1
|
Shamala V, Asha Devi S. Deciphering the genetic impact of signal peptide missense CTLA-4 polymorphism with rheumatoid arthritis in the Indian population: A case-control and in silico studies. Gene 2024; 930:148819. [PMID: 39103060 DOI: 10.1016/j.gene.2024.148819] [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: 06/18/2024] [Revised: 07/15/2024] [Accepted: 08/01/2024] [Indexed: 08/07/2024]
Abstract
Cytoplasmic T Lymphocyte Antigen-4 (CTLA-4) gene encodes for a glycoprotein, expressed on activated T-cells to transfer an inhibitory signal to control T-cell activation and proliferation. Techniques coupled with Real-time Polymerase Chain Reaction (PCR) and High-Resolution Melting Analysis (HRMA) were used to screen a missense signal peptide polymorphism (CTLA-4 + 49 A/G rs231775) in the Indian population to detect its association with Rheumatoid Arthritis (RA). Further, the resulting outcome was confirmed by Sanger's sequencing technique, and genotype frequencies were calculated. In eukaryotic cells, the M domain of the Signal Recognition Particle (SRP-54) recognizes the N-terminal region of the Signal Peptide (SP) sequence. SP directs the polypeptide chain into the Sec-61 translocon of the Endoplasmic Reticulum (ER) for further protein modification. As the Single Nucleotide Polymorphism (SNP) rs231775 lies in the signal peptide region of CTLA-4, an in-silico study was also performed to predict the mRNA stability and SP-SRP protein interaction. From the study, it was observed that the genotype frequency of rs231775 SNP G/G homozygous dominant was significantly higher in RA patients than G/A heterozygous dominant and A/A homozygous recessive conditions (Odd Ratio (OR) = 2.0862; 95 % Confidence Interval (C.I) = 1.2584 to 3.4584; Relative Risk (RR) = 1.8507; p = 0.0044). Moreover, the rs231775 SNP G allele frequency was higher in RA than the control group G = 0.407 (40.7 %) vs 0.32 (32 %). In silico approaches of Protein-Protein docking and Molecular Dynamics (MD) simulation reveal CTLA-4 rs231775 SNP (G allele) has destabilized the SP-SRP protein complex, which may affect the translocation of CTLA-4 nascent polypeptide chains into the ER via activating Regulation of Aberrant Protein Production (RAPP) pathway.
Collapse
Affiliation(s)
- V Shamala
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, TN, India
| | - S Asha Devi
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, TN, India.
| |
Collapse
|
2
|
Li M, Qing R, Tao F, Xu P, Zhang S. Inhibitory effect of truncated isoforms on GPCR dimerization predicted by combinatorial computational strategy. Comput Struct Biotechnol J 2024; 23:278-286. [PMID: 38173876 PMCID: PMC10762321 DOI: 10.1016/j.csbj.2023.12.008] [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: 10/20/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
G protein-coupled receptors (GPCRs) play a pivotal role in fundamental biological processes and disease development. GPCR isoforms, derived from alternative splicing, can exhibit distinct signaling patterns. Some highly-truncated isoforms can impact functional performance of full-length receptors, suggesting their intriguing regulatory roles. However, how these truncated isoforms interact with full-length counterparts remains largely unexplored. Here, we computationally investigated the interaction patterns of three human GPCRs from three different classes, ADORA1 (Class A), mGlu2 (Class C) and SMO (Class F) with their respective truncated isoforms because their homodimer structures have been experimentally determined, and they have truncated isoforms deposited and identified at protein level in Uniprot database. Combining the neural network-based AlphaFold2 and two physics-based protein-protein docking tools, we generated multiple complex structures and assessed the binding affinity in the context of atomistic molecular dynamics simulations. Our computational results suggested all the four studied truncated isoforms showed potent binding to their counterparts and overlapping interfaces with homodimers, indicating their strong potential to block homodimerization of their counterparts. Our study offers insights into functional significance of GPCR truncated isoforms and supports the ubiquity of their regulatory roles.
