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Wang K, Wang J, Chen L, Hou J, Lu F, Liu Y. Effect of sanxan as novel natural gel modifier on the physicochemical and structural properties of microbial transglutaminase-induced mung bean protein isolate gels. Food Chem 2024; 449:139147. [PMID: 38581784 DOI: 10.1016/j.foodchem.2024.139147] [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: 01/04/2024] [Revised: 03/04/2024] [Accepted: 03/24/2024] [Indexed: 04/08/2024]
Abstract
Mung bean protein isolate (MBPI) has attracted much attention as an emerging plant protein. However, its application was limited by the poor gelling characteristics. Thus, the effect of sanxan (SAN) on the gelling behavior of MBPI under microbial transglutaminase (MTG)-induced condition were explored in this study. The results demonstrated that SAN remarkably enhanced the storage modulus, water-holding capacity and mechanical strength. Furthermore, SAN changed the microstructure of MBPI gels to become more dense and ordered. The results of zeta potential indicated the electrostatic interactions existed between SAN and MBPI. The incorporation of SAN altered the secondary structure and molecular conformation of MBPI, and hydrophobic interactions and hydrogen bonding were necessary to maintain the network structure. Additionally, in vitro digestion simulation results exhibited that SAN remarkably improved the capability of MBPI gels to deliver bioactive substances. These findings provided a practical strategy to use natural SAN to improve legume protein gels.
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Affiliation(s)
- Kangning Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jiahui Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Lei Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jiayi Hou
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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2
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Colombo RB, Maxit C, Martinelli D, Anderson M, Masone D, Mayorga L. PURA and GLUT1: Sweet partners for brain health. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167261. [PMID: 38777099 DOI: 10.1016/j.bbadis.2024.167261] [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: 12/26/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
PURA, also known as Pur-alpha, is an evolutionarily conserved DNA/RNA-binding protein crucial for various cellular processes, including DNA replication, transcriptional regulation, and translational control. Comprising three PUR domains, it engages with nucleic acids and has a role in protein-protein interactions. The manifestation of PURA syndrome, arising from mutations in the PURA gene, presents neurologically with developmental delay, hypotonia, and seizures. In our prior work from 2018, we highlighted the unique case of a PURA patient displaying hypoglycorrhachia, suggesting a potential association with GLUT1 dysfunction in this syndrome. In this current study, we expand the patient cohort with PURA mutations exhibiting hypoglycorrhachia and aim to unravel the molecular basis of this phenomenon. We established an in vitro model in HeLa cells to modulate PURA expression and investigated GLUT1 function and expression. Our findings indicate that PURA levels directly impact glucose uptake through the functioning of GLUT1, without influencing significantly GLUT1 expression. Moreover, our study reveals evidence for a possible physical interaction between PURA and GLUT1, demonstrated by colocalization and co-immunoprecipitation of both proteins. Computational analyses, employing molecular dynamics, further corroborates these findings, demonstrating that PURA:GLUT1 interactions are plausible, and that the stability of the complex is altered when PURA is truncated and/or mutated. In conclusion, our results suggest that PURA plays a pivotal role in driving the function of GLUT1 for glucose uptake, potentially forming a regulatory complex. Additional investigations are warranted to elucidate the precise mechanisms governing this complex and its significance in ensuring proper GLUT1 function.
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Affiliation(s)
- Rocío B Colombo
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina; Facultad De Química, Bioquímica y Farmacia, Universidad Nacional De San Luis, San Luis, Argentina
| | - Clarisa Maxit
- Servicio de Neurología infantil, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Diego Martinelli
- Division of Metabolism, Bambino Gesù Children's Hospital, Rome, Italy
| | - Mel Anderson
- PURA Foundation Australia, Plenty Victoria, Australia
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina; Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
| | - Lía Mayorga
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina; Instituto de Neurología Infantojuvenil (Neuroinfan), Mendoza, Argentina.
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3
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Min TT, Choowongkomon K, Htoo HH, Nonejuie P, Haltrich D, Yamabhai M. Anti-CAMP1 IgG promotes macrophage phagocytosis of Cutibacterium acnes type II. Microbiol Res 2024; 285:127749. [PMID: 38761490 DOI: 10.1016/j.micres.2024.127749] [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: 03/20/2024] [Revised: 04/28/2024] [Accepted: 05/03/2024] [Indexed: 05/20/2024]
Abstract
Among 5 types of the Christie-Atkins-Munch-Petersen factor (CAMP) of Cutibacterium acnes, CAMP1 is highly expressed in phylotype II as well as IB, and thought to be a virulence factor of opportunistic but fatal blood, soft tissue, and implant-related infections. The target of a human single-chain variable antibody fragment (scFv), recently isolated from a phage display library, has been identified as CAMP1 of phylotype II, using immunoprecipitation followed by mass spectrometry, phage display peptide biopanning, 3D-modelling, and ELISA. The IgG1 format of the antibody could enhance phagocytosis of C. acnes DMST 14916 by THP-1 human monocytes. Our results suggest that the antibody-dependent phagocytosis process is mediated by the caveolae membrane system and involves the induction of IL-1β. This is the first report on the study of a human antibody against CAMP1 of C. acnes phylotype II, of which a potential use as therapeutic antibody against virulence C. acnes infection is postulated.
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Affiliation(s)
- Thae Thae Min
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Htut Htut Htoo
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Dietmar Haltrich
- Department of Food Sciences and Technology, University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Montarop Yamabhai
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.
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4
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Chiawpanit C, Wathikthinnakorn M, Sawasdee N, Phanthaphol N, Sujjitjoon J, Junking M, Yamabhai M, Panaampon J, Yenchitsomanus PT, Panya A. Precision immunotherapy for cholangiocarcinoma: Pioneering the use of human-derived anti-cMET single chain variable fragment in anti-cMET chimeric antigen receptor (CAR) NK cells. Int Immunopharmacol 2024; 136:112273. [PMID: 38810311 DOI: 10.1016/j.intimp.2024.112273] [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: 12/31/2023] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
Cholangiocarcinoma (CCA) presents a significant clinical challenge which is often identified in advanced stages, therby restricting the effectiveness of surgical interventions for most patients. The high incidence of cancer recurrence and resistance to chemotherapy further contribute to a bleak prognosis and low survival rates. To address this pressing need for effective therapeutic strategies, our study focuses on the development of an innovative cellular immunotherapy, specifically utilizing chimeric antigen receptor (CAR)-engineered natural killer (NK) cells designed to target the cMET receptor tyrosine kinase. In this investigation, we initiated the screening of a phage library displaying human single-chain variable fragment (ScFv) to identify novel ScFv molecules with specificity for cMET. Remarkably, ScFv11, ScFv72, and ScFv114 demonstrated exceptional binding affinity, confirmed by molecular docking analysis. These selected ScFvs, in addition to the well-established anti-cMET ScFvA, were integrated into a CAR cassette harboring CD28 transmembrane region-41BB-CD3ζ domains. The resulting anti-cMET CAR constructs were transduced into NK-92 cells, generating potent anti-cMET CAR-NK-92 cells. To assess the specificity and efficacy of these engineered cells, we employed KKU213A cells with high cMET expression and KKU055 cells with low cMET levels. Notably, co-culture of anti-cMET CAR-NK-92 cells with KKU213A cells resulted in significantly increased cell death, whereas no such effect was observed with KKU055 cells. In summary, our study identified cMET as a promising therapeutic target for CCA. The NK-92 cells, armed with the anti-cMET CAR molecule, have shown strong ability to kill cancer cells specifically, indicating their potential as a promising treatment for CCA in the future.
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Affiliation(s)
- Chutipa Chiawpanit
- Cell Engineering for Cancer Therapy Research Group, Chiang Mai University, Chiang Mai, Thailand; Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand; Office of Research Administration, Chiang Mai University, Chiang Mai, Thailand
| | - Methi Wathikthinnakorn
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nunghathai Sawasdee
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nattaporn Phanthaphol
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Jatuporn Sujjitjoon
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Mutita Junking
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Montarop Yamabhai
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agriculture Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Jutatip Panaampon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Aussara Panya
- Cell Engineering for Cancer Therapy Research Group, Chiang Mai University, Chiang Mai, Thailand; Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.
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Banjan B, Krishnan D, Koshy AJ, Soman S, Leelamma A, Raju R, Revikumar A. In-silico screening and identification of potential drug-like compounds for dengue-associated thrombocytopenia from Carica papaya leaf extracts. J Biomol Struct Dyn 2024; 42:5963-5981. [PMID: 37394810 DOI: 10.1080/07391102.2023.2230293] [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: 03/28/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023]
Abstract
Dengue virus is a mosquito-borne pathogen that causes a variety of illnesses ranging from mild fever to severe and fatal dengue haemorrhagic fever or dengue shock syndrome. One of the major clinical manifestations of severe dengue infection is thrombocytopenia. The dengue non-structural protein 1 (NS1) is the primary protein that stimulates immune cells via toll-like receptor 4 (TLR4), induces platelets, and promotes aggregation, which could result in thrombocytopenia. The leaf extracts of Carica papaya seem to have therapeutic benefits in managing thrombocytopenia associated with dengue. The present study focuses on understanding the underlying mechanism of the use of papaya leaf extracts in treating thrombocytopenia. We have identified 124 phytocompounds that are present in the papaya leaf extract. The pharmacokinetics, molecular docking, binding free energy calculations, and molecular dynamic simulations were performed to investigate the drug-like properties, binding affinities, and interaction of phytocompounds with NS1 protein as well as the interactions of NS1 with TLR4. Three phytocompounds were found to bind with the ASN130, a crucial amino acid residue in the active site of the NS1 protein. Thus, we conclude that Rutin, Myricetin 3-rhamnoside, or Kaempferol 3-(2''-rhamnosylrutinoside) may serve as promising molecules by ameliorating thrombocytopenia in dengue-infected patients by interfering the interaction of NS1 with TLR4. These molecules can serve as drugs in the management of dengue-associated thrombocytopenia after verifying their effectiveness and assessing the drug potency, through additional in-vitro assays.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bhavya Banjan
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, India
| | - Deepak Krishnan
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India
| | - Abel John Koshy
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, India
| | - Sowmya Soman
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, India
| | - Anila Leelamma
- Department of Biochemistry, NSS College, Nilamel, Kollam, Kerala, India
| | - Rajesh Raju
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, India
| | - Amjesh Revikumar
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, India
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6
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Tan Y, Xiao Y, Hao T. Carbon fixation via volatile fatty acids recovery from sewage sludge through electrochemical-pretreatment-based anaerobic digestion. WATER RESEARCH 2024; 258:121736. [PMID: 38754300 DOI: 10.1016/j.watres.2024.121736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
Capturing the carbon in volatile fatty acids (VFA) produced from the anaerobic digestion (AD) of sewage sludge has the potential to not only provide economic benefits but also reduce greenhouse gas production. This study demonstrates a chemical-free method to collect VFA from an AD instead of methane that involves electrochemical pretreatment (EPT) of sludge. Experimental results show that applying 15 V EPT for 45 min enhances acidogenesis and selectively inhibits methanogenesis, leading to a substantial VFA accumulation (2563.1 ± 307.9 mg COD/L) and achieving 2.5 times more carbon fixation than via methane production. Interfacial thermodynamic analysis shows that EPT induces a decrease in both the repulsive electrostatic energy (from 152.9 kT to 12.2 kT) and the energy barrier (from 57.0 kT to 2.6 kT) in the sludge, leading to increased sludge aggregation and entrapment of microorganisms. Molecular docking sheds lights on how the methanogens interacts with the organic matter released from EPT (e.g., alanine-tRNA ligase), showing that these interactions potentially interfere with the proteins that are associated with the activities of the methanogens and the electron transfer pathways, thereby impeding methanogenesis. Integrating EPT into AD therefore facilitates the recovery of valuable VFA and the capture of carbon from freshwater sludge, providing notable economic and environmental benefits in sewage sludge treatment.
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Affiliation(s)
- Yunkai Tan
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, PR China
| | - Yihang Xiao
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, PR China
| | - Tianwei Hao
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, PR China.
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7
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Murmu S, Archak S. In-silico study of protein-protein interactions in wheat blast using docking and molecular dynamics simulation approach. J Biomol Struct Dyn 2024; 42:5747-5757. [PMID: 37357445 DOI: 10.1080/07391102.2023.2228907] [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: 02/06/2023] [Accepted: 06/17/2023] [Indexed: 06/27/2023]
Abstract
Despite advancements in agricultural research and the introduction of modern biotechnological and farming techniques, food security remains a significant issue. Although the efforts of farmers to meet the demands of a growing population, many plant diseases caused by pathogens, through their effects on cell division and tissue growth, lead to the annual loss of countless food crops. The recently emerged wheat blast fungus Magnaporthe oryzae pathotype Triticum (MoT) poses a significant danger to worldwide wheat cultivation. The fungus is a highly varied lineage of the M. oryzae, responsible for causing rice blast disease. In spite of being a significant challenge to successful wheat production in South America since 1985, the underlying biology of the wheat blast pathogen is still not fully understood. The initial outbreak of the wheat blast in South Asia had a severe impact on wheat production, resulting in a complete loss of yield in affected fields. For the purpose of enhancing disease management, it's vital to acquire a comprehensive comprehension of the infection biology of the fungus and its interaction with wheat plants on molecular levels. Host-pathogen protein interactions (HPIs) have the potential to reveal the pathogens' mechanism for overcoming the host organism. The current study delves into the interactions between the host plant wheat and MoT through protein-protein interactions, molecular docking, and 100 ns molecular dynamic simulations. This research uncovers the structural and functional basis of these proteins, leading to improved plant health and production.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sneha Murmu
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sunil Archak
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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Lin J, Gu M, Wang X, Chen Y, Chau NV, Li J, Chu Q, Qing L, Wu W. Huanglian Jiedu decoction inhibits vascular smooth muscle cell-derived foam cell formation by activating autophagy via suppressing P2RY12. JOURNAL OF ETHNOPHARMACOLOGY 2024; 328:118125. [PMID: 38561055 DOI: 10.1016/j.jep.2024.118125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Huanglian Jiedu Decoction (HLJDD) is a Chinese medicine with a long history of therapeutic application. It is widely used in treating atherosclerosis (AS) in Chinese medicine theory and clinical practice. However, the mechanism of HLJDD in treating AS remains unclear. AIM OF THE STUDY To investigate the efficacy and mechanism of HLJDD in treating AS. MATERIALS AND METHODS AS was induced on high-fat diet-fed ApoE-/- mice, with the aorta pathological changes evaluated with lipid content and plaque progression. In vitro, foam cells were induced by subjecting primary mouse aortic vascular smooth muscle cells (VSMCs) to oxLDL incubation. After HLJDD intervention, VSMCs were assessed with lipid stack, apoptosis, oxidative stress, and the expression of foam cell markers. The effects of P2RY12 were tested by adopting clopidogrel hydrogen sulfate (CDL) in vivo and transfecting P2RY12 over-expressive plasmid in vitro. Autophagy was inhibited by Chloroquine or transfecting siRNA targeting ATG7 (siATG7). The mechanism of HLJDD treating atherosclerosis was explored using network pharmacology and validated with molecular docking and co-immunoprecipitation. RESULTS HLJDD exhibited a dose-dependent reduction in lipid deposition, collagen loss, and necrosis within plaques. It also reversed lipid accumulation and down-regulated the expression of foam cell markers. P2RY12 inhibition alleviated AS, while P2RY12 overexpression enhanced foam cell formation and blocked the therapeutic effects of HLJDD. Network pharmacological analysis suggested that HLJDD might mediate PI3K/AKT signaling pathway-induced autophagy. P2RY12 overexpression also impaired autophagy. Similarly, inhibiting autophagy counteracted the effect of CDL, exacerbated AS in vivo, and promoted foam cell formation in vitro. However, HLJDD treatment mitigated these detrimental effects by suppressing the PI3K/AKT signaling pathway. Immunofluorescence and molecular docking revealed a high affinity between P2RY12 and PIK3CB, while co-immunoprecipitation assays illustrated their interaction. CONCLUSIONS HLJDD inhibited AS in vivo and foam cell formation in vitro by restoring P2RY12/PI3K/AKT signaling pathway-suppressed autophagy. This study is the first to reveal an interaction between P2RY12 and PI3K3CB.
