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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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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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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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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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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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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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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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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; 15:399-411. [PMID: 38686829 DOI: 10.4155/tde-2023-0107] [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: 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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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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68
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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: 5] [Impact Index Per Article: 5.0] [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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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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70
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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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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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77
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Shor B, Schneidman-Duhovny D. CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2. Nat Methods 2024; 21:477-487. [PMID: 38326495 PMCID: PMC10927564 DOI: 10.1038/s41592-024-02174-0] [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: 05/17/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024]
Abstract
Deep learning models, such as AlphaFold2 and RosettaFold, enable high-accuracy protein structure prediction. However, large protein complexes are still challenging to predict due to their size and the complexity of interactions between multiple subunits. Here we present CombFold, a combinatorial and hierarchical assembly algorithm for predicting structures of large protein complexes utilizing pairwise interactions between subunits predicted by AlphaFold2. CombFold accurately predicted (TM-score >0.7) 72% of the complexes among the top-10 predictions in two datasets of 60 large, asymmetric assemblies. Moreover, the structural coverage of predicted complexes was 20% higher compared to corresponding Protein Data Bank entries. We applied the method on complexes from Complex Portal with known stoichiometry but without known structure and obtained high-confidence predictions. CombFold supports the integration of distance restraints based on crosslinking mass spectrometry and fast enumeration of possible complex stoichiometries. CombFold's high accuracy makes it a promising tool for expanding structural coverage beyond monomeric proteins.
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Affiliation(s)
- Ben Shor
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dina Schneidman-Duhovny
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
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78
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Peng L, Gao P, Xiong W, Li Z, Chen X. Identifying potential ligand-receptor interactions based on gradient boosted neural network and interpretable boosting machine for intercellular communication analysis. Comput Biol Med 2024; 171:108110. [PMID: 38367445 DOI: 10.1016/j.compbiomed.2024.108110] [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: 10/30/2023] [Revised: 01/24/2024] [Accepted: 02/04/2024] [Indexed: 02/19/2024]
Abstract
Cell-cell communication is essential to many key biological processes. Intercellular communication is generally mediated by ligand-receptor interactions (LRIs). Thus, building a comprehensive and high-quality LRI resource can significantly improve intercellular communication analysis. Meantime, due to lack of a "gold standard" dataset, it remains a challenge to evaluate LRI-mediated intercellular communication results. Here, we introduce CellGiQ, a high-confident LRI prediction framework for intercellular communication analysis. Highly confident LRIs are first inferred by LRI feature extraction with BioTriangle, LRI selection using LightGBM, and LRI classification based on ensemble of gradient boosted neural network and interpretable boosting machine. Subsequently, known and identified high-confident LRIs are filtered by combining single-cell RNA sequencing (scRNA-seq) data and further applied to intercellular communication inference through a quartile scoring strategy. To validation the predictions, CellGiQ exploited several evaluation strategies: using AUC and AUPR, it surpassed six competing LRI prediction models on four LRI datasets; through Venn diagrams and molecular docking, its predicted LRIs were validated by five other popular intercellular communication inference methods; based on the overlapping LRIs, it computed high Jaccard index with six other state-of-the-art intercellular communication prediction tools within human HNSCC tissues; by comparing with classical models and literature retrieve, its inferred HNSCC-related intercellular communication results was further validated. The novelty of this study is to identify high-confident LRIs based on machine learning as well as design several LRI validation ways, providing reference for computational LRI prediction. CellGiQ provides an open-source and useful tool to decompose LRI-mediated intercellular communication at single cell resolution. CellGiQ is freely available at https://github.com/plhhnu/CellGiQ.
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Affiliation(s)
- Lihong Peng
- College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou, 412007, Hunan, China
| | - Pengfei Gao
- College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou, 412007, Hunan, China
| | - Wei Xiong
- College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou, 412007, Hunan, China
| | - Zejun Li
- School of Computer Science and Engineering, Hunan Institute of Technology, Hengyang, 421002, Hunan, China.
| | - Xing Chen
- School of Science, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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79
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Chen L, Hou P, Zou YL, Wang Y, Zhou LL, Hu L, Hu Y, Zhang QY, Huang LP, Lin L. B7-H1 agonists suppress the PI3K/AKT/mtor pathway by degrading p110γ and independently induce cell death. Cancer Lett 2024; 584:216615. [PMID: 38199586 DOI: 10.1016/j.canlet.2024.216615] [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: 08/08/2023] [Revised: 12/03/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
The biological role of B7-H1 intrinsic signal is reportedly diverse and controversial, its signal pathway remains unclear. Although B7-H1 blocking antibodies were found to have agonist capacity, their binding features and agonist mechanisms need further investigation. Here, by constructing cell strains with full-length or truncated B7-H1, we found that B7-H1 functioned as a receptor to transmit cell death signal from PD-1 protein or anti-B7-H1s through its cytoplasmic domain. Specific binding to the IgV-like domain of B7-H1 was required for the downstream signal. Upon agonists interaction, B7-H1 regulated the degradation of phosphoinositide 3-kinases (PI3Ks) subunit p110γ, subsequently inhibited the PI3K/AKT/mTOR pathway, and significantly increased autophagy. Moreover, B7-H1 agonists also suppressed ubiquitylation in B7-H1+cells by reducing ubiquitin-activating enzyme (E1), eventually leading to cell death. Finally, we validated the receptor role of B7-H1 in multiple tumor cells and demonstrated that B7-H1 agonists could suppress tumor progression independent of T cells in vivo. Our findings revealed that B7-H1 agonists functions as a PI3K inhibitor and may offer new strategies for PI3K targeting therapy.
