers Med 2022; 12:jpm12071030. [PMID: 35887528 PMCID: PMC9319133 DOI: 10.3390/jpm12071030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 01/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic causes many morbidity and mortality cases. Despite several developed vaccines and antiviral therapies, some patients experience severe conditions that need intensive care units (ICU); therefore, precision medicine is necessary to predict and treat these patients using novel biomarkers and targeted drugs. In this study, we proposed a multi-level biological network analysis framework to identify key genes via protein–protein interaction (PPI) network analysis as well as survival analysis based on differentially expressed genes (DEGs) in leukocyte transcriptomic profiles, discover novel biomarkers using microRNAs (miRNA) from regulatory network analysis, and provide candidate drugs targeting the key genes using drug–gene interaction network and structural analysis. The results show that upregulated DEGs were mainly enriched in cell division, cell cycle, and innate immune signaling pathways. Downregulated DEGs were primarily concentrated in the cellular response to stress, lysosome, glycosaminoglycan catabolic process, and mature B cell differentiation. Regulatory network analysis revealed that hsa-miR-6792-5p, hsa-let-7b-5p, hsa-miR-34a-5p, hsa-miR-92a-3p, and hsa-miR-146a-5p were predicted biomarkers. CDC25A, GUSB, MYBL2, and SDAD1 were identified as key genes in severe COVID-19. In addition, drug repurposing from drug–gene and drug–protein database searching and molecular docking showed that camptothecin and doxorubicin were candidate drugs interacting with the key genes. In conclusion, multi-level systems biology analysis plays an important role in precision medicine by finding novel biomarkers and targeted drugs based on key gene identification.
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Affiliation(s)
- Pakorn Sagulkoo
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand; (P.S.); (H.C.); (T.R.)
- Center of Biomedical Informatics, Department of Family Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Hathaichanok Chuntakaruk
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand; (P.S.); (H.C.); (T.R.)
- Center of Excellence in Biocatalyst and Sustainable Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand; (P.S.); (H.C.); (T.R.)
- Center of Excellence in Biocatalyst and Sustainable Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Apichat Suratanee
- Department of Mathematics, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok, Bangkok 10800, Thailand;
- Intelligent and Nonlinear Dynamics Innovations Research Center, Science and Technology Research Institute, King Mongkut’s University of Technology North Bangkok, Bangkok 10800, Thailand
| | - Kitiporn Plaimas
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand; (P.S.); (H.C.); (T.R.)
- Advance Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence:
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14
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The Interleukin-1 (IL-1) Superfamily Cytokines and Their Single Nucleotide Polymorphisms (SNPs). J Immunol Res 2022; 2022:2054431. [PMID: 35378905 PMCID: PMC8976653 DOI: 10.1155/2022/2054431] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/24/2022] [Accepted: 03/08/2022] [Indexed: 12/19/2022] Open
Abstract
Interleukins (ILs)—which are important members of cytokines—consist of a vast group of molecules, including a wide range of immune mediators that contribute to the immunological responses of many cells and tissues. ILs are immune-glycoproteins, which directly contribute to the growth, activation, adhesion, differentiation, migration, proliferation, and maturation of immune cells; and subsequently, they are involved in the pro and anti-inflammatory responses of the body, by their interaction with a wide range of receptors. Due to the importance of immune system in different organisms, the genes belonging to immune elements, such as ILs, have been studied vigorously. The results of recent investigations showed that the genes pertaining to the immune system undergo progressive evolution with a constant rate. The occurrence of any mutation or polymorphism in IL genes may result in substantial changes in their biology and function and may be associated with a wide range of diseases and disorders. Among these abnormalities, single nucleotide polymorphisms (SNPs) can represent as important disruptive factors. The present review aims at concisely summarizing the current knowledge available on the occurrence, properties, role, and biological consequences of SNPs within the IL-1 family members.
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