Collapse
Affiliation(s)
- Mengke Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rui Qing
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| |
Collapse
|
3
|
Zheng F, Jiang X, Wen Y, Yang Y, Li M. Systematic investigation of machine learning on limited data: A study on predicting protein-protein binding strength. Comput Struct Biotechnol J 2024; 23:460-472. [PMID: 38235359 PMCID: PMC10792694 DOI: 10.1016/j.csbj.2023.12.018] [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: 10/03/2023] [Revised: 12/14/2023] [Accepted: 12/16/2023] [Indexed: 01/19/2024] Open
Abstract
The application of machine learning techniques in biological research, especially when dealing with limited data availability, poses significant challenges. In this study, we leveraged advancements in method development for predicting protein-protein binding strength to conduct a systematic investigation into the application of machine learning on limited data. The binding strength, quantitatively measured as binding affinity, is vital for understanding the processes of recognition, association, and dysfunction that occur within protein complexes. By incorporating transfer learning, integrating domain knowledge, and employing both deep learning and traditional machine learning algorithms, we mitigated the impact of data limitations and made significant advancements in predicting protein-protein binding affinity. In particular, we developed over 20 models, ultimately selecting three representative best-performing ones that belong to distinct categories. The first model is structure-based, consisting of a random forest regression and thirteen handcrafted features. The second model is sequence-based, employing an architecture that combines transferred embedding features with a multilayer perceptron. Finally, we created an ensemble model by averaging the predictions of the two aforementioned models. The comparison with other predictors on three independent datasets confirms the significant improvements achieved by our models in predicting protein-protein binding affinity. The programs for running these three models are available at https://github.com/minghuilab/BindPPI.
Collapse
Affiliation(s)
- Feifan Zheng
- MOE Key Laboratory of Geriatric Diseases and Immunology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province 215123, China
| | - Xin Jiang
- MOE Key Laboratory of Geriatric Diseases and Immunology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province 215123, China
| | - Yuhao Wen
- MOE Key Laboratory of Geriatric Diseases and Immunology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province 215123, China
| | - Yan Yang
- MOE Key Laboratory of Geriatric Diseases and Immunology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province 215123, China
| | - Minghui Li
- MOE Key Laboratory of Geriatric Diseases and Immunology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province 215123, China
| |
Collapse
|
4
|
Tan C, xiao Y, Liu T, Chen S, Zhou J, Zhang S, Hu Y, Wu A, Li C. Development of multi-epitope mRNA vaccine against Clostridioides difficile using reverse vaccinology and immunoinformatics approaches. Synth Syst Biotechnol 2024; 9:667-683. [PMID: 38817826 PMCID: PMC11137598 DOI: 10.1016/j.synbio.2024.05.008] [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: 01/08/2024] [Revised: 04/28/2024] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Clostridioides difficile (C. difficile), as the major pathogen of diarrhea in healthcare settings, has become increasingly prevalent within community populations, resulting in significant morbidity and mortality. However, the therapeutic options for Clostridioides difficile infection (CDI) remain limited, and as of now, no authorized vaccine is available to combat this disease. Therefore, the development of a novel vaccine against C. difficile is of paramount importance. In our study, the complete proteome sequences of 118 strains of C. difficile were downloaded and analyzed. We found four antigenic proteins that were highly conserved and can be used for epitope identification. We designed two vaccines, WLcd1 and WLcd2, that contain the ideal T-cell and B-cell epitopes, adjuvants, and the pan HLA DR-binding epitope (PADRE) sequences. The biophysical and chemical assessments of these vaccine candidates indicated that they were suitable for immunogenic applications. Molecular docking analyses revealed that WLcd1 bonded with higher affinity to Toll-like receptors (TLRs) than WLcd2. Furthermore, molecular dynamics (MD) simulations, performed using Gmx_MMPBSA v1.56, confirmed the binding stability of WLcd1 with TLR2 and TLR4. The preliminary findings suggested that this multi-epitope vaccine could be a promising candidate for protection against CDI; however, experimental studies are necessary to confirm these predictions.