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Affiliation(s)
- Ling Chen
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, Fujian, 350102, China.
| | - Ping Hou
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, Fujian, 350102, China
| | - Yu-Lian Zou
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, Fujian, 350102, China
| | - Yang Wang
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, Fujian, 350102, China
| | - Lin-Lin Zhou
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, Fujian, 350102, China
| | - Li Hu
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, Fujian, 350102, China
| | - Yan Hu
- Public Technology Service Center, Fujian Medical University, Fuzhou, Fujian, 350102, China
| | - Qiu-Yu Zhang
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, Fujian, 350102, China; Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, 350102, China
| | - Li-Ping Huang
- Department of Obstetrics, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350001, Fujian, China
| | - Lin Lin
- Department of Obstetrics, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350001, Fujian, China
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80
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Wang Q, Guo P, Cheng W, Liu Y, Zhang Y, Huo P, Feng S, Zhang W. An efficient and universal In silico screening strategy for acquisition of high-affinity Aptamer and its application in analytical utility. Talanta 2024; 269:125535. [PMID: 38091739 DOI: 10.1016/j.talanta.2023.125535] [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: 06/25/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024]
Abstract
Numerous aptamers against various targets have been identified through the technology of systematic evolution of ligands by exponential enrichment (SELEX), but the affinity of these aptamers are often insufficient due to the limitations of SELEX. Therefore, a more rational in silico screening strategy (ISS) was developed for efficient screening of high affinity aptamers, which took shape complementarity and thermodynamic stability into consideration. Neuron specific enolase (NSE), a tumor marker, was selected as the target molecule. In the screening process, three aptamer candidates with good shape complementarity, lower ΔG values, and higher ZDOCK scores were produced. The dissociation constant (Kd) of these candidates to NSE was determined to be 10.13 nM, 14.82 nM, and 2.76 nM, respectively. Each of them exhibited higher affinity to NSE than the parent aptamer (Kd = 23.83 nM). Finally, an antibody-free fluorescence aptasensor assay, based on the aptamer with the highest affinity, P-5C8G, was conducted, resulting in a limit of detection (LOD) value of 1.8 nM, which was much lower than the parental aptamer (P, LOD = 12.6 nM). The proposed ISS approach provided an efficient and universal strategy to improve the aptamer to have a high affinity and good analytical utility.
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Affiliation(s)
- Qionglin Wang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China
| | - Pengbo Guo
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China
| | - Weyland Cheng
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China
| | - Yuchun Liu
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China
| | - Yaodong Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China
| | - Peng Huo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Shubin Feng
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China.
| | - Wancun Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China.
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81
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Sengar AS, Kumar M, Rai C, Chakraborti S, Kumar D, Kumar P, Mukherjee S, Mondal K, Stewart A, Maity B. RGS6 drives cardiomyocyte death following nucleolar stress by suppressing Nucleolin/miRNA-21. J Transl Med 2024; 22:204. [PMID: 38409136 PMCID: PMC10895901 DOI: 10.1186/s12967-024-04985-3] [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: 11/26/2023] [Accepted: 02/12/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND Prior evidence demonstrated that Regulator of G protein Signaling 6 (RGS6) translocates to the nucleolus in response to cytotoxic stress though the functional significance of this phenomenon remains unknown. METHODS Utilizing in vivo gene manipulations in mice, primary murine cardiac cells, human cell lines and human patient samples we dissect the participation of a RGS6-nucleolin complex in chemotherapy-dependent cardiotoxicity. RESULTS Here we demonstrate that RGS6 binds to a key nucleolar protein, Nucleolin, and controls its expression and activity in cardiomyocytes. In the human myocyte AC-16 cell line, induced pluripotent stem cell derived cardiomyocytes, primary murine cardiomyocytes, and the intact murine myocardium tuning RGS6 levels via overexpression or knockdown resulted in diametrically opposed impacts on Nucleolin mRNA, protein, and phosphorylation.RGS6 depletion provided marked protection against nucleolar stress-mediated cell death in vitro, and, conversely, RGS6 overexpression suppressed ribosomal RNA production, a key output of the nucleolus, and triggered death of myocytes. Importantly, overexpression of either Nucleolin or Nucleolin effector miRNA-21 counteracted the pro-apoptotic effects of RGS6. In both human and murine heart tissue, exposure to the genotoxic stressor doxorubicin was associated with an increase in the ratio of RGS6/Nucleolin. Preventing RGS6 induction via introduction of RGS6-directed shRNA via intracardiac injection proved cardioprotective in mice and was accompanied by restored Nucleolin/miRNA-21 expression, decreased nucleolar stress, and decreased expression of pro-apoptotic, hypertrophy, and oxidative stress markers in heart. CONCLUSION Together, these data implicate RGS6 as a driver of nucleolar stress-dependent cell death in cardiomyocytes via its ability to modulate Nucleolin. This work represents the first demonstration of a functional role for an RGS protein in the nucleolus and identifies the RGS6/Nucleolin interaction as a possible new therapeutic target in the prevention of cardiotoxicity.
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Affiliation(s)
- Abhishek Singh Sengar
- Centre of Biomedical Research (CBMR), SGPGI Campus, Raebareli Road, Lucknow, Uttar Pradesh, 226014, India
| | - Manish Kumar
- Centre of Biomedical Research (CBMR), SGPGI Campus, Raebareli Road, Lucknow, Uttar Pradesh, 226014, India
| | - Chetna Rai
- Centre of Biomedical Research (CBMR), SGPGI Campus, Raebareli Road, Lucknow, Uttar Pradesh, 226014, India
| | - Sreemoyee Chakraborti
- Centre of Biomedical Research (CBMR), SGPGI Campus, Raebareli Road, Lucknow, Uttar Pradesh, 226014, India
- Forensic Science Laboratory, Department of Home and Hill Affairs, Kolkata, West Bengal, 700037, India
| | - Dinesh Kumar
- Centre of Biomedical Research (CBMR), SGPGI Campus, Raebareli Road, Lucknow, Uttar Pradesh, 226014, India
| | - Pranesh Kumar
- Institute of Pharmaceutical Science, University of Lucknow, Lucknow, Uttar Pradesh, 226007, India
| | - Sukhes Mukherjee
- Biochemistry, AIIMS Bhopal, Saket Nagar, Bhopal, Madhya Pradesh, 462026, India
| | - Kausik Mondal
- Zoology, University of Kalyani, Nadia, West Bengal, 741235, India
| | - Adele Stewart
- Biomedical Science, Florida Atlantic University, Jupiter, FL, 33458, USA
| | - Biswanath Maity
- Centre of Biomedical Research (CBMR), SGPGI Campus, Raebareli Road, Lucknow, Uttar Pradesh, 226014, India.