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Affiliation(s)
- Jinhai Lin
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou, 510405, Guangdong, China; Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou, 510405, Guangdong, China.
| | - Mingyang Gu
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou, 510405, Guangdong, China.
| | - Xiaolong Wang
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou, 510405, Guangdong, China.
| | - Yuanyuan Chen
- Qinchengda Community Health Service Center, Shenzhen Bao'an Traditional Chinese Medicine Hospital Group, No. 225, Block 10A, Qinchengda Yueyuan Commercial and Residential Building, Shenzhen, 518100, Guangdong, China.
| | - Nhi Van Chau
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou, 510405, Guangdong, China; Traditional Medicine Department, Can Tho University of Medicine and Pharmacy, 179 Nguyen Van Cu Street, An Khanh, Ninh Kieu, Can Tho, 94000, Viet Nam.
| | - Junlong Li
- The Department of Cardiology, First Affiliated Hospital, Guangzhou University of Chinese Medicine, 16 Jichang Road, Guangzhou, 510405, Guangdong, China.
| | - Qingmin Chu
- The Department of Cardiology, First Affiliated Hospital, Guangzhou University of Chinese Medicine, 16 Jichang Road, Guangzhou, 510405, Guangdong, China.
| | - Lijin Qing
- The Department of Cardiology, First Affiliated Hospital, Guangzhou University of Chinese Medicine, 16 Jichang Road, Guangzhou, 510405, Guangdong, China.
| | - Wei Wu
- The Department of Cardiology, First Affiliated Hospital, Guangzhou University of Chinese Medicine, 16 Jichang Road, Guangzhou, 510405, Guangdong, China.
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Feng Y, Qian R, Cui D, Luan J, Xu M, Wang L, Li R, Wu X, Chang C. Mutant TP53 promotes invasion of lung cancer cells by regulating desmoglein 3. J Cancer Res Clin Oncol 2024; 150:312. [PMID: 38900156 DOI: 10.1007/s00432-024-05778-3] [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: 02/21/2024] [Accepted: 05/03/2024] [Indexed: 06/21/2024]
Abstract
PURPOSE Targeted therapies have markedly improved the prognosis of lung cancer patients; nevertheless, challenges persist, including limited beneficiary populations and the emergence of drug resistance. This study investigates the molecular mechanisms of mutant TP53 in lung cancer, aiming to contribute to novel strategies for targeted therapy. METHODS The TCGA database was employed to delineate the mutational landscape of TP53 in lung cancer patients. Differential gene expression between TP53-mutant and wild-type patients was analyzed, followed by functional enrichment. DSG3 protein expression in lung cancer patients was assessed using IHC, and its impact on prognosis was analyzed in the TCGA database. The influence of TP53 on the downstream gene DSG3 was investigated using qPCR, ChIP-qPCR, and luciferase reporter gene assays. Protein enrichment in the DSG3 promoter region was examined through IP-MS, and the regulatory role of the HIF1-α/TP53 complex on DSG3 was explored using Co-IP, luciferase assays, and ChIP-qPCR. Molecular interactions between TP53 (R273H) and HIF1-α were detected through immunoprecipitation and molecular docking. The effects and mechanisms of DSG3 on lung cancer phenotypes were assessed through WB, transwell, and wound healing assays. RESULTS TP53 mutations were present in 47.44% of patients, predominantly as missense mutations. DSG3 exhibited high expression in TP53-mutant lung cancer patients, and this elevated expression correlated with a poorer prognosis. TP53 interference led to a reduction in DSG3 mRNA expression, with TP53 mutant P53 enriching at the P2 site of the DSG3 promoter region, a recruitment facilitated by HIF1-α. The DBD region of TP53 (R273H) demonstrated interaction with HIF1-α. DSG3, activated through Ezrin phosphorylation, played a role in promoting invasion and metastasis. CONCLUSIONS Mutant TP53 facilitates lung cancer cell invasion by modulating desmoglein 3.
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Affiliation(s)
- Yu Feng
- Department of Thoracic Surgery, Henan Provincial Chest Hospital, Zhengzhou University, No. 1 Weiwu Road, Zhengzhou, 450000, People's Republic of China
- Department of Clinical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450000, People's Republic of China
| | - Rulin Qian
- Department of Thoracic Surgery, Henan Provincial Chest Hospital, Zhengzhou University, No. 1 Weiwu Road, Zhengzhou, 450000, People's Republic of China
| | - Dong Cui
- Department of Thoracic Surgery, Henan Provincial Chest Hospital, Zhengzhou University, No. 1 Weiwu Road, Zhengzhou, 450000, People's Republic of China.
| | - Jiaqiang Luan
- Department of Thoracic Surgery, Henan Provincial Chest Hospital, Zhengzhou University, No. 1 Weiwu Road, Zhengzhou, 450000, People's Republic of China
| | - Mingxing Xu
- Department of Thoracic Surgery, Henan Provincial Chest Hospital, Zhengzhou University, No. 1 Weiwu Road, Zhengzhou, 450000, People's Republic of China
| | - Ling Wang
- Department of Clinical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450000, People's Republic of China
| | - Ruijie Li
- Department of Medical Oncology, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450000, People's Republic of China
| | - Xiao Wu
- Department of Thoracic Surgery, Henan Provincial Chest Hospital, Zhengzhou University, No. 1 Weiwu Road, Zhengzhou, 450000, People's Republic of China
| | - Chaoying Chang
- Department of Thoracic Surgery, Henan Provincial Chest Hospital, Zhengzhou University, No. 1 Weiwu Road, Zhengzhou, 450000, People's Republic of China
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10
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Liao Z, Zeng X, Guo X, Shi Q, Tang Z, Li P, Chen C, Chen M, Chen J, Xu J, Cai Y. Targeting the aryl hydrocarbon receptor with FICZ regulates IL-2 and immune infiltration to alleviate Hashimoto's thyroiditis in mice. Eur J Pharmacol 2024; 973:176588. [PMID: 38621508 DOI: 10.1016/j.ejphar.2024.176588] [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: 12/11/2023] [Revised: 03/25/2024] [Accepted: 04/11/2024] [Indexed: 04/17/2024]
Abstract
Hashimoto's thyroiditis (HT) is the most frequent autoimmune disorder. Growing work points to the involvement of aryl hydrocarbon receptor (AhR), a ligand-dependent transcription factor, in the regulation of immune homeostasis. However, the roles of AhR and its ligands in HT remains unclear. In this study, we leveraged public human database analyses to postulate that the AhR expression was predominantly in thyroid follicular cells, correlating significantly with the thyroid infiltration levels of multiple immune cells in HT patients. Using a thyroglobulin-induced HT mouse model and in vitro thyroid follicular epithelial cell cultures, we found a significant downregulation of AhR expression in thyrocytes both in vivo and in vitro. Conversely, activating AhR by FICZ, a natural AhR ligand, mitigated inflammation and apoptosis in thyrocytes in vitro and conferred protection against HT in mice. RNA sequencing (RNA-seq) of thyroid tissues indicated that AhR activation moderated HT-associated immune or inflammatory signatures. Further, immunoinfiltration analysis indicated that AhR activation regulated immune cell infiltration in the thyroid of HT mice, such as suppressing cytotoxic CD8+ T cell infiltration and promoting anti-inflammatory M2 macrophage polarization. Concomitantly, the expression levels of interleukin-2 (IL-2), a lymphokine that downregulates immune responses, were typically decreased in HT but restored upon AhR activation. In silico validation substantiated the binding interaction between AhR and IL-2. In conclusion, targeting the AhR with FICZ regulates IL-2 and immune infiltration to alleviate experimental HT, shedding new light on the therapeutic intervention of this prevalent disease.
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Affiliation(s)
- Zhengzheng Liao
- Department of Pharmacy, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Xianzhong Zeng
- Department of Endocrinology, Ganzhou People's Hospital, Ganzhou, 341000, People's Republic of China
| | - Xiaoling Guo
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Qing Shi
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Ziyun Tang
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Ping Li
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China; Jiangxi Clinical Research Center for Endocrine and Metabolic Disease, Nanchang, 330006, People's Republic of China; Jiangxi Branch of National Clinical Research Center for Metabolic Disease, Nanchang, 330006, People's Republic of China
| | - Cuiyun Chen
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China; Jiangxi Clinical Research Center for Endocrine and Metabolic Disease, Nanchang, 330006, People's Republic of China; Jiangxi Branch of National Clinical Research Center for Metabolic Disease, Nanchang, 330006, People's Republic of China
| | - Mengxia Chen
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China; Jiangxi Clinical Research Center for Endocrine and Metabolic Disease, Nanchang, 330006, People's Republic of China; Jiangxi Branch of National Clinical Research Center for Metabolic Disease, Nanchang, 330006, People's Republic of China
| | - Jianrong Chen
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China; Jiangxi Clinical Research Center for Endocrine and Metabolic Disease, Nanchang, 330006, People's Republic of China; Jiangxi Branch of National Clinical Research Center for Metabolic Disease, Nanchang, 330006, People's Republic of China
| | - Jixiong Xu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China; Jiangxi Clinical Research Center for Endocrine and Metabolic Disease, Nanchang, 330006, People's Republic of China; Jiangxi Branch of National Clinical Research Center for Metabolic Disease, Nanchang, 330006, People's Republic of China.
| | - Yaojun Cai
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China; Jiangxi Clinical Research Center for Endocrine and Metabolic Disease, Nanchang, 330006, People's Republic of China; Jiangxi Branch of National Clinical Research Center for Metabolic Disease, Nanchang, 330006, People's Republic of China.
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11
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Luo XY, Hu CM, Yin Q, Zhang XM, Liu ZZ, Zhou CK, Zhang JG, Chen W, Yang YJ. Dual-Mechanism Peptide SR25 has Broad Antimicrobial Activity and Potential Application for Healing Bacteria-infected Diabetic Wounds. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401793. [PMID: 38874469 DOI: 10.1002/advs.202401793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/12/2024] [Indexed: 06/15/2024]
Abstract
The rise of antibiotic resistance poses a significant public health crisis, particularly due to limited antimicrobial options for the treatment of infections with Gram-negative pathogens. Here, an antimicrobial peptide (AMP) SR25 is characterized, which effectively kills both Gram-negative and Gram-positive bacteria through a unique dual-targeting mechanism without detectable resistance. Meanwhile, an SR25-functionalized hydrogel is developed for the efficient treatment of infected diabetic wounds. SR25 is obtained through genome mining from an uncultured bovine enteric actinomycete named Nonomuraea Jilinensis sp. nov. Investigations reveal that SR25 has two independent cellular targets, disrupting bacterial membrane integrity and restraining the activity of succinate:quinone oxidoreductase (SQR). In a diabetic mice wound infection model, the SR25-incorporated hydrogel exhibits high efficacy against mixed infections of Escherichia coli (E. coli) and methicillin-resistant Staphylococcus aureus (MRSA), accelerating wound healing. Overall, these findings demonstrate the therapeutic potential of SR25 and highlight the value of mining drugs with multiple mechanisms from uncultured animal commensals for combating challenging bacterial pathogens.