Collapse
Affiliation(s)
- Caixia Tan
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Yuanyuan xiao
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Ting Liu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Siyao Chen
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Juan Zhou
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Sisi Zhang
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Yiran Hu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Anhua Wu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Chunhui Li
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| |
Collapse
|
5
|
Costa GCA, Torquato RJS, de Morais Gomes V, Rosa-Fernandes L, Palmisano G, Tanaka AS. Functional characterization of a cystatin A from the bat Myotis davidii. Comp Biochem Physiol B Biochem Mol Biol 2024; 274:111003. [PMID: 38936799 DOI: 10.1016/j.cbpb.2024.111003] [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: 04/19/2024] [Revised: 06/06/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
Myotis davidii cystatin A (MdCSTA), a stefin A-like from the Chinese native bat species M. davidii, was expressed as a recombinant protein and functionally characterized as a strong inhibitor of the cysteine proteases papain, human cathepsins L and B and the tick cathepsin L-like BmCL1. Despite the highly conserved amino acid sequences among stefins A from different vertebrates, MdCSTA presents a Methionine-2 residue at the N-terminal region and the second binding loop (pos 73-79) that differs from human stefin A (HsCSTA) and might be related to the lower inhibition constant (Ki) value presented by this inhibitor in comparison to human stefin A inhibition to cathepsin B. Therefore, to investigate the importance of these variable regions in cathepsin B inhibition, recombinant stefins A MdCSTA and HsCSTA containing mutations at the second amino acid residue and second binding loop were expressed and evaluated in kinetic assays. Enzymatic inhibition assays with cathepsin B revealed that switching the amino acid residues at position 2 and second binding loop region between bat and human CSTAs improved the HsCSTA's and reduced MdCSTA's inhibitory activity. Additionally, molecular docking analysis estimated lower energy values for the complex between MdCSTA-cathepsin B, in comparison to human CSTA-cathepsin B, while the mutants presented intermediate values, suggesting that other regions might contribute to the higher inhibitory activity against cathepsin B by MdCSTA. In conclusion, MdCSTA, the first bat's stefin A-like inhibitor to be functionally characterized, presented a higher inhibitory activity against cathepsin B in comparison to the human inhibitor, which is partially related to the glutamine-rich second binding loop and Met-2. Further structural analysis should be performed to elucidate potential inhibitor effects on cysteine proteinases.
Collapse
Affiliation(s)
| | | | - Vinícius de Morais Gomes
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, SP, Brazil
| | - Lívia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, SP, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, SP, Brazil
| | - Aparecida Sadae Tanaka
- Department of Biochemistry, Federal University of Sao Paulo (UNIFESP), SP, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), RJ, Brazil.
| |
Collapse
|
6
|
Cai M, Deng J, Wu S, Cao Y, Chen H, Tang H, Zou C, Zhu H, Qi L. Alpha-1 antitrypsin targeted neutrophil elastase protects against sepsis-induced inflammation and coagulation in mice via inhibiting neutrophil extracellular trap formation. Life Sci 2024; 353:122923. [PMID: 39032690 DOI: 10.1016/j.lfs.2024.122923] [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: 05/07/2024] [Revised: 07/05/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
AIMS Sepsis pathophysiology is complex and identifying effective treatments for sepsis remains challenging. The study aims to identify effective drugs and targets for sepsis through transcriptomic analysis of sepsis patients, repositioning analysis of compounds, and validation by animal models. MAIN METHODS GSE185263 obtained from the GEO database that includes gene expression profiles of 44 healthy controls and 348 sepsis patients categorized by severity. Bioinformatic algorithms revealed the molecular, function, and immune characteristics of the sepsis, and constructed sepsis-related protein-protein interaction networks. Subsequently, Random Walk with Restart analysis was applied to identify candidate drugs for sepsis, which were tested in animal models for survival, inflammation, coagulation, and multi-organ damage. KEY FINDINGS Our analysis found 1862 genes linked to sepsis development, enriched in functions like neutrophil extracellular trap formation (NETs) and complement/coagulation cascades. With disease progression, immune activation-associated cells were inhibited, while immune suppression-associated cells were activated. Next, the drug repositioning method identified candidate drugs, such as alpha-1 antitrypsin, that may play a therapeutic role by targeting neutrophil elastase (NE) to inhibit NETs. Animal experiments proved that alpha-1 antitrypsin treatment can improve the survival rate, reduce sepsis score, reduce the levels of inflammation markers in serum, and alleviate muti-organ morphological damage in mice with sepsis. The further results showed that α-1 antitrypsin can inhibit the NETs by suppressing the NE for the treatment of sepsis. SIGNIFICANCE Alpha-1 antitrypsin acted on the NE to inhibit NETs thereby protecting mice from sepsis-induced inflammation and coagulation.