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82
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Xu L, Xu X, Xia J, Zhang H, Liang Y, Duan L. Phage Display Screening of Anchor Peptides for Red Blood Cell-Derived Extracellular Vesicles. ACS OMEGA 2024; 9:6492-6504. [PMID: 38371813 PMCID: PMC10870408 DOI: 10.1021/acsomega.3c06527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/26/2023] [Accepted: 01/03/2024] [Indexed: 02/20/2024]
Abstract
Extracellular vesicles (EVs) are increasingly used for disease diagnosis and treatment. Among them, red blood cell-derived EVs (RBC-EVs) have attracted great attention due to their abundant sources and low risks of gene transfer (RBC-EVs lack nuclear and mitochondrial DNA). Here, we first revealed the high expression level of membrane protein solute carrier family 4 member 1 (SLC4A1) in RBC-EVs through proteomic analysis. We then identified several binding peptides with high affinity for the SLC4A1 extracellular domain (SLC4A1-EC) from phage display library screening. A high affinity of SLC4A1-EC and the three peptides (XRB2, XRE4, and XRH7) were assessed in vitro using surface plasmon resonance analysis and SDS-polyacrylamide gel electrophoresis (SDS-PAGE). The binding sites of SLC4A1-EC and polypeptides were further predicted by LigPlot + analysis, and the results showed that these three polypeptides could bind to part of the hydrophobic residues of SLC4A1-EC. The binding efficiency of the anchor peptides to the RBC-EVs was further verified by flow cytometry and fluorescence imaging. In conclusion, we successfully screened three specific RBC-EV-targeting peptides which could potentially be utilized for isolating RBC-derived EVs from serum samples. More importantly, this peptide could be coupled with targeting peptides to modify RBC-EVs for drug delivery. Our work will provide a viable method for optimizing the function of RBC-EVs.
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Affiliation(s)
- Limei Xu
- Department
of Orthopedics, the First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Guangdong
Provincial Research Center for Artificial Intelligence and Digital
Orthopedic Technology, Shenzhen 518035, Guangdong, China
- Affiliated
Hospital of Jining Medical University, Jining
Medical University, Jining 272029, Shandong, China
| | - Xiao Xu
- Department
of Orthopedics, the First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Guangdong
Provincial Research Center for Artificial Intelligence and Digital
Orthopedic Technology, Shenzhen 518035, Guangdong, China
- Affiliated
Hospital of Jining Medical University, Jining
Medical University, Jining 272029, Shandong, China
| | - Jiang Xia
- Department
of Chemistry, The Chinese University of
Hong Kong, Shatin 999077, Hong Kong SAR, China
| | - Huawei Zhang
- Shenzhen
Institute of Advanced Technology, Chinese
Academy of Sciences, Shenzhen 518055, Guangdong, China
- Department
of Biomedical Engineering, South University
of Science and Technology of China, Shenzhen 518055, Guangdong, China
| | - Yujie Liang
- Department
of Child and Adolescent Psychiatry, Shenzhen Institute of Mental Health,
Shenzhen Mental Health Center, ShenzhenKangning
Hospital, Shenzhen 518020, Guangdong, China
| | - Li Duan
- Department
of Orthopedics, the First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Guangdong
Provincial Research Center for Artificial Intelligence and Digital
Orthopedic Technology, Shenzhen 518035, Guangdong, China
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83
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Dikhit MR, Sen A. Elucidation of conserved multi-epitope vaccine against Leishmania donovani using reverse vaccinology. J Biomol Struct Dyn 2024; 42:1293-1306. [PMID: 37054523 DOI: 10.1080/07391102.2023.2201630] [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: 11/02/2022] [Accepted: 03/29/2023] [Indexed: 04/15/2023]
Abstract
Visceral leishmaniasis (VL) is a tropical disease that causes severe public health problems in humans when untreated. As no licensed vaccine exists against VL, we aimed to formulate a potential MHC-restricted chimeric vaccine construct against this dreadful parasitic disease. Amastin-like protein derived from L. donovani is considered to be stable, immunogenic and non-allergic. A comprehensive established framework was used to explore the set of immunogenic epitopes with estimated population coverage of 96.08% worldwide. The rigorous assessment revealed 6 promiscuous T-epitopes which can plausibly be presented by more than 66 diverse HLA alleles. Further docking and simulation study of peptide receptor complexes identified a strong and stable binding interaction with better structural compactness. The predicted epitopes were combined with appropriate linkers and adjuvant molecules and their translation efficiency was evaluated in pET28+(a), an bacterial expression vector using in-silico cloning. Molecular docking followed by MD simulation study revealed a stable interaction between chimeric vaccine construct with TLRs. Immune simulation of the chimeric vaccine constructs showed an elevated Th1 immune response against both B and T epitopes. With this, the detailed computational analysis suggested that the chimeric vaccine construct can evoke a robust immune response against Leishmania donovani infection. Future studies are required to validate the role of amastin as a promising vaccine target.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manas Ranjan Dikhit
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Abhik Sen
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
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84
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Zhong J, Dos Santos RF, Abdelgaffar H, de Bortoli CP, Raza A, Jurat-Fuentes JL. Individual transmembrane domains of SfABCC2 from Spodoptera frugiperda do not serve as functional Cry1F receptors. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 199:105777. [PMID: 38458684 DOI: 10.1016/j.pestbp.2024.105777] [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: 10/31/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 03/10/2024]
Abstract
The fall armyworm (Spodoptera frugiperda) is a major global pest causing severe damage to various crops, especially corn. Transgenic corn producing the Cry1F pesticidal protein from the bacterium Bacillus thuringiensis (Cry1F corn) showed effectiveness in controlling this pest until S. frugiperda populations at locations in North and South America evolved practical resistance. The mechanism for practical resistance involved disruptive mutations in an ATP binding cassette transporter subfamily C2 gene (SfABCC2), which serves as a functional Cry1F receptor in the midgut cells of susceptible S. frugiperda. The SfABCC2 protein contains two transmembrane domains (TMD1 and TMD2), each with a cytosolic nucleotide (ATP) binding domain (NBD1 and NBD2, respectively). Previous reports have demonstrated that disruptive mutations in TMD2 were linked with resistance to Cry1F, yet whether the complete SfABCC2 structure is needed for receptor functionality or if a single TMD-NBD protein can serve as functional Cry1F receptor remains unknown. In the present study, we separately expressed TMD1 and TMD2 with their corresponding NBDs in cultured insect cells and tested their Cry1F receptor functionality. Our results show that the complete SfABCC2 structure is required for Cry1F receptor functionality. Moreover, binding competition assays revealed that Cry1F specifically bound to SfABCC2, whereas neither SfTMD1-NBD1 nor SfTMD2-NBD2 exhibited any significant binding. These results provide insights into the molecular mechanism of Cry1F recognition by SfABCC2 in S. frugiperda, which could facilitate the development of more effective insecticidal proteins.