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Affiliation(s)
- Xue-Yue Luo
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Chun-Mei Hu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Qi Yin
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Xiao-Mei Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Zhen-Zhen Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Cheng-Kai Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Jian-Gang Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Wei Chen
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Yong-Jun Yang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
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12
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Bai Y, Zhang Z, Bi J, Tang Q, Jiang K, Yao C, Wang W. miR-181c-5p/DERL1 pathway controls breast cancer progression mediated by TRAF6-linked K63 ubiquitination of AKT. Cancer Cell Int 2024; 24:204. [PMID: 38858669 PMCID: PMC11165795 DOI: 10.1186/s12935-024-03395-1] [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: 03/11/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Aberrant Derlin-1 (DERL1) expression is associated with an overactivation of p-AKT, whose involvement in breast cancer (BRCA) development has been widely speculated. However, the precise mechanism that links DERL1 expression and AKT activation is less well-studied. METHODS Bioinformatic analyses hold a promising approach by which to detect genes' expression levels and their association with disease prognoses in patients. In the present work, a dual-luciferase assay was employed to investigate the relationship between DERL1 expression and the candidate miRNA by both in vitro and in vivo methods. Further in-depth studies involving immunoprecipitation-mass spectrum (IP-MS), co-immunoprecipitation (Co-IP), as well as Zdock prediction were performed. RESULTS Overexpression of DERL1 was detected in all phenotypes of BRCA, and its knockdown showed an inhibitory effect on BRCA cells both in vitro and in vivo. The Cancer Genome Atlas (TCGA) database reported that DERL1 overexpression was correlated with poor overall survival in BRCA cases, and so the quantification of DERL1 expression could be a potential marker for the clinical diagnosis of BRCA. On the other hand, miR-181c-5p was downregulated in BRCA, suggesting that its overexpression could be a potent therapeutic route to improve the overall survival of BRCA cases. Prior bioinformatic analyses indicated a somewhat positive correlation between DERL1 and TRAF6 as well as between TRAF6 and AKT, but not between miR-181c-5p and DERL1. In retrospect, DERL1 overexpression promoted p-AKT activation through K63 ubiquitination. DERL1 was believed to directly interact with the E3 ligase TRAF6. As Tyr77Ala or Tyr77Ala/Gln81Ala/Arg85Ala/Val158Ala attempts to prevent the interaction between DERL1 and TRAF domain of TRAF6, resulted in a significant reduction in K63-ubiquitinated p-AKT production. However, mutations in Gln81Ala, Arg85Ala, or Val158Ala could possibly interrupt with these processes. CONCLUSIONS Our data confirm that mediation of the miR-181c-5p/DERL1 pathway by TRAF6-linked AKT K63 ubiquitination holds one of the clues to set our focus on toward meeting the therapeutic goals of BRCA.
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Affiliation(s)
- Yang Bai
- Laboratory of Department of Surgery, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Zhanqiang Zhang
- Department of Thyroid, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Jiong Bi
- Laboratory of Department of Surgery, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Qian Tang
- Department of Anesthesiology, Guiqian International General Hospital, Guiyang, 550000, Guizhou, China
| | - Keying Jiang
- Laboratory of Department of Surgery, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Chen Yao
- Laboratory of Department of Surgery, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Wenjian Wang
- Laboratory of Department of Surgery, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
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13
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Xiong W, Chai J, Wu J, Li J, Lu W, Tian M, Jmel MA, Ippel JH, Kotsyfakis M, Dijkgraaf I, Liu S, Xu X. Cathelicidin-HG Alleviates Sepsis-Induced Platelet Dysfunction by Inhibiting GPVI-Mediated Platelet Activation. RESEARCH (WASHINGTON, D.C.) 2024; 7:0381. [PMID: 38840901 PMCID: PMC11151873 DOI: 10.34133/research.0381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 04/15/2024] [Indexed: 06/07/2024]
Abstract
Platelet activation contributes to sepsis development, leading to microthrombosis and increased inflammation, which results in disseminated intravascular coagulation and multiple organ dysfunction. Although Cathelicidin can alleviate sepsis, its role in sepsis regulation remains largely unexplored. In this study, we identified Cath-HG, a novel Cathelicidin from Hylarana guentheri skin, and analyzed its structure using nuclear magnetic resonance spectroscopy. The modulatory effect of Cath-HG on the symptoms of mice with sepsis induced by cecal ligation and puncture was evaluated in vivo, and the platelet count, degree of organ damage, and microthrombosis were measured. The antiplatelet aggregation activity of Cath-HG was studied in vitro, and its target was verified. Finally, we further investigated whether Cath-HG could regulate thrombosis in vivo in a FeCl3 injury-induced carotid artery model. The results showed that Cath-HG exhibited an α-helical structure in sodium dodecyl sulfate solution and effectively reduced organ inflammation and damage, improving survival in septic mice. It alleviated sepsis-induced thrombocytopenia and microthrombosis. In vitro, Cath-HG specifically inhibited collagen-induced platelet aggregation and modulated glycoprotein VI (GPVI) signaling pathways. Dot blotting, enzyme-linked immunosorbent assay, and pull-down experiments confirmed GPVI as the target of Cath-HG. Molecular docking and amino acid residue truncations/mutations identified crucial sites of Cath-HG. These findings suggest that GPVI represents a promising therapeutic target for sepsis, and Cath-HG may serve as a potential treatment for sepsis-related thrombocytopenia and thrombotic events. Additionally, identifying Cath-HG as a GPVI inhibitor provides insights for developing novel antithrombotic therapies targeting platelet activation mediated by GPVI.
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Affiliation(s)
- Weichen Xiong
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences,
Southern Medical University, Guangzhou 510515, China
| | - Jinwei Chai
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences,
Southern Medical University, Guangzhou 510515, China
| | - Jiena Wu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences,
Southern Medical University, Guangzhou 510515, China
| | - Jiali Li
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences,
Southern Medical University, Guangzhou 510515, China
| | - Wancheng Lu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences,
Southern Medical University, Guangzhou 510515, China
| | - Maolin Tian
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences,
Southern Medical University, Guangzhou 510515, China
| | - Mohamed Amine Jmel
- Institute of Parasitology,
Biology Centre of the Czech Academy of Sciences, Branisovska 31, Budweis (Ceske Budejovice) 37005, Czech Republic
| | - Johannes H. Ippel
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM),
Maastricht University, 6229 ER Maastricht, Netherlands
| | - Michail Kotsyfakis
- Institute of Parasitology,
Biology Centre of the Czech Academy of Sciences, Branisovska 31, Budweis (Ceske Budejovice) 37005, Czech Republic
- Institute of Molecular Biology and Biotechnology,
Foundation for Research and Technology-Hellas, 70013 Heraklion, Crete, Greece
| | - Ingrid Dijkgraaf
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM),
Maastricht University, 6229 ER Maastricht, Netherlands
| | - Shuwen Liu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences,
Southern Medical University, Guangzhou 510515, China
| | - Xueqing Xu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences,
Southern Medical University, Guangzhou 510515, China
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14
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Chourasia R, Dabrha G, Abedin MM, Phukon LC, Singh AK, Sahoo D, Singh SP, Rai AK. Exploring peptidomes of by-products generated during chhurpi production using Lactobacillus delbrueckii WS4 for identification of novel bioactive peptides. Food Funct 2024; 15:5987-5999. [PMID: 38742436 DOI: 10.1039/d4fo00405a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The considerable value of whey is evident from its significant potential applications and contributions to the functional food and nutraceutical market. The by-products were individually obtained during functional chhurpi and novel soy chhurpi cheese production using defined lactic acid bacterial strains of Sikkim Himalaya's traditional chhurpi. Hydrolysis of substrate proteins by starter proteinases resulted in a comparable peptide content in whey and soy whey which was associated with antioxidant and ACE inhibition potential. Peptidome analysis of Lactobacillus delbrueckii WS4 whey and soy whey revealed the presence of several bioactive peptides including the multifunctional peptides PVVVPPFLQPE and YQEPVLGPVRGPFPIIV. In silico analyses predicted the antihypertensive potential of whey and soy whey peptides with strong binding affinity for ACE active sites. QSAR models predicted the highest ACE inhibition potential (IC50) for the β-casein-derived decapeptide PVRGPFPIIV (0.95 μM) and the Kunitz trypsin inhibitor protein-derived nonapeptide KNKPLVVQF (16.64 μM). Chhurpi whey and soy whey can be explored as a valuable source of diverse and novel bioactive peptides for applications in designer functional foods development.
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Affiliation(s)
- Rounak Chourasia
- National Agri-food Biotechnology Institute, SAS Nagar, Mohali, India.
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Gayatri Dabrha
- National Agri-food Biotechnology Institute, SAS Nagar, Mohali, India.
| | | | | | - Ashish Kumar Singh
- Center of Innovative and Applied Bioprocessing, SAS Nagar, Mohali, India.
| | - Dinabandhu Sahoo
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
- Department of Botany, University of Delhi, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, SAS Nagar, Mohali, India.
- Gujarat Biotechnology University, Shahpur, Gandhinagar, Gujarat, India
| | - Amit Kumar Rai
- National Agri-food Biotechnology Institute, SAS Nagar, Mohali, India.
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
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15
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Wang L, Wen Z, Liu SW, Zhang L, Finley C, Lee HJ, Fan HJS. Overview of AlphaFold2 and breakthroughs in overcoming its limitations. Comput Biol Med 2024; 176:108620. [PMID: 38761500 DOI: 10.1016/j.compbiomed.2024.108620] [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: 10/29/2023] [Revised: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
Predicting three-dimensional (3D) protein structures has been challenging for decades. The emergence of AlphaFold2 (AF2), a deep learning-based machine learning method developed by DeepMind, became a game changer in the protein folding community. AF2 can predict a protein's three-dimensional structure with high confidence based on its amino acid sequence. Accurate prediction of protein structures can dramatically accelerate our understanding of biological mechanisms and provide a solid foundation for reliable drug design. Although AF2 breaks through the barriers in predicting protein structures, many rooms remain to be further studied. This review provides a brief historical overview of the development of protein structure prediction, covering template-based, template-free, and machine learning-based methods. In addition to reviewing the potential benefits (Pros) and considerations (Cons) of using AF2, this review summarizes the diverse applications, including protein structure predictions, dynamic changes, point mutation, integration of language model and experimental data, protein complex, and protein-peptide interaction. It underscores recent advancements in efficiency, reliability, and broad application of AF2. This comprehensive review offers valuable insights into the applications of AF2 and AF2-inspired AI methods in structural biology and its potential for clinically significant drug target discovery.
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Affiliation(s)
- Lei Wang
- College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong City, Sichuan Province, 64300, China
| | - Zehua Wen
- College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong City, Sichuan Province, 64300, China
| | - Shi-Wei Liu
- College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong City, Sichuan Province, 64300, China
| | - Lihong Zhang
- Digestive Department, Binhai New Area Hospital of TCM Tianjin, Tianjin, 300451, China
| | - Cierra Finley
- Department of Natural Sciences, Southwest Tennessee Community College, Memphis, TN, 38015, USA
| | - Ho-Jin Lee
- Department of Natural Sciences, Southwest Tennessee Community College, Memphis, TN, 38015, USA; Division of Natural & Mathematical Sciences, LeMoyne-Own College, Memphis, TN, 38126, USA.
| | - Hua-Jun Shawn Fan
- College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong City, Sichuan Province, 64300, China.
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16
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Yang Q, Jin X, Zhou H, Ying J, Zou J, Liao Y, Lu X, Ge S, Yu H, Min X. SurfPro-NN: A 3D point cloud neural network for the scoring of protein-protein docking models based on surfaces features and protein language models. Comput Biol Chem 2024; 110:108067. [PMID: 38714420 DOI: 10.1016/j.compbiolchem.2024.108067] [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: 01/18/2024] [Revised: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 05/09/2024]
Abstract
Protein-protein interactions (PPI) play a crucial role in numerous key biological processes, and the structure of protein complexes provides valuable clues for in-depth exploration of molecular-level biological processes. Protein-protein docking technology is widely used to simulate the spatial structure of proteins. However, there are still challenges in selecting candidate decoys that closely resemble the native structure from protein-protein docking simulations. In this study, we introduce a docking evaluation method based on three-dimensional point cloud neural networks named SurfPro-NN, which represents protein structures as point clouds and learns interaction information from protein interfaces by applying a point cloud neural network. With the continuous advancement of deep learning in the field of biology, a series of knowledge-rich pre-trained models have emerged. We incorporate protein surface representation models and language models into our approach, greatly enhancing feature representation capabilities and achieving superior performance in protein docking model scoring tasks. Through comprehensive testing on public datasets, we find that our method outperforms state-of-the-art deep learning approaches in protein-protein docking model scoring. Not only does it significantly improve performance, but it also greatly accelerates training speed. This study demonstrates the potential of our approach in addressing protein interaction assessment problems, providing strong support for future research and applications in the field of biology.
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Affiliation(s)
- Qianli Yang
- Institute of Artifical Intelligence, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China.
| | - Xiaocheng Jin
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China; School of Public Health, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China
| | - Haixia Zhou
- School of Public Health, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China
| | - Junjie Ying
- Institute of Artifical Intelligence, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China
| | - JiaJun Zou
- School of Informatics, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China
| | - Yiyang Liao
- School of Informatics, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China
| | - Xiaoli Lu
- Information and Networking Center, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China
| | - Shengxiang Ge
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China; School of Public Health, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China
| | - Hai Yu
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China; School of Public Health, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China.
| | - Xiaoping Min
- School of Informatics, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, XiaMen University, No. 422, Siming South Road, XiaMen, 361005, Fujian, China.
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17
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Kamal H, Zafar MM, Parvaiz A, Razzaq A, Elhindi KM, Ercisli S, Qiao F, Jiang X. Gossypium hirsutum calmodulin-like protein (CML 11) interaction with geminivirus encoded protein using bioinformatics and molecular techniques. Int J Biol Macromol 2024; 269:132095. [PMID: 38710255 DOI: 10.1016/j.ijbiomac.2024.132095] [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: 12/09/2023] [Revised: 03/24/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
Plant viruses are the most abundant destructive agents that exist in every ecosystem, causing severe diseases in multiple crops worldwide. Currently, a major gap is present in computational biology determining plant viruses interaction with its host. We lay out a strategy to extract virus-host protein interactions using various protein binding and interface methods for Geminiviridae, a second largest virus family. Using this approach, transcriptional activator protein (TrAP/C2) encoded by Cotton leaf curl Kokhran virus (CLCuKoV) and Cotton leaf curl Multan virus (CLCuMV) showed strong binding affinity with calmodulin-like (CML) protein of Gossypium hirsutum (Gh-CML11). Higher negative value for the change in Gibbs free energy between TrAP and Gh-CML11 indicated strong binding affinity. Consensus from gene ontology database and in-silico nuclear localization signal (NLS) tools identified subcellular localization of TrAP in the nucleus associated with Gh-CML11 for virus infection. Data based on interaction prediction and docking methods present evidences that full length and truncated C2 strongly binds with Gh-CML11. This computational data was further validated with molecular results collected from yeast two-hybrid, bimolecular fluorescence complementation system and pull down assay. In this work, we also show the outcomes of full length and truncated TrAP on plant machinery. This is a first extensive report to delineate a role of CML protein from cotton with begomoviruses encoded transcription activator protein.