Collapse
Affiliation(s)
- Minghui Cai
- Basic Medical College, Harbin Medical University, Harbin, China
| | - Jiaxing Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shangjie Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yang Cao
- Basic Medical College, Harbin Medical University, Harbin, China
| | - Hong Chen
- The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Hao Tang
- The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Chendan Zou
- Basic Medical College, Harbin Medical University, Harbin, China
| | - Hui Zhu
- Basic Medical College, Harbin Medical University, Harbin, China; Heilongjiang Academy of Medical Sciences, Harbin, China.
| | - Lishuang Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
| |
Collapse
|
7
|
Kotipalli A, Koulgi S, Jani V, Sonavane U, Joshi R. Early Events in β 2AR Dimer Dynamics Mediated by Activation-Related Microswitches. J Membr Biol 2024:10.1007/s00232-024-00324-1. [PMID: 39240374 DOI: 10.1007/s00232-024-00324-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 08/24/2024] [Indexed: 09/07/2024]
Abstract
G-Protein-Coupled Receptors (GPCRs) make up around 3-4% of the human genome and are the targets of one-third of FDA-approved drugs. GPCRs typically exist as monomers but also aggregate to form higher-order oligomers, including dimers. β2AR, a pharmacologically relevant GPCR, is known to be targeted for the treatment of asthma and cardiovascular diseases. The activation of β2AR at the dimer level remains under-explored. In the current study, molecular dynamics (MD) simulations have been performed to understand activation-related structural changes in β2AR at the dimer level. The transition from inactive to active and vice versa has been studied by starting the simulations in the apo, agonist-bound, and inverse agonist-bound β2AR dimers for PDB ID: 2RH1 and PDB ID: 3P0G, respectively. A cumulative total of around 21-μs simulations were performed. Residue-based distances, RMSD, and PCA calculations suggested that either of the one monomer attained activation-related features for the apo and agonist-bound β2AR dimers. The TM5 and TM6 helices within the two monomers were observed to be in significant variation in all the simulations. TM5 bulge and proximity of TM2 and TM7 helices may be contributing to one of the early events in activation. The dimeric interface between TM1 and helix 8 were observed to be well maintained in the apo and agonist-bound simulations. The presence of inverse agonists favored inactive features in both the monomers. These key features of activation known for monomers were observed to have an impact on β2AR dimers, thereby providing an insight into the oligomerization mechanism of GPCRs.
Collapse
Affiliation(s)
- Aneesh Kotipalli
- HPC-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, India, 411008
| | - Shruti Koulgi
- HPC-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, India, 411008
| | - Vinod Jani
- HPC-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, India, 411008
| | - Uddhavesh Sonavane
- HPC-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, India, 411008
| | - Rajendra Joshi
- HPC-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, India, 411008.