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Affiliation(s)
- Jianfeng Zhong
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Key Laboratory for Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture and Rural Affairs, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | | | - Heba Abdelgaffar
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | | | - Ahmad Raza
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Juan Luis Jurat-Fuentes
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA.
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85
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Vincenzi M, Mercurio FA, Leone M. Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools. Int J Mol Sci 2024; 25:1798. [PMID: 38339078 PMCID: PMC10855943 DOI: 10.3390/ijms25031798] [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: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).
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Affiliation(s)
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy; (M.V.); (F.A.M.)
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Xiong D, Qiu Y, Zhao J, Zhou Y, Lee D, Gupta S, Torres M, Lu W, Liang S, Kang JJ, Eng C, Loscalzo J, Cheng F, Yu H. Structurally-informed human interactome reveals proteome-wide perturbations by disease mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.24.538110. [PMID: 37162909 PMCID: PMC10168245 DOI: 10.1101/2023.04.24.538110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Human genome sequencing studies have identified numerous loci associated with complex diseases. However, translating human genetic and genomic findings to disease pathobiology and therapeutic discovery remains a major challenge at multiscale interactome network levels. Here, we present a deep-learning-based ensemble framework, termed PIONEER (Protein-protein InteractiOn iNtErfacE pRediction), that accurately predicts protein binding partner-specific interfaces for all known protein interactions in humans and seven other common model organisms, generating comprehensive structurally-informed protein interactomes. We demonstrate that PIONEER outperforms existing state-of-the-art methods. We further systematically validated PIONEER predictions experimentally through generating 2,395 mutations and testing their impact on 6,754 mutation-interaction pairs, confirming the high quality and validity of PIONEER predictions. We show that disease-associated mutations are enriched in PIONEER-predicted protein-protein interfaces after mapping mutations from ~60,000 germline exomes and ~36,000 somatic genomes. We identify 586 significant protein-protein interactions (PPIs) enriched with PIONEER-predicted interface somatic mutations (termed oncoPPIs) from pan-cancer analysis of ~11,000 tumor whole-exomes across 33 cancer types. We show that PIONEER-predicted oncoPPIs are significantly associated with patient survival and drug responses from both cancer cell lines and patient-derived xenograft mouse models. We identify a landscape of PPI-perturbing tumor alleles upon ubiquitination by E3 ligases, and we experimentally validate the tumorigenic KEAP1-NRF2 interface mutation p.Thr80Lys in non-small cell lung cancer. We show that PIONEER-predicted PPI-perturbing alleles alter protein abundance and correlates with drug responses and patient survival in colon and uterine cancers as demonstrated by proteogenomic data from the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium. PIONEER, implemented as both a web server platform and a software package, identifies functional consequences of disease-associated alleles and offers a deep learning tool for precision medicine at multiscale interactome network levels.
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Affiliation(s)
- Dapeng Xiong
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Innovative Proteomics, Cornell University, Ithaca, NY 14853, USA
| | - Yunguang Qiu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Junfei Zhao
- Department of Systems Biology, Herbert Irving Comprehensive Center, Columbia University, New York, NY 10032, USA
| | - Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Dongjin Lee
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Shobhita Gupta
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Innovative Proteomics, Cornell University, Ithaca, NY 14853, USA
- Biophysics Program, Cornell University, Ithaca, NY 14853, USA
| | - Mateo Torres
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Innovative Proteomics, Cornell University, Ithaca, NY 14853, USA
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Siqi Liang
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jin Joo Kang
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Innovative Proteomics, Cornell University, Ithaca, NY 14853, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Joseph Loscalzo
- Channing Division of Network Medicine, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Innovative Proteomics, Cornell University, Ithaca, NY 14853, USA
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Min J, Rong X, Zhang J, Su R, Wang Y, Qi W. Computational Design of Peptide Assemblies. J Chem Theory Comput 2024; 20:532-550. [PMID: 38206800 DOI: 10.1021/acs.jctc.3c01054] [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: 01/13/2024]
Abstract
With the ongoing development of peptide self-assembling materials, there is growing interest in exploring novel functional peptide sequences. From short peptides to long polypeptides, as the functionality increases, the sequence space is also expanding exponentially. Consequently, attempting to explore all functional sequences comprehensively through experience and experiments alone has become impractical. By utilizing computational methods, especially artificial intelligence enhanced molecular dynamics (MD) simulation and de novo peptide design, there has been a significant expansion in the exploration of sequence space. Through these methods, a variety of supramolecular functional materials, including fibers, two-dimensional arrays, nanocages, etc., have been designed by meticulously controlling the inter- and intramolecular interactions. In this review, we first provide a brief overview of the current main computational methods and then focus on the computational design methods for various self-assembled peptide materials. Additionally, we introduce some representative protein self-assemblies to offer guidance for the design of self-assembling peptides.
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Affiliation(s)
- Jiwei Min
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Xi Rong
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Jiaxing Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
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88
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Zhao N, Han B, Zhao C, Xu J, Gong X. ABAG-docking benchmark: a non-redundant structure benchmark dataset for antibody-antigen computational docking. Brief Bioinform 2024; 25:bbae048. [PMID: 38385879 PMCID: PMC10883643 DOI: 10.1093/bib/bbae048] [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: 11/13/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 02/23/2024] Open
Abstract
Accurate prediction of antibody-antigen complex structures is pivotal in drug discovery, vaccine design and disease treatment and can facilitate the development of more effective therapies and diagnostics. In this work, we first review the antibody-antigen docking (ABAG-docking) datasets. Then, we present the creation and characterization of a comprehensive benchmark dataset of antibody-antigen complexes. We categorize the dataset based on docking difficulty, interface properties and structural characteristics, to provide a diverse set of cases for rigorous evaluation. Compared with Docking Benchmark 5.5, we have added 112 cases, including 14 single-domain antibody (sdAb) cases and 98 monoclonal antibody (mAb) cases, and also increased the proportion of Difficult cases. Our dataset contains diverse cases, including human/humanized antibodies, sdAbs, rodent antibodies and other types, opening the door to better algorithm development. Furthermore, we provide details on the process of building the benchmark dataset and introduce a pipeline for periodic updates to keep it up to date. We also utilize multiple complex prediction methods including ZDOCK, ClusPro, HDOCK and AlphaFold-Multimer for testing and analyzing this dataset. This benchmark serves as a valuable resource for evaluating and advancing docking computational methods in the analysis of antibody-antigen interaction, enabling researchers to develop more accurate and effective tools for predicting and designing antibody-antigen complexes. The non-redundant ABAG-docking structure benchmark dataset is available at https://github.com/Zhaonan99/Antibody-antigen-complex-structure-benchmark-dataset.