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Affiliation(s)
- Hira Kamal
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Muhammad Mubashar Zafar
- Sanya Institute of Breeding and Multiplication/School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
| | - Aqsa Parvaiz
- Department of Biochemistry and Biotechnology, The Women University Multan, Multan. Pakistan
| | - Abdul Razzaq
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan..
| | - Khalid M Elhindi
- Plant Production Department, College of Food & Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Fei Qiao
- Sanya Institute of Breeding and Multiplication/School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
| | - Xuefei Jiang
- Sanya Institute of Breeding and Multiplication/School of Tropical Agriculture and Forestry, Hainan University, Sanya, China..
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18
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Fan W, Hu L, Yang Y, Liu P, Feng Y, Gu RX, Liu Q. Engineering of the start condensation domain with improved N-decanoyl catalytic activity for daptomycin biosynthesis. Biotechnol J 2024; 19:e2400202. [PMID: 38896411 DOI: 10.1002/biot.202400202] [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: 04/01/2024] [Revised: 05/19/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
Daptomycin, a lipopeptide comprising an N-decanoyl fatty acyl chain and a peptide core, is used clinically as an antimicrobial agent. The start condensation domain (dptC1) is an enzyme that catalyzes the lipoinitiation step of the daptomycin synthesis. In this study, we integrated enzymology, protein engineering, and computer simulation to study the substrate selectivity of the start condensation domain (dptC1) and to screen mutants with improved activity for decanoyl loading. Through molecular docking and computer simulation, the fatty acyl substrate channel and the protein-protein interaction interface of dptC1 are analyzed. Key residues at the protein-protein interface between dptC1 and the acyl carrier were mutated, and a single-point mutant showed more than three-folds improved catalytic efficiency of the target n-decanoyl substrate in comparing with the wild type. Moreover, molecular dynamics simulations suggested that mutants with increased catalytic activity may correlated with a more "open" and contracted substrate binding channel. Our work provides a new perspective for the elucidation of lipopeptide natural products biosynthesis, and also provides new resources to enrich its diversity and optimize the production of important components.
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Affiliation(s)
- Wenjie Fan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lyubin Hu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Panpan Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ruo-Xu Gu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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19
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Zhang W, Sha Z, Tang Y, Jin C, Gao W, Chen C, Yu L, Lv N, Liu S, Xu F, Wang D, Shi L. Defective Lamtor5 Leads to Autoimmunity by Deregulating v-ATPase and Lysosomal Acidification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400446. [PMID: 38639386 PMCID: PMC11165510 DOI: 10.1002/advs.202400446] [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: 01/12/2024] [Revised: 04/02/2024] [Indexed: 04/20/2024]
Abstract
Despite accumulating evidence linking defective lysosome function with autoimmune diseases, how the catabolic machinery is regulated to maintain immune homeostasis remains unknown. Late endosomal/lysosomal adaptor, MAPK and mTOR activator 5 (Lamtor5) is a subunit of the Ragulator mediating mechanistic target of rapamycin complex 1 (mTORC1) activation in response to amino acids, but its action mode and physiological role are still unclear. Here it is demonstrated that Lamtor5 level is markedly decreased in peripheral blood mononuclear cells (PBMCs) of patients with systemic lupus erythematosus (SLE). In parallel, the mice with myeloid Lamtor5 ablation developed SLE-like manifestation. Impaired lysosomal function and aberrant activation of mTORC1 are evidenced in Lamtor5 deficient macrophages and PBMCs of SLE patients, accompanied by blunted autolysosomal pathway and undesirable inflammatory responses. Mechanistically, it is shown that Lamtor5 is physically associated with ATP6V1A, an essential subunit of vacuolar H+-ATPase (v-ATPase), and promoted the V0/V1 holoenzyme assembly to facilitate lysosome acidification. The binding of Lamtor5 to v-ATPase affected the lysosomal tethering of Rag GTPase and weakened its interaction with mTORC1 for activation. Overall, Lamtor5 is identified as a critical factor for immune homeostasis by intergrading v-ATPase activity, lysosome function, and mTOR pathway. The findings provide a potential therapeutic target for SLE and/or other autoimmune diseases.
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Affiliation(s)
- Wei Zhang
- School of MedicineNanjing University of Chinese MedicineNanjing210046China
| | - Zhou Sha
- School of MedicineNanjing University of Chinese MedicineNanjing210046China
| | - Yunzhe Tang
- School of MedicineNanjing University of Chinese MedicineNanjing210046China
| | - Cuiyuan Jin
- Key lab of Artificial Organs and Computational MedicineInstitute of Translational MedicineZhejiang Shuren UniversityHangzhou310022China
| | - Wenhua Gao
- School of MedicineNanjing University of Chinese MedicineNanjing210046China
| | - Changmai Chen
- School of PharmacyFujian Medical UniversityFuzhou350122China
| | - Lang Yu
- School of MedicineNanjing University of Chinese MedicineNanjing210046China
| | - Nianyin Lv
- School of MedicineNanjing University of Chinese MedicineNanjing210046China
| | - Shijia Liu
- The Affiliated Hospital of Nanjing University of Chinese MedicineNanjing210029China
| | - Feng Xu
- Department of Infectious DiseasesThe Second Affiliated HospitalZhejiang University School of MedicineHangzhou310009China
| | - Dandan Wang
- Department of Rheumatology and ImmunologyThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing210093China
| | - Liyun Shi
- School of MedicineNanjing University of Chinese MedicineNanjing210046China
- Key lab of Artificial Organs and Computational MedicineInstitute of Translational MedicineZhejiang Shuren UniversityHangzhou310022China
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20
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Aslan A, Ari Yuka S. Therapeutic peptides for coronary artery diseases: in silico methods and current perspectives. Amino Acids 2024; 56:37. [PMID: 38822212 PMCID: PMC11143054 DOI: 10.1007/s00726-024-03397-3] [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: 01/25/2024] [Accepted: 05/06/2024] [Indexed: 06/02/2024]
Abstract
Many drug formulations containing small active molecules are used for the treatment of coronary artery disease, which affects a significant part of the world's population. However, the inadequate profile of these molecules in terms of therapeutic efficacy has led to the therapeutic use of protein and peptide-based biomolecules with superior properties, such as target-specific affinity and low immunogenicity, in critical diseases. Protein‒protein interactions, as a consequence of advances in molecular techniques with strategies involving the combined use of in silico methods, have enabled the design of therapeutic peptides to reach an advanced dimension. In particular, with the advantages provided by protein/peptide structural modeling, molecular docking for the study of their interactions, molecular dynamics simulations for their interactions under physiological conditions and machine learning techniques that can work in combination with all these, significant progress has been made in approaches to developing therapeutic peptides that can modulate the development and progression of coronary artery diseases. In this scope, this review discusses in silico methods for the development of peptide therapeutics for the treatment of coronary artery disease and strategies for identifying the molecular mechanisms that can be modulated by these designs and provides a comprehensive perspective for future studies.
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Affiliation(s)
- Ayca Aslan
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Esenler, Istanbul, Turkey
- Health Biotechnology Joint Research and Application Center of Excellence, Esenler, Istanbul, Turkey
| | - Selcen Ari Yuka
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Esenler, Istanbul, Turkey.
- Health Biotechnology Joint Research and Application Center of Excellence, Esenler, Istanbul, Turkey.
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21
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Liu Z, Liu H, Huang C, Zhou Q, Luo Y. Hybrid Cas12a Variants with Relaxed PAM Requirements Expand Genome Editing Compatibility. ACS Synth Biol 2024. [PMID: 38819403 DOI: 10.1021/acssynbio.4c00103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Cas12a is a widely used programmable nuclease for genome editing across a variety of organisms, but its application is limited by its PAM recognition restriction. To alleviate these PAM constraints, protein engineering efforts have been applied to expand the PAM recognition range. In this study, we designed and constructed 990 synthetic hybrid Cas12a chimeras through domain shuffling and screened an efficient hybrid Cas12a (ehCas12a) that could recognize a broad range PAM of 5'-TYYN-3' (Y is T or C and N is A, T, C, or G). Furthermore, we constructed an ehCas12a variant, ehCas12a RRVR (T167R/N572R/K578V/N582R), with expanded PAM preference to 5'-TNYN, TWRV-3' (W is A or T, R is A or G, and V is A, C, or G), which can efficiently recognize -2* A/G PAMs that are barely recognized by Cas12a-type proteins and their mutants. Finally, we demonstrated that the DNase-inactivated ehCas12a RRVR base editor (dehCas12a RRVR-BE) was capable of targeting noncanonical PAMs in vivo and disease-related loci for potential therapeutic applications. Overall, our findings highlight the modular design and reconfiguration of Cas proteins for enhanced functionality.
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Affiliation(s)
- Zhenyu Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Huayi Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chaoqun Huang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Qun Zhou
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yunzi Luo
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Tangxing Road 133, Nanshan District, Shenzhen 518071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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22
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Lima CP, Barreiros GM, Oliveira ASA, de Souza MM, Manieri TM, Moro AM. A Dual Strategy-In Vitro and In Silico-To Evaluate Human Antitetanus mAbs Addressing Their Potential Protective Action on TeNT Endocytosis in Primary Rat Neuronal Cells. Int J Mol Sci 2024; 25:5788. [PMID: 38891974 PMCID: PMC11171557 DOI: 10.3390/ijms25115788] [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: 03/21/2024] [Revised: 05/01/2024] [Accepted: 05/10/2024] [Indexed: 06/21/2024] Open
Abstract
Tetanus disease, caused by C. tetani, starts with wounds or mucous layer contact. Prevented by vaccination, the lack of booster shots throughout life requires prophylactic treatment in case of accidents. The incidence of tetanus is high in underdeveloped countries, requiring the administration of antitetanus antibodies, usually derived from immunized horses or humans. Heterologous sera represent risks such as serum sickness. Human sera can carry unknown viruses. In the search for human monoclonal antibodies (mAbs) against TeNT (Tetanus Neurotoxin), we previously identified a panel of mAbs derived from B-cell sorting, selecting two nonrelated ones that binded to the C-terminal domain of TeNT (HCR/T), inhibiting its interaction with the cellular receptor ganglioside GT1b. Here, we present the results of cellular assays and molecular docking tools. TeNT internalization in neurons is prevented by more than 50% in neonatal rat spinal cord cells, determined by quantitative analysis of immunofluorescence punctate staining of Alexa Fluor 647 conjugated to TeNT. We also confirmed the mediator role of the Synaptic Vesicle Glycoprotein II (SV2) in TeNT endocytosis. The molecular docking assays to predict potential TeNT epitopes showed the binding of both antibodies to the HCR/T domain. A higher incidence was found between N1153 and W1297 when evaluating candidate residues for conformational epitope.
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Affiliation(s)
- Cauã Pacheco Lima
- Laboratory of Biopharmaceuticals, Butantan Institute, Sao Paulo 05503-900, Brazil; (C.P.L.); (G.M.B.); (A.S.A.O.)
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo 05508-270, Brazil
| | - Gabriela Massaro Barreiros
- Laboratory of Biopharmaceuticals, Butantan Institute, Sao Paulo 05503-900, Brazil; (C.P.L.); (G.M.B.); (A.S.A.O.)
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo 05508-270, Brazil
| | - Adriele Silva Alves Oliveira
- Laboratory of Biopharmaceuticals, Butantan Institute, Sao Paulo 05503-900, Brazil; (C.P.L.); (G.M.B.); (A.S.A.O.)
| | - Marcelo Medina de Souza
- CENTD—Centre of Excellence in New Target Discovery, Butantan Institute, São Paulo 05503-900, Brazil;
| | - Tania Maria Manieri
- Laboratory of Biopharmaceuticals, Butantan Institute, Sao Paulo 05503-900, Brazil; (C.P.L.); (G.M.B.); (A.S.A.O.)
- CeRDI—Center for Research and Development in Immunobiologicals, Butantan Institute, São Paulo 05503-900, Brazil
| | - Ana Maria Moro
- Laboratory of Biopharmaceuticals, Butantan Institute, Sao Paulo 05503-900, Brazil; (C.P.L.); (G.M.B.); (A.S.A.O.)
- CeRDI—Center for Research and Development in Immunobiologicals, Butantan Institute, São Paulo 05503-900, Brazil
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23
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Zhu Y, Li X, Zhang Q, Yang X, Sun X, Pan Y, Yuan X, Ma Y, Xu B, Yang Z. Aptamer AS411 interacts with the KRAS promoter/hnRNP A1 complex and shows increased potency against drug-resistant lung cancer. RSC Med Chem 2024; 15:1515-1526. [PMID: 38784467 PMCID: PMC11110790 DOI: 10.1039/d3md00752a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/15/2024] [Accepted: 02/22/2024] [Indexed: 05/25/2024] Open
Abstract
G-quadruplex (G4) aptamers that can competitively binding protein with oncogene promoter G4 hold promise for cancer treatment. In this study, a neutral cytidinyl lipid, DNCA, was shown to transfect and deliver G4 aptamers (AS1411, TBA) into tumour cells, including multidrug-resistant tumour cells, and their nuclear localizations were clearly detected. Both AS1411/DNCA and TBA/DNCA showed excellent antitumour efficacies in the drug-resistant non-small cell lung cancer cell line A549/TXL at a low concentration (100 nM). Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) was identified as a new target of AS1411 and TBA. The binding affinities were measured, and the Kd values of AS1411/hnRNP A1 and TBA/hnRNP A1 were 17.5 nM and 21.1 nM, respectively. Then the expression of KRAS mRNA in A549/TXL cells was found to be higher than that in A549 cells, and KRAS mRNA was reduced by approximately 40% after administration of AS1411 or TBA in A549/TXL cells. Further, it was confirmed for the first time that AS1411 targeted not only hnRNP A1 but also the KRAS promoter/hnRNP A1 complexes. And although TBA cannot target the KRAS promoter/hnRNP A1 complexes, the biolayer interferometry (BLI) experiment showed that TBA and AS1411 have similar effects on several key proteins in tumour cells, especially hnRNP A1. Molecular docking and molecular dynamics simulation showed that AS1411 and the KRAS promoter bound to the same domain of hnRNP A1 protein, while TBA bound to another domain.