| |
Collapse
|
8
|
Ren Z, Li M, Chen J, Gong X, Song S, Li D, Yang M, Yu J, Asghar S, Cui Y, Niu S, Liao Z, Jiang Y, Liu J, Li Y, Zhang B, Zhao W, Peng J, Yang Y, Shen C. Identification of mpox M1R and B6R monoclonal and bispecific antibodies that efficiently neutralize authentic mpox virus. Emerg Microbes Infect 2024:2401931. [PMID: 39233480 DOI: 10.1080/22221751.2024.2401931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
In 2022, the monkeypox virus (mpox virus, MPXV) exhibited global dissemination across six continents, representing a notable challenge owing to the scarcity of targeted antiviral interventions. Passive immunotherapy, such as the use of monoclonal antibodies (mAbs) and bispecific antibodies (bsAbs), has emerged as a promising option for antiviral regimens. Here, we generated several mAbs against M1R and B6R of MPXV, and subsequently characterized the antiviral activity of these antibodies both in vitro and in vivo. Two neutralizing mAbs, M1H11 and M3B2, targeting M1R, and one B6R-specific mAb, B7C9, were identified. They exhibited varying antiviral efficacy against MPXV and vaccinia virus (VACV) in vitro and orthopoxvirus infection in vivo. A cocktail comprising M1H11 and M3B2 demonstrated a superior protective effect in vivo. A bsAb, Bis-M1M3, was engineered by conjugating the fragment crystallizable (Fc) region of the human-mouse chimeric engineered M1H11 with the single-chain fragment variable (scFv) of M3B2. In mice challenged with MPXV, Bis-M1M3 showed a notable protective effects, including the absence of mortality. Analysis of neutralization mechanism showed that these mAbs and Bis-M1M3 exerted virus-neutralizing effects before the virus infects cells. In vivo pharmacokinetic experiments showed that Bis-M1M3 has a long half-life in rhesus macaques. This study provides crucial insights for further research on -broad-spectrum antiviral drugs against MPXV and other orthopoxviruses.
Collapse
Affiliation(s)
- Zuning Ren
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health; Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou, People's Republic of China
| | - Mengjun Li
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health; Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou, People's Republic of China
| | - Jiayin Chen
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health; Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou, People's Republic of China
| | - Xiaohua Gong
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Shuo Song
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Delin Li
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Minghui Yang
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing, China
| | - Jianhai Yu
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health; Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou, People's Republic of China
| | - Sadia Asghar
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Pakistan
| | - Yanxin Cui
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Shiyu Niu
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Zhonghui Liao
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Yushan Jiang
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health; Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou, People's Republic of China
| | - Jiahui Liu
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health; Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou, People's Republic of China
| | - Yuqing Li
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health; Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou, People's Republic of China
| | - Bao Zhang
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health; Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou, People's Republic of China
| | - Wei Zhao
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health; Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou, People's Republic of China
| | - Jie Peng
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Chenguang Shen
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health; Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou, People's Republic of China
- Key Laboratory of Infectious Diseases Research in South China (Southern Medical University), Ministry of Education, People's Republic of China
| |
Collapse
|
9
|
Diplock N, Baudin M, Xiang XD, Liang LY, Dai W, Murphy JM, Lucet IS, Hassan JA, Lewis JD. Molecular dissection of the pseudokinase ZED1 expands effector recognition to the tomato immune receptor ZAR1. PLANT PHYSIOLOGY 2024; 196:651-666. [PMID: 38748589 DOI: 10.1093/plphys/kiae268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/11/2024] [Indexed: 09/03/2024]
Abstract
The highly conserved angiosperm immune receptor HOPZ-ACTIVATED RESISTANCE 1 (ZAR1) is a bacterial pathogen recognition hub that mediates resistance by guarding host kinases for modification by pathogen effectors. The pseudokinase HOPZ-ETI DEFICIENT 1 (ZED1) is the only known ZAR1-guarded protein that interacts directly with a pathogen effector, HopZ1a, from the bacterial pathogen Pseudomonas syringae, making it a promising system for rational design of effector recognition for plant immunity. Here, we conducted an in-depth molecular analysis of ZED1. We generated a library of 164 random ZED1 mutants and identified 50 mutants that could not recognize the effector HopZ1a when transiently expressed in Nicotiana benthamiana. Based on our random mutants, we generated a library of 27 point mutants and found evidence of minor functional divergence between Arabidopsis (Arabidopsis thaliana) and N. benthamiana ZAR1 orthologs. We leveraged our point mutant library to identify regions in ZED1 critical for ZAR1 and HopZ1a interactions and identified two likely ZED1-HopZ1a binding conformations. We explored ZED1 nucleotide and cation binding activity and showed that ZED1 is a catalytically dead pseudokinase, functioning solely as an allosteric regulator upon effector recognition. We used our library of ZED1 point mutants to identify the ZED1 activation loop regions as the most likely cause of interspecies ZAR1-ZED1 incompatibility. Finally, we identified a mutation that abolished ZAR1-ZED1 interspecies incompatibility while retaining the ability to mediate HopZ1a recognition, which enabled recognition of HopZ1a through tomato (Solanum lycopersicum) ZAR1. This provides an example of expanded effector recognition through a ZAR1 ortholog from a non-model species.