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Affiliation(s)
- Nan Zhao
- Institute for Mathematical Sciences, School of Mathematics, Renmin University of China, Beijing, China
| | - Bingqing Han
- Institute for Mathematical Sciences, School of Mathematics, Renmin University of China, Beijing, China
| | - Cuicui Zhao
- Institute for Mathematical Sciences, School of Mathematics, Renmin University of China, Beijing, China
| | - Jinbo Xu
- MoleculeMind Ltd., Beijing, China
| | - Xinqi Gong
- Institute for Mathematical Sciences, School of Mathematics, Renmin University of China, Beijing, China
- Beijing Academy of Artificial Intelligence, Beijing, China
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89
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Xiong L, Gong Y, Liu H, Huang L, Zeng Z, Zheng X, Li W, Liang Z, Kang L. circGlis3 promotes β-cell dysfunction by binding to heterogeneous nuclear ribonucleoprotein F and encoding Glis3-348aa protein. iScience 2024; 27:108680. [PMID: 38226164 PMCID: PMC10788204 DOI: 10.1016/j.isci.2023.108680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/12/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024] Open
Abstract
Circular RNAs (circRNAs) are crucial regulators of β-cell function and are involved in lipotoxicity-induced β-cell damage in type 2 diabetes mellitus (T2DM). We previously identified that circGlis3, a circRNA derived from exon 4 of the diabetes susceptibility gene Glis3, was upregulated in lipotoxic β cells. However, the functional role and molecular mechanism of circGlis3 in β cells remain largely unknown. Here, we revealed that the splicing factor CUGBP Elav-Like Family Member 1 (CELF1) facilitated the biogenesis of circGlis3. Moreover, we established a transgenic mouse model and confirmed that the overexpression of circGlis3 impaired β-cell function. Mechanistically, circGlis3 bound to heterogeneous nuclear ribonucleoprotein F (hnRNPF) and blocked its nuclear translocation, thereby reducing Sirt1 levels. Additionally, circGlis3 encoded a 348aa protein that interacted with GLIS3 and inhibited its transcriptional activity. Our data uncover a critical role of circGlis3 in β-cell dysfunction, suggesting that circGlis3 may be a potential therapeutic target for T2DM.
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Affiliation(s)
- Li Xiong
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yingying Gong
- Department of Geriatrics, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Huashan Liu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liang Huang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ziwei Zeng
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaobin Zheng
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenxin Li
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhenxing Liang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liang Kang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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90
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Wan H, Yang YD, Zhang Q, Chen YH, Hu XM, Huang YX, Shang L, Xiong K. VDAC1, as a downstream molecule of MLKL, participates in OGD/R-induced necroptosis by inducing mitochondrial damage. Heliyon 2024; 10:e23426. [PMID: 38173512 PMCID: PMC10761567 DOI: 10.1016/j.heliyon.2023.e23426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Ischemia-reperfusion (I/R) injury constitutes a significant risk factor for a range of diseases, including ischemic stroke, myocardial infarction, and trauma. Following the restoration of blood flow post-tissue ischemia, oxidative stress can lead to various forms of cell death, including necrosis, apoptosis, autophagy, and necroptosis. Recent evidence has highlighted the crucial role of mitochondrial dysfunction in I/R injury. Nevertheless, there remains much to be explored regarding the molecular signaling network governing cell death under conditions of oxidative stress. Voltage-dependent anion channel 1 (VDAC1), a major component in the outer mitochondrial membrane, is closely involved in the regulation of cell death. In a cellular model of oxygen-glucose deprivation and reoxygenation (OGD/R), which effectively simulates I/R injury in vitro, our study reveals that OGD/R induces VDAC1 oligomerization, consequently exacerbating cell death. Furthermore, we have revealed the translocation of mixed lineage kinase domain-like protein (MLKL) to the mitochondria, where it interacts with VDAC1 following OGD/R injury, leading to an increased mitochondrial membrane permeability. Notably, the inhibition of MLKL by necrosulfonamide hinders the binding of MLKL to VDAC1, primarily by affecting the membrane translocation of MLKL, and reduces OGD/R-induced VDAC1 oligomerization. Collectively, our findings provide preliminary evidence of the functional association between MLKL and VDAC1 in the regulation of necroptosis.
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Affiliation(s)
- Hao Wan
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Yan-di Yang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Qi Zhang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Yu-hua Chen
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
- Department of Central Laboratory, Xi'an Peihua University, Xi'an, China
| | - Xi-min Hu
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Yan-xia Huang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Lei Shang
- Jiangxi Research Institute of Ophthalmology and Visual Sciences, Affiliated Eye Hospital of Nanchang University, Nanchang, China
| | - Kun Xiong
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Changsha, China
- Key Laboratory of Emergency and Trauma, Ministry of Education, College of Emergency and Trauma, Hainan Medical University, Haikou, China
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91
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Zhang C, Zhao Z, Jia YJ, Zhang PQ, Sun Y, Zhou YC, Wang GX, Zhu B. Rationally Designed Self-Assembling Nanovaccines Elicit Robust Mucosal and Systemic Immunity against Rhabdovirus. ACS APPLIED MATERIALS & INTERFACES 2024; 16:228-244. [PMID: 38055273 DOI: 10.1021/acsami.3c14305] [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: 12/07/2023]
Abstract
Viral diseases have constantly caused great threats to global public health, resulting in an urgent need for effective vaccines. However, the current viral vaccines often show low immunogenicity. To counter this, we report a smart strategy of a well-designed modular nanoparticle (LSG-TDH) that recapitulates the dominant antigen SG, low-molecular-weight protamine, and tetralysine-modified H-chain apoferritin (TDH). The constructed LSG-TDH nanovaccine could self-assemble into a nanocage structure, which confers excellent mucus-penetrating, cellular affinity, and uptake ability. Studies demonstrate that the LSG-TDH nanovaccine could strongly activate both mucosal and systemic immune responses. Importantly, by immunizing wild-type and TLR2 knockout (TLR2-KO) zebrafish, we found that TLR2 could mediate LSG-TDH-induced adaptive mucosal and systemic immune responses by activating antigen-presenting cells. Collectively, our findings offer new insights into rational viral vaccine design and provide additional evidence of the vital role of TLR2 in regulating adaptive immunity.