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Affiliation(s)
- Yuejie Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Xiang Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Qi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Xiantao Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
- School of Pharmacy, Chengdu Medical College 783 Xindu Avenue, Xindu District Chengdu 610500 China
| | - Xudong Sun
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Yi Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Xia Yuan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Yuan Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Bo Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
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24
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Zhao H, Petrey D, Murray D, Honig B. ZEPPI: Proteome-scale sequence-based evaluation of protein-protein interaction models. Proc Natl Acad Sci U S A 2024; 121:e2400260121. [PMID: 38743624 PMCID: PMC11127014 DOI: 10.1073/pnas.2400260121] [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: 01/08/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024] Open
Abstract
We introduce ZEPPI (Z-score Evaluation of Protein-Protein Interfaces), a framework to evaluate structural models of a complex based on sequence coevolution and conservation involving residues in protein-protein interfaces. The ZEPPI score is calculated by comparing metrics for an interface to those obtained from randomly chosen residues. Since contacting residues are defined by the structural model, this obviates the need to account for indirect interactions. Further, although ZEPPI relies on species-paired multiple sequence alignments, its focus on interfacial residues allows it to leverage quite shallow alignments. ZEPPI can be implemented on a proteome-wide scale and is applied here to millions of structural models of dimeric complexes in the Escherichia coli and human interactomes found in the PrePPI database. PrePPI's scoring function is based primarily on the evaluation of protein-protein interfaces, and ZEPPI adds a new feature to this analysis through the incorporation of evolutionary information. ZEPPI performance is evaluated through applications to experimentally determined complexes and to decoys from the CASP-CAPRI experiment. As we discuss, the standard CAPRI scores used to evaluate docking models are based on model quality and not on the ability to give yes/no answers as to whether two proteins interact. ZEPPI is able to detect weak signals from PPI models that the CAPRI scores define as incorrect and, similarly, to identify potential PPIs defined as low confidence by the current PrePPI scoring function. A number of examples that illustrate how the combination of PrePPI and ZEPPI can yield functional hypotheses are provided.
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Affiliation(s)
- Haiqing Zhao
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY10032
| | - Donald Petrey
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY10032
| | - Diana Murray
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY10032
| | - Barry Honig
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY10032
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY10032
- Department of Medicine, Columbia University, New York, NY10032
- Zuckerman Institute, Columbia University, New York, NY10027
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25
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Fecht S, Paracuellos P, Subramoni S, Tan CAZ, Ilangovan A, Costa TRD, Filloux A. Functionality of chimeric TssA proteins in the type VI secretion system reveals sheath docking specificity within their N-terminal domains. Nat Commun 2024; 15:4283. [PMID: 38769318 PMCID: PMC11106082 DOI: 10.1038/s41467-024-48487-8] [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: 03/19/2023] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
The genome of Pseudomonas aeruginosa encodes three type VI secretion systems, each comprising a dozen distinct proteins, which deliver toxins upon T6SS sheath contraction. The least conserved T6SS component, TssA, has variations in size which influence domain organisation and structure. Here we show that the TssA Nt1 domain interacts directly with the sheath in a specific manner, while the C-terminus is essential for oligomerisation. We built chimeric TssA proteins by swapping C-termini and showed that these can be functional even when made of domains from different TssA sub-groups. Functional specificity requires the Nt1 domain, while the origin of the C-terminal domain is more permissive for T6SS function. We identify two regions in short TssA proteins, loop and hairpin, that contribute to sheath binding. We propose a docking mechanism of TssA proteins with the sheath, and a model for how sheath assembly is coordinated by TssA proteins from this position.
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Affiliation(s)
- Selina Fecht
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Patricia Paracuellos
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Sujatha Subramoni
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Casandra Ai Zhu Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Aravindan Ilangovan
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Tiago R D Costa
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Alain Filloux
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
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26
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Toh JM, Yong J, Abrams ST, Wang L, Schofield J, Lane S, La Corte AC, Wang SS, Ariëns RAS, Philippou H, Xie J, Yu W, Wang G, Toh CH. Fibrinogen binding to histones in circulation protects against adverse cellular and clinical outcomes. J Thromb Haemost 2024:S1538-7836(24)00292-7. [PMID: 38777257 DOI: 10.1016/j.jtha.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/17/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Circulating histones are released by extensive tissue injury or cell death and play important pathogenic roles in critical illnesses. Their interaction with circulating plasma components and the potential roles in the clinical setting are not fully understood. OBJECTIVES We aimed to characterize the interaction of histones with fibrinogen and explore its roles in vitro, in vivo, and in patient samples. METHODS Histone-fibrinogen binding was assessed by electrophoresis and enzyme-linked immunosorbent assay-based affinity assay. Functional significance was explored using washed platelets and endothelial cells in vitro and histone-infusion mouse models in vivo. To determine clinical translatability, a retrospective single-center cohort study was conducted on patients requiring intensive care admission (n = 199) and validated in a cohort of hospitalized patients with COVID-19 (n = 69). RESULTS Fibrinogen binds histones through its D-domain with high affinity (calf thymus histones, KD = 18.0 ± 5.6 nM; histone 3, KD = 2.7 ± 0.8 nM; and histone 4, KD = 2.0 ± 0.7 nM) and significantly reduces histone-induced endothelial damage and platelet aggregation in vitro and in vivo in a histone-infusion mouse model. Physiologic concentrations of fibrinogen can neutralize low levels of circulating histones and increase the cytotoxicity threshold of histones to 50 μg/mL. In a cohort of patients requiring intensive care, a histone:fibrinogen ratio of ≥6 on admission was associated with moderate-severe thrombocytopenia and independently predicted mortality. This finding was validated in a cohort of hospitalized patients with COVID-19. CONCLUSION Fibrinogen buffers the cytotoxic properties of circulating histones. Detection and monitoring of circulating histones and histone:fibrinogen ratios will help identify critically ill patients at highest risk of adverse outcomes who might benefit from antihistone therapy.
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Affiliation(s)
- Julien M Toh
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK; Department of Anaesthetics and Critical Care, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Jun Yong
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK; Roald Dahl Haemostasis & Thrombosis Centre, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Simon T Abrams
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK; Department of Haematology, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Lijun Wang
- The Medical School, Southeast University, Nanjing, China
| | - Jeremy Schofield
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK; Roald Dahl Haemostasis & Thrombosis Centre, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Steven Lane
- Department of Medical Statistics, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Amy Cilia La Corte
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Susan S Wang
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK; William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | - Robert A S Ariëns
- Leeds Institute of Cardiovascular & Metabolic Medicine, University of Leeds, Leeds, West Yorkshire, UK
| | - Helen Philippou
- Leeds Institute of Cardiovascular & Metabolic Medicine, University of Leeds, Leeds, West Yorkshire, UK
| | - Jianfeng Xie
- The Medical School, Southeast University, Nanjing, China
| | - Weiping Yu
- The Medical School, Southeast University, Nanjing, China
| | - Guozheng Wang
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK; Department of Haematology, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK.
| | - Cheng-Hock Toh
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK; Roald Dahl Haemostasis & Thrombosis Centre, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK.
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27
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Wossnig L, Furtmann N, Buchanan A, Kumar S, Greiff V. Best practices for machine learning in antibody discovery and development. Drug Discov Today 2024; 29:104025. [PMID: 38762089 DOI: 10.1016/j.drudis.2024.104025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/25/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
In the past 40 years, therapeutic antibody discovery and development have advanced considerably, with machine learning (ML) offering a promising way to speed up the process by reducing costs and the number of experiments required. Recent progress in ML-guided antibody design and development (D&D) has been hindered by the diversity of data sets and evaluation methods, which makes it difficult to conduct comparisons and assess utility. Establishing standards and guidelines will be crucial for the wider adoption of ML and the advancement of the field. This perspective critically reviews current practices, highlights common pitfalls and proposes method development and evaluation guidelines for various ML-based techniques in therapeutic antibody D&D. Addressing challenges across the ML process, best practices are recommended for each stage to enhance reproducibility and progress.
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Affiliation(s)
- Leonard Wossnig
- LabGenius Ltd, The Biscuit Factory, 100 Drummond Road, London SE16 4DG, UK; Department of Computer Science, University College London, 66-72 Gower St, London WC1E 6EA, UK.
| | - Norbert Furtmann
- R&D Large Molecules Research Platform, Sanofi Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Andrew Buchanan
- Biologics Engineering, R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Sandeep Kumar
- Computational Protein Design and Modeling Group, Computational Science, Moderna Therapeutics, 200 Technology Square, Cambridge, MA 02139, USA
| | - Victor Greiff
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
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Liu H, Yao M, Ren J. Codonopsis pilosula-derived glycopeptide dCP1 promotes the polarization of tumor-associated macrophage from M2-like to M1 phenotype. Cancer Immunol Immunother 2024; 73:128. [PMID: 38743074 PMCID: PMC11093951 DOI: 10.1007/s00262-024-03694-6] [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: 07/21/2023] [Accepted: 03/28/2024] [Indexed: 05/16/2024]
Abstract
The majority of the immune cell population in the tumor microenvironment (TME) consists of tumor-associated macrophages (TAM), which are the main players in coordinating tumor-associated inflammation. TAM has a high plasticity and is divided into two main phenotypes, pro-inflammatory M1 type and anti-inflammatory M2 type, with tumor-suppressive and tumor-promoting functions, respectively. Considering the beneficial effects of M1 macrophages for anti-tumor and the high plasticity of macrophages, the conversion of M2 TAM to M1 TAM is feasible and positive for tumor treatment. This study sought to evaluate whether the glycopeptide derived from simulated digested Codonopsis pilosula extracts could regulate the polarization of M2-like TAM toward the M1 phenotype and the potential regulatory mechanisms. The results showed that after glycopeptide dCP1 treatment, the mRNA relative expression levels of some M2 phenotype marker genes in M2-like TAM in simulated TME were reduced, and the relative expression levels of M1 phenotype marker genes and inflammatory factor genes were increased. Analysis of RNA-Seq of M2-like TAM after glycopeptide dCP1 intervention showed that the gene sets such as glycolysis, which is associated with macrophage polarization in the M1 phenotype, were significantly up-regulated, whereas those of gene sets such as IL-6-JAK-STAT3 pathway, which is associated with polarization in the M2 phenotype, were significantly down-regulated. Moreover, PCA analysis and Pearson's correlation also indicated that M2-like TAM polarized toward the M1 phenotype at the transcriptional level after treatment with the glycopeptide dCP1. Lipid metabolomics was used to further explore the efficacy of the glycopeptide dCP1 in regulating the polarization of M2-like TAM to the M1 phenotype. It was found that the lipid metabolite profiles in dCP1-treated M2-like TAM showed M1 phenotype macrophage lipid metabolism profiles compared with blank M2-like TAM. Analysis of the key differential lipid metabolites revealed that the interconversion between phosphatidylcholine (PC) and diacylglycerol (DG) metabolites may be the central reaction of the glycopeptide dCP1 in regulating the conversion of M2-like TAM to the M1 phenotype. The above results suggest that the glycopeptide dCP1 has the efficacy to regulate the polarization of M2-like TAM to M1 phenotype in simulated TME.
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Affiliation(s)
- Hongxu Liu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, Guangdong, People's Republic of China
| | - Maojin Yao
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, People's Republic of China.
| | - Jiaoyan Ren
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, Guangdong, People's Republic of China.
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29
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Chen X, Liu J, Park N, Cheng J. A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models. Biomolecules 2024; 14:574. [PMID: 38785981 PMCID: PMC11117562 DOI: 10.3390/biom14050574] [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: 03/01/2024] [Revised: 04/07/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
The quality prediction of quaternary structure models of a protein complex, in the absence of its true structure, is known as the Estimation of Model Accuracy (EMA). EMA is useful for ranking predicted protein complex structures and using them appropriately in biomedical research, such as protein-protein interaction studies, protein design, and drug discovery. With the advent of more accurate protein complex (multimer) prediction tools, such as AlphaFold2-Multimer and ESMFold, the estimation of the accuracy of protein complex structures has attracted increasing attention. Many deep learning methods have been developed to tackle this problem; however, there is a noticeable absence of a comprehensive overview of these methods to facilitate future development. Addressing this gap, we present a review of deep learning EMA methods for protein complex structures developed in the past several years, analyzing their methodologies, data and feature construction. We also provide a prospective summary of some potential new developments for further improving the accuracy of the EMA methods.
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Affiliation(s)
- Xiao Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
| | - Jian Liu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
- NextGen Precision Health Institute, University of Missouri, Columbia, MO 65211, USA
| | - Nolan Park
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
- NextGen Precision Health Institute, University of Missouri, Columbia, MO 65211, USA
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Ma L, Ma J, Tian Y, Li X, Tai B, Xing F. Fus3 Interacts with Gal83, Revealing the MAPK Crosstalk to Snf1/AMPK to Regulate Secondary Metabolic Substrates in Aspergillus flavus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10065-10075. [PMID: 38634532 DOI: 10.1021/acs.jafc.4c01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Aflatoxins (AFs), highly carcinogenic natural products, are produced by the secondary metabolism of fungi such as Aspergillus flavus. Essential for the fungi to respond to environmental changes and aflatoxin synthesis, the pheromone mitogen-activated protein kinase (MAPK) is a potential regulator of aflatoxin biosynthesis. However, the mechanism by which pheromone MAPK regulates aflatoxin biosynthesis is not clear. Here, we showed Gal83, a new target of Fus3, and identified the pheromone Fus3-MAPK signaling pathway as a regulator of the Snf1/AMPK energy-sensing pathway modulating aflatoxins synthesis substrates. The screening for Fus3 target proteins identified the β subunit of Snf1/AMPK complexes using tandem affinity purification and multiomics. This subunit physically interacted with Fus3 both in vivo and in vitro and received phosphorylation from Fus3. Although the transcript levels of aflatoxin synthesis genes were not noticeably downregulated in both gal83 and fus3 deletion mutant strains, the levels of aflatoxin B1 and its synthesis substrates and gene expression levels of primary metabolizing enzymes were significantly reduced. This suggests that both the Fus3-MAPK and Snf1/AMPK pathways respond to energy signals. In conclusion, all the evidence unlocks a novel pathway of Fus3-MAPK to regulate AFs synthesis substrates by cross-talking with the Snf1/AMPK complexes.