Collapse
Affiliation(s)
- Nathan Diplock
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Maël Baudin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Xincheng Derek Xiang
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Lung-Yu Liang
- Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne 3052, Australia
| | - Weiwen Dai
- Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne 3052, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne 3052, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Isabelle S Lucet
- Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne 3052, Australia
| | - Jana A Hassan
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jennifer D Lewis
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Plant Gene Expression Center, United States Department of Agriculture, Agriculture Research Service, Albany, CA 94710, USA
| |
Collapse
|
10
|
Lee J, Kim B, Woo HM, Kim JW, Jung I, Park SW, Kim YS, Na JH, Jung ST. Enhanced Omicron Variant Neutralization by a Human Antibody Tailored to Wild-Type and Delta-Variant SARS-CoV-2 RBDs. Mol Pharm 2024; 21:4336-4346. [PMID: 39058261 DOI: 10.1021/acs.molpharmaceut.4c00297] [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: 07/28/2024]
Abstract
Given the previous SARS-CoV-2 pandemic and the inherent unpredictability of viral antigenic drift and shift, preemptive development of diverse neutralizing antibodies targeting a broad spectrum of epitopes is essential to ensure immediate therapeutic and prophylactic interventions during emerging outbreaks. In this study, we present a monoclonal antibody engineered for cross-reactivity to both wild-type and Delta RBDs, which, surprisingly, demonstrates enhanced neutralizing activity against the Omicron variant despite a significant number of mutations. Using an Escherichia coli inner membrane display of a human naïve antibody library, we identified antibodies specific to the wild-type SARS-CoV-2 receptor binding domain (RBD). Subsequent directed evolution via yeast surface display yielded JS18.1, an antibody with high binding affinity for both the Delta and Kappa RBDs, as well as enhanced binding to other RBDs (wild-type, Alpha, Beta, Gamma, Kappa, and Mu). Notably, JS18.1 (engineered for wild-type and Delta RBDs) exhibits enhanced neutralizing capability against the Omicron variant and binds to RBDs noncompetitively with ACE2, distinguishing it from other previously reported antibodies. This underscores the potential of pre-existing antibodies to neutralize emerging SARS-CoV-2 strains and offers insights into strategies to combat emerging viruses.
Collapse
Affiliation(s)
- Jisun Lee
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Bomi Kim
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Hye-Min Woo
- Division of Emerging Virus and Vector Research, Center for Emerging Virus Research, National Institute of Health, Korea Centers for Disease Control and Prevention Agency, Osong, Cheongju 28159, Republic of Korea
| | - Jun-Won Kim
- Division of Emerging Virus and Vector Research, Center for Emerging Virus Research, National Institute of Health, Korea Centers for Disease Control and Prevention Agency, Osong, Cheongju 28159, Republic of Korea
| | - Inji Jung
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Seong-Wook Park
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi-do 16499, Republic of Korea
| | - Yong-Sung Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi-do 16499, Republic of Korea
- Department of Allergy and Clinical Immunology, Ajou University Medical School, Suwon, Gyeonggi-do 16499, Republic of Korea
| | - Jung-Hyun Na
- School of Biopharmaceutical and Medical Sciences, Sungshin Women's University, Seoul 01133, Republic of Korea
| | - Sang Taek Jung
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Biomedical Research Center, Korea University Anam Hospital, Seoul 02841, Republic of Korea
- Institute of Human Genetics, Korea University College of Medicine, Seoul 02841, Republic of Korea
| |
Collapse
|
11
|