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Affiliation(s)
- Chen Zhang
- Collaborative Innovation Center of Marine Science and Technology, Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, Haikou 570228, P. R. China
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Zhao Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Yi-Jun Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Peng-Qi Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Yun Sun
- Collaborative Innovation Center of Marine Science and Technology, Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, Haikou 570228, P. R. China
| | - Yong-Can Zhou
- Collaborative Innovation Center of Marine Science and Technology, Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, Haikou 570228, P. R. China
| | - Gao-Xue Wang
- College of Animal Science and Technology, Key Laboratory of Livestock Biology, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Bin Zhu
- College of Animal Science and Technology, Key Laboratory of Livestock Biology, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
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Mori AA, Malaquias VB, Bonjour K, Ferreira GM, Bortolin RH, Borges JB, Oliveira VFD, Gonçalves RM, Faludi AA, Bastos GM, Thurow H, Sampaio MF, Ciconelli RM, Cury AN, Fajardo CM, Hirata RDC, Hirata MH. Effects of LDLR variants rs5928, rs750518671 and rs879254797 on protein structure and functional activity in HepG2 cells transfected with CRISPR/Cas9 constructs. Gene 2024; 890:147821. [PMID: 37739193 DOI: 10.1016/j.gene.2023.147821] [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: 07/12/2023] [Revised: 08/24/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Familial Hypercholesterolemia (FH) is a genetic disorder associated with premature atherosclerosis and increased risk of cardiovascular diseases. LDLR deleterious mutations are associated with FH, however the role of some missense variants in FH pathogenicity remains to be elucidated. This study explored the predictive impact of LDLR missense variants on protein structure and investigated their functional effects on LDLR expression in HepG2 cells transfected with CRISPR/Cas9 constructs. FH (n = 287) and non-FH patients (n = 45) were selected, and lipid profile was obtained from medical records. LDLR variants were identified using an exon-targeted gene sequencing strategy, considering its cost-effective to increase accuracy in the identification step of the most likely FH-related variants in a less laborious process. LDLR variants were selected based on conflicting pathogenicity results found in Clinvar, in silico prediction tools, affected LDLR domains, and less common variants considering minor allele frequency < 0.05. Molecular modeling studies were used to predict the effects of LDLR missense variants on protein structure. Recombinant LDLR variants were constructed using CRISPR/Cas9 system and were used to transfect HepG2 cells. Functional assays in transfected cells were performed to assess LDLR expression using flow cytometry and western blotting, and LDLR activity using flow cytometry and confocal microscopy. The variants rs121908039 (c.551G>A, p.C184Y), rs879254797 (c.1118G>A, p.G373D), rs28941776 (c.1646G>A, p.G549D), rs750518671 (c.2389G>C, p.V797L), rs5928 (c.2441G>A, p.R814Q) and rs137853964 (c.2479G>A, p.V827I) were selected for molecular docking analysis. The p.C184Y exhibited a favorable energy change for protein stability due to its interaction with EGF-A/EGF-B regions; p.G373D and p.G549D displayed intermediate energy changes; and p.R814Q and p.V827I showed smaller energy changes. The results of functional assays showed that p.G373D, p.V797L and p.R814Q reduced LDLR expression and activity (p < 0.05). Microscopic analysis of the p.V797L and p.G373D variants revealed altered lipid localization and accumulation in transfected HepG2 cells. Carriers of p.G549D, p.V797L and p.R814Q had higher LDL cholesterol levels than non-FH group, and (p < 0.05). p.G373D and p.G549D were associated with clinical manifestations of FH. In conclusion, the p.C184Y, p.G373D, p.G549D and p.R814Q variants alter protein stability and intramolecular interactions, while p.V797L has a minimal impact on protein stability, and p.V827I has no significant intramolecular interactions. p.G373D, p.V767L and p.R814Q are associated with impaired LDLR expression and activity.
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Affiliation(s)
- Augusto Akira Mori
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Vanessa Barbosa Malaquias
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Kennedy Bonjour
- Laboratory of Molecular and Morphological Pathology, Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo 05508-000, Brazil; Laboratory Membrane Biochemistry and Transport, Department of Cell Biology and Infection, Institut Pasteur, Paris 75724 Paris Cedex 15, France
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | | | - Jéssica Bassani Borges
- Laboratory of Molecular Research in Cardiology, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil; Department of Research, Hospital Beneficência Portuguesa de Sao Paulo, Sao Paulo 01323-001, Brazil
| | - Victor Fernandes de Oliveira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil; Laboratory of Physiological Genomics of Mental Health, Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo 05508-000, Brazil
| | | | - Andre Arpad Faludi
- Medical Clinic Division, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil
| | - Gisele Monteiro Bastos
- Department of Research, Hospital Beneficência Portuguesa de Sao Paulo, Sao Paulo 01323-001, Brazil
| | - Helena Thurow
- Department of Research, Hospital Beneficência Portuguesa de Sao Paulo, Sao Paulo 01323-001, Brazil
| | - Marcelo Ferraz Sampaio
- Department of Cardiology, Hospital Beneficência Portuguesa de São Paulo, Sao Paulo 01323-001, Brazil
| | | | - Adriano Namo Cury
- Department of Endocrinology, Hospital Beneficência Portuguesa de Sao Paulo, Sao Paulo 01323-001, Brazil
| | - Cristina Moreno Fajardo
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Rosario Dominguez Crespo Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil.
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93
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Melancon K, Pliushcheuskaya P, Meiler J, Künze G. Targeting ion channels with ultra-large library screening for hit discovery. Front Mol Neurosci 2024; 16:1336004. [PMID: 38249296 PMCID: PMC10796734 DOI: 10.3389/fnmol.2023.1336004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 01/23/2024] Open
Abstract
Ion channels play a crucial role in a variety of physiological and pathological processes, making them attractive targets for drug development in diseases such as diabetes, epilepsy, hypertension, cancer, and chronic pain. Despite the importance of ion channels in drug discovery, the vastness of chemical space and the complexity of ion channels pose significant challenges for identifying drug candidates. The use of in silico methods in drug discovery has dramatically reduced the time and cost of drug development and has the potential to revolutionize the field of medicine. Recent advances in computer hardware and software have enabled the screening of ultra-large compound libraries. Integration of different methods at various scales and dimensions is becoming an inevitable trend in drug development. In this review, we provide an overview of current state-of-the-art computational chemistry methodologies for ultra-large compound library screening and their application to ion channel drug discovery research. We discuss the advantages and limitations of various in silico techniques, including virtual screening, molecular mechanics/dynamics simulations, and machine learning-based approaches. We also highlight several successful applications of computational chemistry methodologies in ion channel drug discovery and provide insights into future directions and challenges in this field.