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Affiliation(s)
- Longxue Ma
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences / Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Junning Ma
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences / Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Yuanyuan Tian
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences / Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Xu Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences / Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Bowen Tai
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences / Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Fuguo Xing
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences / Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
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Delgado-Maldonado T, González-González A, Moreno-Rodríguez A, Bocanegra-García V, Martinez-Vazquez AV, de Luna-Santillana EDJ, Pujadas G, Rojas-Verde G, Lara-Ramírez EE, Rivera G. Ligand- and Structure-Based Virtual Screening Identifies New Inhibitors of the Interaction of the SARS-CoV-2 Spike Protein with the ACE2 Host Receptor. Pharmaceutics 2024; 16:613. [PMID: 38794275 PMCID: PMC11124852 DOI: 10.3390/pharmaceutics16050613] [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: 03/30/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a fast-spreading viral pathogen and poses a serious threat to human health. New SARS-CoV-2 variants have been arising worldwide; therefore, is necessary to explore more therapeutic options. The interaction of the viral spike (S) protein with the angiotensin-converting enzyme 2 (ACE2) host receptor is an attractive drug target to prevent the infection via the inhibition of virus cell entry. In this study, Ligand- and Structure-Based Virtual Screening (LBVS and SBVS) was performed to propose potential inhibitors capable of blocking the S receptor-binding domain (RBD) and ACE2 interaction. The best five lead compounds were confirmed as inhibitors through ELISA-based enzyme assays. The docking studies and molecular dynamic (MD) simulations of the selected compounds maintained the molecular interaction and stability (RMSD fluctuations less than 5 Å) with key residues of the S protein. The compounds DRI-1, DRI-2, DRI-3, DRI-4, and DRI-5 efficiently block the interaction between the SARS-CoV-2 spike protein and receptor ACE2 (from 69.90 to 99.65% of inhibition) at 50 µM. The most potent inhibitors were DRI-2 (IC50 = 8.8 µM) and DRI-3 (IC50 = 2.1 µM) and have an acceptable profile of cytotoxicity (CC50 > 90 µM). Therefore, these compounds could be good candidates for further SARS-CoV-2 preclinical experiments.
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Affiliation(s)
- Timoteo Delgado-Maldonado
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (T.D.-M.); (A.G.-G.); (E.E.L.-R.)
| | - Alonzo González-González
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (T.D.-M.); (A.G.-G.); (E.E.L.-R.)
| | - Adriana Moreno-Rodríguez
- Laboratorio de Estudios Epidemiológicos, Clínicos, Diseños Experimentales e Investigación, Facultad de Ciencias Químicas, Universidad Autónoma “Benito Juárez” de Oaxaca, Avenida Universidad S/N, Ex Hacienda Cinco Señores, Oaxaca 68120, Mexico;
| | - Virgilio Bocanegra-García
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (V.B.-G.); (A.V.M.-V.); (E.d.J.d.L.-S.)
| | - Ana Verónica Martinez-Vazquez
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (V.B.-G.); (A.V.M.-V.); (E.d.J.d.L.-S.)
| | | | - Gerard Pujadas
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain;
| | - Guadalupe Rojas-Verde
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Monterrey 66451, Mexico;
| | - Edgar E. Lara-Ramírez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (T.D.-M.); (A.G.-G.); (E.E.L.-R.)
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (T.D.-M.); (A.G.-G.); (E.E.L.-R.)
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Wang K, Sun H, Cui Z, Wang J, Hou J, Lu F, Liu Y. Synergistic effects of microbial transglutaminase and apple pectin on the gelation properties of pea protein isolate and its application to probiotic encapsulation. Food Chem 2024; 439:138232. [PMID: 38118228 DOI: 10.1016/j.foodchem.2023.138232] [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: 09/23/2023] [Revised: 12/02/2023] [Accepted: 12/15/2023] [Indexed: 12/22/2023]
Abstract
The low gelation capacity of pea protein isolate (PPI) limits their use in food industry. Therefore, microbial transglutaminase (MTG) and apple pectin (AP) were combined to modify PPI to enhance its gelling characteristics, and the mechanism of MTG-induced PPI-AP composite gel generation was investigated. PPI (10 wt%) could not form a gel at 40 °C, while MTG-treated PPI (10 wt%) formed a self-supporting gel at 40 °C. Subsequently, the addition of AP further promoted the crosslinking of PPI and significantly improved the water holding capacity, rheology, and strength of PPI gels, which was attributed to both hydrogen and isopeptide bonds in the composite gel. Additionally, the PPI-AP composite gel showed excellent protection ability, and the survival rate of probiotics could reach over 90%, which could be used as an effective delivery system. This study verified that MTG and AP were efficient in enhancing the functional quality of PPI gels.
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Affiliation(s)
- Kangning Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Hui Sun
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Zhihan Cui
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jiahui Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jiayi Hou
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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Wang J, Hong M, Cheng Y, Wang X, Li D, Chen G, Bao B, Song J, Du X, Yang C, Zheng L, Tong Q. Targeting c-Myc transactivation by LMNA inhibits tRNA processing essential for malate-aspartate shuttle and tumour progression. Clin Transl Med 2024; 14:e1680. [PMID: 38769668 PMCID: PMC11106511 DOI: 10.1002/ctm2.1680] [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: 11/25/2023] [Revised: 03/28/2024] [Accepted: 04/19/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND A series of studies have demonstrated the emerging involvement of transfer RNA (tRNA) processing during the progression of tumours. Nevertheless, the roles and regulating mechanisms of tRNA processing genes in neuroblastoma (NB), the prevalent malignant tumour outside the brain in children, are yet unknown. METHODS Analysis of multi-omics results was conducted to identify crucial regulators of downstream tRNA processing genes. Co-immunoprecipitation and mass spectrometry methods were utilised to measure interaction between proteins. The impact of transcriptional regulators on expression of downstream genes was measured by dual-luciferase reporter, chromatin immunoprecipitation, western blotting and real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR) methods. Studies have been conducted to reveal impact and mechanisms of transcriptional regulators on biological processes of NB. Survival differences were analysed using the log-rank test. RESULTS c-Myc was identified as a transcription factor driving tRNA processing gene expression and subsequent malate-aspartate shuttle (MAS) in NB cells. Mechanistically, c-Myc directly promoted the expression of glutamyl-prolyl-tRNA synthetase (EPRS) and leucyl-tRNA synthetase (LARS), resulting in translational up-regulation of glutamic-oxaloacetic transaminase 1 (GOT1) as well as malate dehydrogenase 1 (MDH1) via inhibiting general control nonrepressed 2 or activating mechanistic target of rapamycin signalling. Meanwhile, lamin A (LMNA) inhibited c-Myc transactivation via physical interaction, leading to suppression of MAS, aerobic glycolysis, tumourigenesis and aggressiveness. Pre-clinically, lobeline was discovered as a LMNA-binding compound to facilitate its interaction with c-Myc, which inhibited aminoacyl-tRNA synthetase expression, MAS and tumour progression of NB, as well as growth of organoid derived from c-Myc knock-in mice. Low levels of LMNA or elevated expression of c-Myc, EPRS, LARS, GOT1 or MDH1 were linked to a worse outcome and a shorter survival time of clinical NB patients. CONCLUSIONS These results suggest that targeting c-Myc transactivation by LMNA inhibits tRNA processing essential for MAS and tumour progression.
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Affiliation(s)
- Jianqun Wang
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Mei Hong
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Yang Cheng
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Xiaojing Wang
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
- Department of GeriatricsUnion Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanHubei ProvinceChina
| | - Dan Li
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Guo Chen
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Banghe Bao
- Department of PathologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Jiyu Song
- Department of PathologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Xinyi Du
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Chunhui Yang
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Liduan Zheng
- Department of PathologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Qiangsong Tong
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
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Ge S, Dias ACP, Zhang X. Chimerism of avian IgY-scFv and truncated IgG-Fc: A novel strategy in cross-species antibody generation and enhancement. Immunology 2024; 172:46-60. [PMID: 38247105 DOI: 10.1111/imm.13752] [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: 06/10/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024] Open
Abstract
Chicken single-chain fragment variable (IgY-scFv) is a functional fragment and an emerging development in genetically engineered antibodies with a wide range of biomedical applications. However, scFvs have considerably shorter serum half-life due to the absence of antibody Fc region compared with the full-length antibody, and usually requires continuous intravenous administration for efficacy. A promising approach to overcome this limitation is to fuse scFv with immunoglobulin G (IgG) Fc region, for better recognition and mediation by the neonatal Fc receptor (FcRn) in the host. In this study, engineered mammalian ΔFc domains (CH2, CH3, and intact Fc region) were fused with anti-canine parvovirus-like particles avian IgY-scFv to produce chimeric antibodies and expressed in the HEK293 cell expression system. The obtained scFv-CH2, scFv-CH3, and scFv-Fc can bind with antigen specifically and dose-dependently. Surface plasmon resonance investigation confirmed that scFv-CH2, scFv-CH3, and scFv-Fc had different degrees of binding to FcRn, with scFv-Fc showing the highest affinity. scFv-Fc had a significantly longer half-life in mice compared with the unfused scFv. The identified ΔFcs are promising for the development of engineered Fc-based therapeutic antibodies and proteins with longer half-lives. The avian IgY-scFv-mammalian IgG Fc region opens up new avenues for antibody engineering, and it is a novel strategy to enhance the rapid development and screening of functional antibodies in veterinary and human medicine.
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Affiliation(s)
- Shikun Ge
- Department of Biology, Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Alberto Carlos Pires Dias
- Department of Biology, Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal
| | - Xiaoying Zhang
- Department of Biology, Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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Zhou L, Wang X, Peng L, Chen M, Wen H. SEnSCA: Identifying possible ligand-receptor interactions and its application in cell-cell communication inference. J Cell Mol Med 2024; 28:e18372. [PMID: 38747737 PMCID: PMC11095317 DOI: 10.1111/jcmm.18372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/10/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Multicellular organisms have dense affinity with the coordination of cellular activities, which severely depend on communication across diverse cell types. Cell-cell communication (CCC) is often mediated via ligand-receptor interactions (LRIs). Existing CCC inference methods are limited to known LRIs. To address this problem, we developed a comprehensive CCC analysis tool SEnSCA by integrating single cell RNA sequencing and proteome data. SEnSCA mainly contains potential LRI acquisition and CCC strength evaluation. For acquiring potential LRIs, it first extracts LRI features and reduces the feature dimension, subsequently constructs negative LRI samples through K-means clustering, finally acquires potential LRIs based on Stacking ensemble comprising support vector machine, 1D-convolutional neural networks and multi-head attention mechanism. During CCC strength evaluation, SEnSCA conducts LRI filtering and then infers CCC by combining the three-point estimation approach and single cell RNA sequencing data. SEnSCA computed better precision, recall, accuracy, F1 score, AUC and AUPR under most of conditions when predicting possible LRIs. To better illustrate the inferred CCC network, SEnSCA provided three visualization options: heatmap, bubble diagram and network diagram. Its application on human melanoma tissue demonstrated its reliability in CCC detection. In summary, SEnSCA offers a useful CCC inference tool and is freely available at https://github.com/plhhnu/SEnSCA.
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Affiliation(s)
- Liqian Zhou
- School of Life Sciences and ChemistryHunan University of TechnologyHunanChina
| | - Xiwen Wang
- School of Life Sciences and ChemistryHunan University of TechnologyHunanChina
| | - Lihong Peng
- School of Life Sciences and ChemistryHunan University of TechnologyHunanChina
| | - Min Chen
- School of Computer ScienceHunan Institute of TechnologyHengyangChina
| | - Hong Wen
- School of Computer ScienceHunan University of TechnologyHunanChina
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Hajizade MS, Raee MJ, Faraji SN, Farvadi F, Kabiri M, Eskandari S, Tamaddon AM. Targeted drug delivery to the thrombus by fusing streptokinase with a fibrin-binding peptide (CREKA): an in silico study. Ther Deliv 2024:1-13. [PMID: 38686829 DOI: 10.4155/tde-2023-0107] [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: 10/25/2023] [Accepted: 03/18/2024] [Indexed: 05/02/2024] Open
Abstract
Aim: Streptokinase has poor selectivity and provokes the immune response. In this study, we used in silico studies to design a fusion protein to achieve targeted delivery to the thrombus. Materials & methods: Streptokinase was analyzed computationally for mapping. The fusion protein modeling and quality assessment were carried out on several servers. The enzymatic activity and the stability of the fusion protein and its complex with plasminogen were assessed through molecular docking analysis and molecular dynamics simulation respectively. Results: Physicochemical properties analysis, protein quality assessments, protein-protein docking and molecular dynamics simulations predicted that the designed fusion protein is functionally active. Conclusion: Our results showed that this fusion protein might be a prospective candidate as a novel thrombolytic agent with better selectivity.
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Affiliation(s)
- Mohammad Soroosh Hajizade
- Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz, Fars, Iran, PO:7146864685
| | - Mohammad Javad Raee
- Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz, Fars, Iran, PO:7146864685
| | - Seyed Nooreddin Faraji
- School of Advanced Medical Sciences & Technologies, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Fakhrossadat Farvadi
- Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz, Fars, Iran, PO:7146864685
| | - Maryam Kabiri
- Arnold & Marie Schwartz College of Pharmacy & Health Sciences, Long Island University, Brooklyn, NY 11201, USA
| | - Sedigheh Eskandari
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Ali Mohammad Tamaddon
- Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz, Fars, Iran, PO:7146864685
- Department of Pharmaceutical Nanotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
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Wang X, Zhu Y, Tang L, Wang Y, Sun R, Deng X. Arabidopsis HSFA9 Acts as a Regulator of Heat Response Gene Expression and the Acquisition of Thermotolerance and Seed Longevity. PLANT & CELL PHYSIOLOGY 2024; 65:372-389. [PMID: 38123450 PMCID: PMC11020252 DOI: 10.1093/pcp/pcad164] [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: 02/02/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023]
Abstract
Heat-shock transcription factors (HSFs) are crucial for regulating plant responses to heat and various stresses, as well as for maintaining normal cellular functions and plant development. HSFA9 and HSFA2 are two of the Arabidopsis class A HSFs and their expressions are dramatically induced in response to heat shock (HS) stress among all 21 Arabidopsis HSFs. However, the detailed biological roles of their cooperation have not been fully characterized. In this study, we employed an integrated approach that combined bioinformatics, molecular genetics and computational analysis to identify and validate the molecular mechanism that controls seed longevity and thermotolerance in Arabidopsis. The acquisition of tolerance to deterioration was accompanied by a significant transcriptional switch that involved the induction of primary metabolism, reactive oxygen species and unfolded protein response, as well as the regulation of genes involved in response to dehydration, heat and hypoxia. In addition, the cis-regulatory motif analysis in normal stored and controlled deterioration treatment (CDT) seeds confirmed the CDT-repressed genes with heat-shock element (HSE) in their promoters. Using a yeast two-hybrid and molecular dynamic interaction assay, it is shown that HSFA9 acted as a potential regulator that can interact with HSFA2. Moreover, the knock-out mutants of both HSFA9 and HSFA2 displayed a significant reduction in seed longevity. These novel findings link HSF transcription factors with seed deterioration tolerance and longevity.