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Affiliation(s)
- Kortney Melancon
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | | | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
- Medical Faculty, Institute for Drug Discovery, Leipzig University, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence, Leipzig University, Leipzig, Germany
| | - Georg Künze
- Medical Faculty, Institute for Drug Discovery, Leipzig University, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence, Leipzig University, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
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D’Acunto E, Muzi A, Marchese S, Donnici L, Chiarini V, Bucci F, Pavoni E, Ferrara FF, Cappelletti M, Arriga R, Serrao SM, Peluzzi V, Principato E, Compagnone M, Pinto E, Luberto L, Stoppoloni D, Lahm A, Groß R, Seidel A, Wettstein L, Münch J, Goodhead A, Parisot J, De Francesco R, Ciliberto G, Marra E, Aurisicchio L, Roscilli G. Isolation and Characterization of Neutralizing Monoclonal Antibodies from a Large Panel of Murine Antibodies against RBD of the SARS-CoV-2 Spike Protein. Antibodies (Basel) 2024; 13:5. [PMID: 38247569 PMCID: PMC10801580 DOI: 10.3390/antib13010005] [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: 11/15/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
The COVID-19 pandemic, once a global crisis, is now largely under control, a testament to the extraordinary global efforts involving vaccination and public health measures. However, the relentless evolution of SARS-CoV-2, leading to the emergence of new variants, continues to underscore the importance of remaining vigilant and adaptable. Monoclonal antibodies (mAbs) have stood out as a powerful and immediate therapeutic response to COVID-19. Despite the success of mAbs, the evolution of SARS-CoV-2 continues to pose challenges and the available antibodies are no longer effective. New variants require the ongoing development of effective antibodies. In the present study, we describe the generation and characterization of neutralizing mAbs against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein by combining plasmid DNA and recombinant protein vaccination. By integrating genetic immunization for rapid antibody production and the potent immune stimulation enabled by protein vaccination, we produced a rich pool of antibodies, each with unique binding and neutralizing specificities, tested with the ELISA, BLI and FACS assays and the pseudovirus assay, respectively. Here, we present a panel of mAbs effective against the SARS-CoV-2 variants up to Omicron BA.1 and BA.5, with the flexibility to target emerging variants. This approach ensures the preparedness principle is in place to address SARS-CoV-2 actual and future infections.
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Affiliation(s)
- Emanuela D’Acunto
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Alessia Muzi
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Silvia Marchese
- INGM-Istituto Nazionale di Genetica Molecolare “Romeo ed Erica Invernizzi”, 20122 Milan, Italy; (S.M.); (L.D.); (R.D.F.)
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Lorena Donnici
- INGM-Istituto Nazionale di Genetica Molecolare “Romeo ed Erica Invernizzi”, 20122 Milan, Italy; (S.M.); (L.D.); (R.D.F.)
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | | | - Federica Bucci
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Emiliano Pavoni
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Fabiana Fosca Ferrara
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Manuela Cappelletti
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Roberto Arriga
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Silvia Maria Serrao
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Valentina Peluzzi
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
- Department of Engineering, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Eugenia Principato
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
- Department of Experimental and Clinical Medicine, University Magna Graecia, 88100 Catanzaro, Italy
| | | | - Eleonora Pinto
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Laura Luberto
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Daniela Stoppoloni
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Armin Lahm
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.G.); (A.S.); (J.M.)
| | - Alina Seidel
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.G.); (A.S.); (J.M.)
| | - Lukas Wettstein
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.G.); (A.S.); (J.M.)
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.G.); (A.S.); (J.M.)
| | - Andrew Goodhead
- Carterra, 825 N. 300 W., Suite C309, Salt Lake City, UT 84103, USA; (A.G.); (J.P.)
| | - Judicael Parisot
- Carterra, 825 N. 300 W., Suite C309, Salt Lake City, UT 84103, USA; (A.G.); (J.P.)
| | - Raffaele De Francesco
- INGM-Istituto Nazionale di Genetica Molecolare “Romeo ed Erica Invernizzi”, 20122 Milan, Italy; (S.M.); (L.D.); (R.D.F.)
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Gennaro Ciliberto
- Tumor Immunology and Immunotherapy Unit, IRCSS Regina Elena National Cancer Institute, 00144 Rome, Italy;
| | - Emanuele Marra
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Luigi Aurisicchio
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Giuseppe Roscilli
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
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95
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Zhang Y, Wang X, Zhang Z, Huang Y, Kihara D. Assessment of Protein-Protein Docking Models Using Deep Learning. Methods Mol Biol 2024; 2780:149-162. [PMID: 38987469 DOI: 10.1007/978-1-0716-3985-6_10] [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] [Indexed: 07/12/2024]
Abstract
Protein-protein interactions are involved in almost all processes in a living cell and determine the biological functions of proteins. To obtain mechanistic understandings of protein-protein interactions, the tertiary structures of protein complexes have been determined by biophysical experimental methods, such as X-ray crystallography and cryogenic electron microscopy. However, as experimental methods are costly in resources, many computational methods have been developed that model protein complex structures. One of the difficulties in computational protein complex modeling (protein docking) is to select the most accurate models among many models that are usually generated by a docking method. This article reviews advances in protein docking model assessment methods, focusing on recent developments that apply deep learning to several network architectures.
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Affiliation(s)
- Yuanyuan Zhang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Xiao Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Zicong Zhang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Yunhan Huang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, USA.
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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96
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Jarończyk M, Abagyan R, Totrov M. Software and Databases for Protein-Protein Docking. Methods Mol Biol 2024; 2780:129-138. [PMID: 38987467 DOI: 10.1007/978-1-0716-3985-6_8] [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] [Indexed: 07/12/2024]
Abstract
Protein-protein interactions (PPIs) provide valuable insights for understanding the principles of biological systems and for elucidating causes of incurable diseases. One of the techniques used for computational prediction of PPIs is protein-protein docking calculations, and a variety of software has been developed. This chapter is a summary of software and databases used for protein-protein docking.
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Affiliation(s)
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
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97
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Singh A, Copeland MM, Kundrotas PJ, Vakser IA. GRAMM Web Server for Protein Docking. Methods Mol Biol 2024; 2714:101-112. [PMID: 37676594 DOI: 10.1007/978-1-0716-3441-7_5] [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] [Indexed: 09/08/2023]
Abstract
Prediction of the structure of protein complexes by docking methods is a well-established research field. The intermolecular energy landscapes in protein-protein interactions can be used to refine docking predictions and to detect macro-characteristics, such as the binding funnel. A new GRAMM web server for protein docking predicts a spectrum of docking poses that characterize the intermolecular energy landscape in protein interaction. A user-friendly interface provides options to choose free or template-based docking, as well as other advanced features, such as clustering of the docking poses, and interactive visualization of the docked models.
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Affiliation(s)
- Amar Singh
- Computational Biology Program and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Matthew M Copeland
- Computational Biology Program and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Petras J Kundrotas
- Computational Biology Program and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA.
| | - Ilya A Vakser
- Computational Biology Program and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA.
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98
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Krupa MA, Krupa P. Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking. Methods Mol Biol 2024; 2780:27-41. [PMID: 38987462 DOI: 10.1007/978-1-0716-3985-6_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] [Indexed: 07/12/2024]
Abstract
Docking methods can be used to predict the orientations of two or more molecules with respect of each other using a plethora of various algorithms, which can be based on the physics of interactions or can use information from databases and templates. The usability of these approaches depends on the type and size of the molecules, whose relative orientation will be estimated. The two most important limitations are (i) the computational cost of the prediction and (ii) the availability of the structural information for similar complexes. In general, if there is enough information about similar systems, knowledge-based and template-based methods can significantly reduce the computational cost while providing high accuracy of the prediction. However, if the information about the system topology and interactions between its partners is scarce, physics-based methods are more reliable or even the only choice. In this chapter, knowledge-, template-, and physics-based methods will be compared and briefly discussed providing examples of their usability with a special emphasis on physics-based protein-protein, protein-peptide, and protein-fullerene docking in the UNRES coarse-grained model.
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Affiliation(s)
- Magdalena A Krupa
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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99
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Patel KN, Chavda D, Manna M. Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies. Methods Mol Biol 2024; 2780:165-201. [PMID: 38987470 DOI: 10.1007/978-1-0716-3985-6_11] [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] [Indexed: 07/12/2024]
Abstract
Intrinsically disordered proteins (IDPs) are a novel class of proteins that have established a significant importance and attention within a very short period of time. These proteins are essentially characterized by their inherent structural disorder, encoded mainly by their amino acid sequences. The profound abundance of IDPs and intrinsically disordered regions (IDRs) in the biological world delineates their deep-rooted functionality. IDPs and IDRs convey such extensive functionality through their unique dynamic nature, which enables them to carry out huge number of multifaceted biomolecular interactions and make them "interaction hub" of the cellular systems. Additionally, with such widespread functions, their misfunctioning is also intimately associated with multiple diseases. Thus, understanding the dynamic heterogeneity of various IDPs along with their interactions with respective binding partners is an important field with immense potentials in biomolecular research. In this context, molecular docking-based computational approaches have proven to be remarkable in case of ordered proteins. Molecular docking methods essentially model the biomolecular interactions in both structural and energetic terms and use this information to characterize the putative interactions between the two participant molecules. However, direct applications of the conventional docking methods to study IDPs are largely limited by their structural heterogeneity and demands for unique IDP-centric strategies. Thus, in this chapter, we have presented an overview of current methodologies for successful docking operations involving IDPs and IDRs. These specialized methods majorly include the ensemble-based and fragment-based approaches with their own benefits and limitations. More recently, artificial intelligence and machine learning-assisted approaches are also used to significantly reduce the complexity and computational burden associated with various docking applications. Thus, this chapter aims to provide a comprehensive summary of major challenges and recent advancements of molecular docking approaches in the IDP field for their better utilization and greater applicability.Asp (D).
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Affiliation(s)
- Keyur N Patel
- Applied Phycology and Biotechnology Division, CSIR Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Dhruvil Chavda
- Applied Phycology and Biotechnology Division, CSIR Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Moutusi Manna
- Applied Phycology and Biotechnology Division, CSIR Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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100
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Yadav P, Gupta M, Wazahat R, Islam Z, Tsutakawa SE, Kamthan M, Kumar P. Structural basis for the role of C-terminus acidic tail of Saccharomyces cerevisiae ubiquitin-conjugating enzyme (Rad6) in E3 ligase (Bre1) mediated recognition of histones. Int J Biol Macromol 2024; 254:127717. [PMID: 37923031 DOI: 10.1016/j.ijbiomac.2023.127717] [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: 08/15/2023] [Revised: 10/07/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Ubiquitination of histone H2B on chromatin is key to gene regulation. E3 ligase Bre1 and E2 Rad6 in Saccharomyces cerevisiae associate together to catalyze mono-ubiquitination at histone H2BK123. Prior studies identified the role of a highly dynamic C-terminal acidic tail of Rad6 indispensable for H2BK123 mono-ubiquitination. However, the mechanistic basis for the Rad6-acidic tail role remained elusive. Using different structural and biophysical approaches, this study for the first time uncovers the direct role of Rad6-acidic tail in interaction with the Bre1 Rad6-Binding Domain (RBD) and recognition of histones surface to facilitate histone H2B mono-ubiquitination. A combination of NMR, SAXS, ITC, site-directed mutagenesis and molecular dynamics studies reveal that RBD domain of Bre1 interacts with Rad6 to stabilize the dynamics of acidic tail. This Bre1-RBD mediated stability in acidic tail of Rad6 could be one of the key factors for facilitating correct recognition of histone surface and ubiquitin-transfer at H2BK123. We provide biophysical evidence that Rad6-acidic tail and a positivity charged surface on histone H2B are involved in recognition of E2:Histones. Taken together, this study uncovers the mechanistic basis for the role of Rad6-acidic in Bre1-RBD mediated recognition of histone surface that ensure the histone H2B mono-ubiquitination.
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Affiliation(s)
- Pawan Yadav
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi 110062, India
| | - Manish Gupta
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Rushna Wazahat
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi 110062, India
| | - Zeyaul Islam
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mohan Kamthan
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi 110062, India
| | - Pankaj Kumar
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi 110062, India.
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