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Affiliation(s)
- Xiaohua Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Yan Zhu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Ling Tang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runze Sun
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xin Deng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
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Grassmann G, Miotto M, Desantis F, Di Rienzo L, Tartaglia GG, Pastore A, Ruocco G, Monti M, Milanetti E. Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments. Chem Rev 2024; 124:3932-3977. [PMID: 38535831 PMCID: PMC11009965 DOI: 10.1021/acs.chemrev.3c00550] [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: 07/31/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Investigating protein-protein interactions is crucial for understanding cellular biological processes because proteins often function within molecular complexes rather than in isolation. While experimental and computational methods have provided valuable insights into these interactions, they often overlook a critical factor: the crowded cellular environment. This environment significantly impacts protein behavior, including structural stability, diffusion, and ultimately the nature of binding. In this review, we discuss theoretical and computational approaches that allow the modeling of biological systems to guide and complement experiments and can thus significantly advance the investigation, and possibly the predictions, of protein-protein interactions in the crowded environment of cell cytoplasm. We explore topics such as statistical mechanics for lattice simulations, hydrodynamic interactions, diffusion processes in high-viscosity environments, and several methods based on molecular dynamics simulations. By synergistically leveraging methods from biophysics and computational biology, we review the state of the art of computational methods to study the impact of molecular crowding on protein-protein interactions and discuss its potential revolutionizing effects on the characterization of the human interactome.
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Affiliation(s)
- Greta Grassmann
- Department
of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Mattia Miotto
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Fausta Desantis
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- The
Open University Affiliated Research Centre at Istituto Italiano di
Tecnologia, Genoa 16163, Italy
| | - Lorenzo Di Rienzo
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Gian Gaetano Tartaglia
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
- Center
for Human Technologies, Genoa 16152, Italy
| | - Annalisa Pastore
- Experiment
Division, European Synchrotron Radiation
Facility, Grenoble 38043, France
| | - Giancarlo Ruocco
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
| | - Michele Monti
- RNA
System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Edoardo Milanetti
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
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Tang X, Zeng P, Liu K, Qing L, Sun Y, Liu X, Lu L, Wei C, Wang J, Jiang S, Sun J, Chang W, Yu H, Chen H, Zhou J, Xu C, Fan L, Miao YL, Ding J. The PTM profiling of CTCF reveals the regulation of 3D chromatin structure by O-GlcNAcylation. Nat Commun 2024; 15:2813. [PMID: 38561336 PMCID: PMC10985093 DOI: 10.1038/s41467-024-47048-3] [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: 11/28/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
CCCTC-binding factor (CTCF), a ubiquitously expressed and highly conserved protein, is known to play a critical role in chromatin structure. Post-translational modifications (PTMs) diversify the functions of protein to regulate numerous cellular processes. However, the effects of PTMs on the genome-wide binding of CTCF and the organization of three-dimensional (3D) chromatin structure have not been fully understood. In this study, we uncovered the PTM profiling of CTCF and demonstrated that CTCF can be O-GlcNAcylated and arginine methylated. Functionally, we demonstrated that O-GlcNAcylation inhibits CTCF binding to chromatin. Meanwhile, deficiency of CTCF O-GlcNAcylation results in the disruption of loop domains and the alteration of chromatin loops associated with cellular development. Furthermore, the deficiency of CTCF O-GlcNAcylation increases the expression of developmental genes and negatively regulates maintenance and establishment of stem cell pluripotency. In conclusion, these results provide key insights into the role of PTMs for the 3D chromatin structure.
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Affiliation(s)
- Xiuxiao Tang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Pharmacology and Cardiac & Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Pengguihang Zeng
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Kezhi Liu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Li Qing
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yifei Sun
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Xinyi Liu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Lizi Lu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Chao Wei
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jia Wang
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Shaoshuai Jiang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jun Sun
- West China Biomedical Big Data Center, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Wakam Chang
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Haopeng Yu
- West China Biomedical Big Data Center, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Jiaguo Zhou
- Department of Pharmacology and Cardiac & Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Chengfang Xu
- The obstetric and gynecology Department of The third affiliated hospital of Sun Yat-Sen University, Guangzhou, China.
| | - Lili Fan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong, China.
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.
| | - Junjun Ding
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China.
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.
- West China Biomedical Big Data Center, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China.
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Ahmadi N, Zareinejad M, Ameri M, Mahmoudi Maymand E, Nooreddin Faraji S, Ghaderi A, Ramezani A. Enhancing cancer immunotherapy with Anti-NKG2D/IL-15(N72D)/Sushi fusion protein: Targeting cytotoxic immune cells and boosting IL-15 efficacy. Cytokine 2024; 176:156505. [PMID: 38301357 DOI: 10.1016/j.cyto.2024.156505] [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: 10/18/2023] [Revised: 01/07/2024] [Accepted: 01/12/2024] [Indexed: 02/03/2024]
Abstract
BACKGROUND There are a number of distinct challenges and complexities associated with administering IL-15 for cancer immunotherapy that must be taken into consideration. OBJECTIVE The purpose of this study was to design a fusion protein for targeting cytotoxic immune cells and enhance IL-15 efficiency. METHODS A fusokine that contains IL-15(N72D), a Sushi domain, and anti-NKG2D scFv was designed. The fusion protein was in-silico modeled using the Swiss model server, followed by docking and molecular dynamics simulations. The in-vitro purified fusokine was evaluated using dot blot and Western blot. Then, flow cytometry was employed to evaluate biological properties such as proliferation, cytotoxicity, and degranulation. RESULTS Fusokine and IL-15(N72D)/Sushi, which had molecular weights of about 52 kDa and 26 kDa, respectively, were expressed in CHO-K1 cells. The fusokine binds 69.6 % of the CHO-NKG2D+ cells that express 83.1 % NKG2D. Both the fusokine and the IL-15(N72D)/Sushi significantly stimulate the proliferation of lymphocytes. After 14 days of growth, the vitality of untreated cells decreased to about 17.5 %, but 82.2 % and 56.6 % of cells were still alive when fusokine and IL-15(N72D)/Sushi were present. Furthermore, administration of fusokine was associated with the highest rates of target tumor cell cytotoxicity. Additionally, although it was not statistically significant, fusokine increased the expression of CD107a and granzyme B by 1.25 times and 2.4 times, respectively. CONCLUSION The fusokine possesses the capability to stimulate the survival and multiplication of lymphocytes, as well as their ability to eliminate tumors. These characteristics have led to its consideration as a potential treatment for immunotherapy.
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Affiliation(s)
- Nahid Ahmadi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran; Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammadrasul Zareinejad
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehrdad Ameri
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran; Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elham Mahmoudi Maymand
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Nooreddin Faraji
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Ghaderi
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amin Ramezani
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran; Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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41
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Das AP, Agarwal SM. Recent advances in the area of plant-based anti-cancer drug discovery using computational approaches. Mol Divers 2024; 28:901-925. [PMID: 36670282 PMCID: PMC9859751 DOI: 10.1007/s11030-022-10590-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/18/2022] [Indexed: 01/22/2023]
Abstract
Phytocompounds are a well-established source of drug discovery due to their unique chemical and functional diversities. In the area of cancer therapeutics, several phytocompounds have been used till date to design and develop new drugs. One of the desired interests of pharmaceutical companies and researchers globally is that new anti-cancer leads are discovered, for which phytocompounds can be considered a valuable source. Simultaneously, in recent years, the growth of computational approaches like virtual screening (VS), molecular dynamics (MD), pharmacophore modelling, Quantitative structure-activity relationship (QSAR), Absorption Distribution Metabolism Excretion and Toxicity (ADMET), network biology, and machine learning (ML) has gained importance due to their efficiency, reduced time-consuming nature, and cost-effectiveness. Therefore, the present review amalgamates the information on plant-based molecules identified for cancer lead discovery from in silico approaches. The mandate of this review is to discuss studies published in the last 5-6 years that aim to identify the phytomolecules as leads against cancer with the help of traditional computational approaches as well as newer techniques like network pharmacology and ML. This review also lists the databases and webservers available in the public domain for phytocompounds related information that can be harnessed for drug discovery. It is expected that the present review would be useful to pharmacologists, medicinal chemists, molecular biologists, and other researchers involved in the development of natural products (NPs) into clinically effective lead molecules.
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Affiliation(s)
- Agneesh Pratim Das
- Bioinformatics Division, ICMR-National Institute of Cancer Prevention and Research, I-7, Sector-39, Noida, Uttar Pradesh, 201301, India
| | - Subhash Mohan Agarwal
- Bioinformatics Division, ICMR-National Institute of Cancer Prevention and Research, I-7, Sector-39, Noida, Uttar Pradesh, 201301, India.
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Zavarzina II, Kuzmenkov AI, Dobrokhotov NA, Maleeva EE, Korolkova YV, Peigneur S, Tytgat J, Krylov NA, Vassilevski AA, Chugunov AO. The scorpion toxin BeKm-1 blocks hERG cardiac potassium channels using an indispensable arginine residue. FEBS Lett 2024; 598:889-901. [PMID: 38563123 DOI: 10.1002/1873-3468.14850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024]
Abstract
BeKm-1 is a peptide toxin from scorpion venom that blocks the pore of the potassium channel hERG (Kv11.1) in the human heart. Although individual protein structures have been resolved, the structure of the complex between hERG and BeKm-1 is unknown. Here, we used molecular dynamics and ensemble docking, guided by previous double-mutant cycle analysis data, to obtain an in silico model of the hERG-BeKm-1 complex. Adding to the previous mutagenesis study of BeKm-1, our model uncovers the key role of residue Arg20, which forms three interactions (a salt bridge and hydrogen bonds) with the channel vestibule simultaneously. Replacement of this residue even by lysine weakens the interactions significantly. In accordance, the recombinantly produced BeKm-1R20K mutant exhibited dramatically decreased activity on hERG. Our model may be useful for future drug design attempts.
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Affiliation(s)
- Iana I Zavarzina
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | | | - Nikita A Dobrokhotov
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | | | | | | | - Jan Tytgat
- Toxicology and Pharmacology, KU Leuven, Belgium
| | - Nikolay A Krylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Alexander A Vassilevski
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Anton O Chugunov
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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43
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Ghosh M, Shadangi S, Rana S. Rational design of antibody-like peptides for targeting the human complement fragment protein C5a. Proteins 2024; 92:449-463. [PMID: 37933678 DOI: 10.1002/prot.26637] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023]
Abstract
Human complement fragment 5a (C5a) is one of the most potent glycoproteins generated downstream of C3a and C4a during late-stage activation of the complement signaling cascade. C5a recruits receptors like C5aR1 and C5aR2 and is established to play a critical role in complement-mediated inflammation. Thus, excessive C5a in the plasma due to aberrant activation of the complement contributes to the pathophysiology of several chronic inflammatory diseases. Therefore, restricting the excessive interaction of C5a with its receptors by neutralizing C5a has been one of the most effective therapeutic strategies for the management of inflammatory diseases. Indeed, antibodies targeting C5 (Eculizumab), the precursor of C5a, and C5a (Vilobelimab) have already been approved by the FDA. Still, small designer peptides that work like antibodies and can target and stop C5a from interacting with its receptors seem to be a possible therapeutic alternative to antibodies because they are smaller, cheaper to make, more specific to their target, and can get through membrane barriers. As a proof-of-principle, the current study describes the computational design and evaluation of a pair of peptides that are able to form stable high-affinity complexes with the epitope regions of C5a that are important for the recruitment of C5aR1 and C5aR2. The computational data further supports the potential of designer peptides for mimicking the function of antibodies targeting C5a. However, further experimental studies will be required to establish the structure-function relationship of the designer peptides and also to establish the hypothesis of antibody-like peptides targeting C5a.
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Affiliation(s)
- Manaswini Ghosh
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha, India
| | - Sucharita Shadangi
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha, India
| | - Soumendra Rana
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha, India
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Zhang H, Wu Y, Zhu Y, Ge L, Huang J, Qin Z. Identification and functional analysis of a serine protease inhibitor using machine learning strategy. Int J Biol Macromol 2024; 265:130852. [PMID: 38508547 DOI: 10.1016/j.ijbiomac.2024.130852] [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: 01/17/2024] [Revised: 03/03/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
In the intricate realm of animal biology, a multitude of vital processes heavily rely on precisely orchestrated proteinase cascades, but the potential for havoc makes proteinase inhibitors indispensable, with serine proteinase inhibitors (serpins) at the forefront, serving as custodians of homeostasis and participating in various critical biological processes. Importantly, there are still many unexplored facets of serpin functionality. In this study, we focused on the serpin family proteins from Marsupenaeus japonicus, utilizing a fine-tuned pretrained protein language model. This approach led to the identification and evolutionary validation of 28 serpins, one of which, referred to as Mjserpin-1, was both computationally and experimentally demonstrated to show potential as an antiviral and apoptosis inhibitor. Our research unveils exciting prospects for the fusion of state-of-the-art artificial intelligence and rich bioinformatics, holding the promise of significant discoveries that could pave the way for future therapeutic advancements.
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Affiliation(s)
- Heqian Zhang
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China.
| | - Yaxin Wu
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Yanran Zhu
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Liangjun Ge
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Jiaquan Huang
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China.
| | - Zhiwei Qin
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China.
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Kravchenko A, de Vries SJ, Smaïl-Tabbone M, Chauvot de Beauchene I. HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses. BMC Bioinformatics 2024; 25:129. [PMID: 38532339 DOI: 10.1186/s12859-024-05733-6] [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: 05/25/2023] [Accepted: 03/06/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND The RNA-Recognition motif (RRM) is a protein domain that binds single-stranded RNA (ssRNA) and is present in as much as 2% of the human genome. Despite this important role in biology, RRM-ssRNA interactions are very challenging to study on the structural level because of the remarkable flexibility of ssRNA. In the absence of atomic-level experimental data, the only method able to predict the 3D structure of protein-ssRNA complexes with any degree of accuracy is ssRNA'TTRACT, an ssRNA fragment-based docking approach using ATTRACT. However, since ATTRACT parameters are not ssRNA-specific and were determined in 2010, there is substantial opportunity for enhancement. RESULTS Here we present HIPPO, a composite RRM-ssRNA scoring potential derived analytically from contact frequencies in near-native versus non-native docking models. HIPPO consists of a consensus of four distinct potentials, each extracted from a distinct reference pool of protein-trinucleotide docking decoys. To score a docking pose with one potential, for each pair of RNA-protein coarse-grained bead types, each contact is awarded or penalised according to the relative frequencies of this contact distance range among the correct and incorrect poses of the reference pool. Validated on a fragment-based docking benchmark of 57 experimentally solved RRM-ssRNA complexes, HIPPO achieved a threefold or higher enrichment for half of the fragments, versus only a quarter with the ATTRACT scoring function. In particular, HIPPO drastically improved the chance of very high enrichment (12-fold or higher), a scenario where the incremental modelling of entire ssRNA chains from fragments becomes viable. However, for the latter result, more research is needed to make it directly practically applicable. Regardless, our approach already improves upon the state of the art in RRM-ssRNA modelling and is in principle extendable to other types of protein-nucleic acid interactions.
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Affiliation(s)
- Anna Kravchenko
- Université de Lorraine, CNRS, Inria, LORIA, 54000, Nancy, France
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Huang J, Tsang WY, Fang XN, Zhang Y, Luo J, Gong LQ, Zhang BF, Wong CN, Li ZH, Liu BL, Huang JL, Yang YM, Liu S, Ban LX, Chan YH, Guan XY. FASN Inhibition Decreases MHC-I Degradation and Synergizes with PD-L1 Checkpoint Blockade in Hepatocellular Carcinoma. Cancer Res 2024; 84:855-871. [PMID: 38486485 DOI: 10.1158/0008-5472.can-23-0966] [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: 03/29/2023] [Revised: 08/20/2023] [Accepted: 01/08/2024] [Indexed: 03/19/2024]
Abstract
Immune checkpoint inhibitors (ICI) transformed the treatment landscape of hepatocellular carcinoma (HCC). Unfortunately, patients with attenuated MHC-I expression remain refractory to ICIs, and druggable targets for upregulating MHC-I are limited. Here, we found that genetic or pharmacologic inhibition of fatty acid synthase (FASN) increased MHC-I levels in HCC cells, promoting antigen presentation and stimulating antigen-specific CD8+ T-cell cytotoxicity. Mechanistically, FASN inhibition reduced palmitoylation of MHC-I that led to its lysosomal degradation. The palmitoyltransferase DHHC3 directly bound MHC-I and negatively regulated MHC-I protein levels. In an orthotopic HCC mouse model, Fasn deficiency enhanced MHC-I levels and promoted cancer cell killing by tumor-infiltrating CD8+ T cells. Moreover, the combination of two different FASN inhibitors, orlistat and TVB-2640, with anti-PD-L1 antibody robustly suppressed tumor growth in vivo. Multiplex IHC of human HCC samples and bioinformatic analysis of The Cancer Genome Atlas data further illustrated that lower expression of FASN was correlated with a higher percentage of cytotoxic CD8+ T cells. The identification of FASN as a negative regulator of MHC-I provides the rationale for combining FASN inhibitors and immunotherapy for treating HCC. SIGNIFICANCE Inhibition of FASN increases MHC-I protein levels by suppressing its palmitoylation and lysosomal degradation, which stimulates immune activity against hepatocellular carcinoma and enhances the efficacy of immune checkpoint inhibition.
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Affiliation(s)
- Jiao Huang
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Wai Ying Tsang
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong
| | - Xiao-Na Fang
- Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, P.R. China
- State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
- Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, P.R. China
| | - Yu Zhang
- Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, P.R. China
- State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
- Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, P.R. China
| | - Jie Luo
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Lan-Qi Gong
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- Clinical Oncology Center, Shenzhen Key Laboratory for Cancer Metastasis and Personalized Therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Bai-Feng Zhang
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- Clinical Oncology Center, Shenzhen Key Laboratory for Cancer Metastasis and Personalized Therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Ching Ngar Wong
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Zhi-Hong Li
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong
| | - Bei-Lei Liu
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- Clinical Oncology Center, Shenzhen Key Laboratory for Cancer Metastasis and Personalized Therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Jin-Lin Huang
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Yu-Ma Yang
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Shan Liu
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Liu-Xian Ban
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- Clinical Oncology Center, Shenzhen Key Laboratory for Cancer Metastasis and Personalized Therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Yiu Hong Chan
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong
| | - Xin-Yuan Guan
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- Clinical Oncology Center, Shenzhen Key Laboratory for Cancer Metastasis and Personalized Therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, China
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Chen Z, Lin B, Yao X, Weng J, Liu J, He Q, Song K, Zhou C, Zuo Z, Huang X, Liu Z, Huang Q, Xu Q, Guo X. Endothelial β-catenin upregulation and Y142 phosphorylation drive diabetic angiogenesis via upregulating KDR/HDAC9. Cell Commun Signal 2024; 22:182. [PMID: 38491522 PMCID: PMC10941375 DOI: 10.1186/s12964-024-01566-1] [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: 11/07/2023] [Accepted: 03/09/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Diabetic angiogenesis is closely associated with disabilities and death caused by diabetic microvascular complications. Advanced glycation end products (AGEs) are abnormally accumulated in diabetic patients and are a key pathogenic factor for diabetic angiogenesis. The present study focuses on understanding the mechanisms underlying diabetic angiogenesis and identifying therapeutic targets based on these mechanisms. METHODS In this study, AGE-induced angiogenesis serves as a model to investigate the mechanisms underlying diabetic angiogensis. Mouse aortic rings, matrigel plugs, and HUVECs or 293T cells were employed as research objects to explore this pathological process by using transcriptomics, gene promoter reporter assays, virtual screening and so on. RESULTS Here, we found that AGEs activated Wnt/β-catenin signaling pathway and enhanced the β-catenin protein level by affecting the expression of β-catenin degradation-related genes, such as FZDs (Frizzled receptors), LRPs (LDL Receptor Related Proteins), and AXIN1. AGEs could also mediate β-catenin Y142 phosphorylation through VEGFR1 isoform5. These dual effects of AGEs elevated the nuclear translocation of β-catenin and sequentially induced the expression of KDR (Kinase Insert Domain Receptor) and HDAC9 (Histone Deacetylase 9) by POU5F1 and NANOG, respectively, thus mediating angiogenesis. Finally, through virtual screening, Bioymifi, an inhibitor that blocks VEGFR1 isoform5-β-catenin complex interaction and alleviates AGE-induced angiogenesis, was identified. CONCLUSION Collectively, this study offers insight into the pathophysiological functions of β-catenin in diabetic angiogenesis.
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Affiliation(s)
- Zhenfeng Chen
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Bingqi Lin
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaodan Yao
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jie Weng
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jinlian Liu
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Qi He
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Ke Song
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Chuyu Zhou
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zirui Zuo
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoxia Huang
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zhuanhua Liu
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Qiaobing Huang
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Qiulin Xu
- Department of Intensive Care Unit, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Southern Medical University, Guangzhou, 510515, China.
| | - Xiaohua Guo
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
- National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
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Wang Z, Xie X, He Z, Sun Z, Zhang Y, Mao F, Pei H, Zhang S, Hammock BD, Liu X. Development of Shark Single Domain Antibodies Specific for Human α-Fetoprotein and the Multimerization Strategy in Serum Detection. Anal Chem 2024; 96:4242-4250. [PMID: 38408370 DOI: 10.1021/acs.analchem.3c05675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Sensitive detection of cancer biomarkers can contribute to the timely diagnosis and treatment of diseases. In this study, the whitespotted bamboo sharks were immunized with human α-fetoprotein (AFP), and a phage-displayed variable new antigen receptor (VNAR) single domain antibody library was constructed. Then four unique VNARs (VNAR1, VNAR11, VNAR21, and VNAR25) against AFP were isolated from the library by biopanning for the first time. All of the sequences belong to type II of VNAR, and the VNAR11 was much different from the rest of the three sequences. Then VNAR1 and VNAR11 were selected to fuse with the C4-binding protein α chain (C4bpα) sequence and efficiently expressed in the Escherichia coli system. Furthermore, a VNAR-C4bpα-mediated sandwich chemiluminescence immunoassay (VSCLIA) was developed for the detection of AFP in human serum samples. After optimization, the VSCLIA showed a limit of detection of 0.74 ng/mL with good selectivity and accuracy. Moreover, the results of clinical serum samples detected by the VSCLIA were confirmed by an automatic immunoanalyzer in the hospital, indicating its practical application in actual samples. In conclusion, the novel antibody element VNAR exhibits great potential for immunodiagnosis, and this study also provides a new direction and experimental basis for AFP detection.
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Affiliation(s)
- Zheming Wang
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Xiaoxia Xie
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Zhenyun He
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Zhichang Sun
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Yongli Zhang
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Fujing Mao
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Hua Pei
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, China
| | - Sihang Zhang
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Bruce D Hammock
- Department of Entomology and Nematology, and UC Davis Comprehensive Cancer Center, University of California, Davis, California 95616, United States
| | - Xing Liu
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
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Wen X, Qin J, Zhang X, Ye L, Wang Y, Yang R, Di Y, He W, Wang Z. MEK-mediated CHPF2 phosphorylation promotes colorectal cancer cell proliferation and metastasis by activating NF-κB signaling. Cancer Lett 2024; 584:216644. [PMID: 38253217 DOI: 10.1016/j.canlet.2024.216644] [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: 10/02/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
The cytokine tumor necrosis factor (TNF) plays a crucial role in the proliferation and metastasis of colorectal cancer (CRC) cells, but the underlying mechanisms remain poorly understood. Here, we report that chondroitin polymerizing factor 2 (CHPF2) promotes CRC cell proliferation and metastasis mediated by TNF, independently of its enzymatic activity. CHPF2 is highly expressed in CRC, and its elevated expression is associated with poor prognosis of CRC patients. Mechanistically, upon TNF stimulation, CHPF2 is phosphorylated at the T588 residue by MEK, enabling CHPF2 to interact with both TAK1 and IKKα. This interaction enhances the binding of TAK1 and IKKα, leading to increased phosphorylation of the IKK complex and activation of NF-κB signaling. As a result, the expression of early growth factors (EGR1) is upregulated to promote CRC cell proliferation and metastasis. In contrast, introduction of a phospho-deficient T588A mutation in CHPF2 weakened the interaction between CHPF2 and TAK1, thus impairing NF-κB signaling. CHPF2 T588A mutation reduced the ability of CHPF2 to promote the proliferation and metastasis of CRC in vitro and in vivo. Furthermore, the NF-κB RELA subunit promotes CHPF2 expression, further amplifying TNF-induced NF-κB signaling activation. These findings identify a moonlighting function of CHPF2 in promoting tumor cell proliferation and metastasis and provide insights into the mechanism by which CHPF2 amplifies TNF-mediated NF-κB signaling activation. Our study provides a molecular basic for the development of therapeutic strategies for CRC treatment.
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Affiliation(s)
- Xiangqiong Wen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Jiale Qin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Xiang Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Lvlan Ye
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China; Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Youpeng Wang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| | - Ranran Yang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China; Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Yuqin Di
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China; Molecular Diagnosis and Gene Testing Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
| | - Weiling He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China; Department of Gastrointestinal Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361000, China.
| | - Ziyang Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China; Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
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Lv Y, Gong H, Liu X, Hao J, Xu L, Sun Z, Yu C, Xu L. A dual computational and experimental strategy to enhance TSLP antibody affinity for improved asthma treatment. PLoS Comput Biol 2024; 20:e1011984. [PMID: 38536788 PMCID: PMC10971747 DOI: 10.1371/journal.pcbi.1011984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 03/10/2024] [Indexed: 04/05/2024] Open
Abstract
Thymic stromal lymphopoietin is a key cytokine involved in the pathogenesis of asthma and other allergic diseases. Targeting TSLP and its signaling pathways is increasingly recognized as an effective strategy for asthma treatment. This study focused on enhancing the affinity of the T6 antibody, which specifically targets TSLP, by integrating computational and experimental methods. The initial affinity of the T6 antibody for TSLP was lower than the benchmark antibody AMG157. To improve this, we utilized alanine scanning, molecular docking, and computational tools including mCSM-PPI2 and GEO-PPI to identify critical amino acid residues for site-directed mutagenesis. Subsequent mutations and experimental validations resulted in an antibody with significantly enhanced blocking capacity against TSLP. Our findings demonstrate the potential of computer-assisted techniques in expediting antibody affinity maturation, thereby reducing both the time and cost of experiments. The integration of computational methods with experimental approaches holds great promise for the development of targeted therapeutic antibodies for TSLP-related diseases.
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Affiliation(s)
- Yitong Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - He Gong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xuechao Liu
- Beijing Sungen Biomedical Technology Co., Ltd, Beijing, China
| | - Jia Hao
- Beijing Sungen Biomedical Technology Co., Ltd, Beijing, China
| | - Lei Xu
- Beijing Sungen Biomedical Technology Co., Ltd, Beijing, China
| | - Zhiwei Sun
- Beijing Sungen Biomedical Technology Co., Ltd, Beijing, China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lida Xu
- Beijing Sungen Biomedical Technology Co., Ltd, Beijing, China
- Beijing Hotgen Biotech Co., Ltd, Beijing, China
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