Batista C, Cruz JVR, Stipursky J, de Almeida Mendes F, Pesquero JB. Kinin B 1 receptor and TLR4 interaction in inflammatory response. Inflamm Res 2024; 73:1459-1476. [PMID: 38965133 DOI: 10.1007/s00011-024-01909-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/27/2024] [Accepted: 06/19/2024] [Indexed: 07/06/2024] Open
Abstract
OBJECTIVE We aimed to broaden our understanding of a potential interaction between B1R and TLR4, considering earlier studies suggesting that lipopolysaccharide (LPS) may trigger B1R stimulation. METHODS We assessed the impact of DBK and LPS on the membrane potential of thoracic aortas from C57BL/6, B1R, or TLR4 knockout mice. Additionally, we examined the staining patterns of these receptors in the thoracic aortas of C57BL/6 and in endothelial cells (HBMEC). RESULTS DBK does not affect the resting membrane potential of aortic rings in C57BL/6 mice, but it hyperpolarizes preparations in B1KO and TLR4KO mice. The hyperpolarization mechanism in B1KO mice involves B2R, and the TLR4KO response is independent of cytoplasmic calcium influx but relies on potassium channels. Conversely, LPS hyperpolarizes thoracic aorta rings in both C57BL/6 and B1KO mice, with the response unaffected by a B1R antagonist. Interestingly, the absence of B1R alters the LPS response to potassium channels. These activities are independent of nitric oxide synthase (NOS). While exposure to DBK and LPS does not alter B1R and TLR4 mRNA expression, treatment with these agonists increases B1R staining in endothelial cells of thoracic aortic rings and modifies the staining pattern of B1R and TLR4 in endothelial cells. Proximity ligation assay suggests a interaction between the receptors. CONCLUSION Our findings provide additional support for a putative connection between B1R and TLR4 signaling. Given the involvement of these receptors and their agonists in inflammation, it suggests that drugs and therapies targeting their effects could be promising therapeutic avenues worth exploring.
Collapse
Affiliation(s)
- Carolina Batista
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rua César Pernetta, S/N, Prédio do ICB (Anexo ao Bloco F do CCS), 3º andar, sala LJ.03.01, Cidade Universitária, Rio de Janeiro, RJ, CEP: 21941-902, Brazil
- Departamento de Biofísica, Universidade Federal de São Paulo, R. Pedro de Toledo, 669, 9° andar, São Paulo, SP, CEP: 04039-032, Brazil
| | - João Victor Roza Cruz
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rua César Pernetta, S/N, Prédio do ICB (Anexo ao Bloco F do CCS), 3º andar, sala LJ.03.01, Cidade Universitária, Rio de Janeiro, RJ, CEP: 21941-902, Brazil
| | - Joice Stipursky
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rua César Pernetta, S/N, Prédio do ICB (Anexo ao Bloco F do CCS), 3º andar, sala LJ.03.01, Cidade Universitária, Rio de Janeiro, RJ, CEP: 21941-902, Brazil
| | - Fabio de Almeida Mendes
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rua César Pernetta, S/N, Prédio do ICB (Anexo ao Bloco F do CCS), 3º andar, sala LJ.03.01, Cidade Universitária, Rio de Janeiro, RJ, CEP: 21941-902, Brazil.
| | - João Bosco Pesquero
- Departamento de Biofísica, Universidade Federal de São Paulo, R. Pedro de Toledo, 669, 9° andar, São Paulo, SP, CEP: 04039-032, Brazil.
| |
Collapse
|
12
|
Ritaparna P, Ray M, Dhal AK, Mahapatra RK. An immunoinformatics approach for design and validation of multi-subunit vaccine against Plasmodium falciparum from essential hypothetical proteins. J Parasit Dis 2024; 48:593-609. [PMID: 39145352 PMCID: PMC11319695 DOI: 10.1007/s12639-024-01696-w] [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: 04/15/2024] [Accepted: 06/11/2024] [Indexed: 08/16/2024] Open
Abstract
Malaria, caused by Plasmodium falciparum, remains a pressing global health concern. Advancements in combating this parasite involve the development of a protein vaccine. This study employs immunoinformatics to identify potential vaccine candidates within the repertoire of 218 P. falciparum exported essential proteins identified through saturaturation mutagenesis study. Our screening approach narrows down to 65 Plasmodium-exported proteins with uncharacterized functions while exhibiting non-mutability in CDS (coding sequences). The transmembrane helix, antigenicity, allergenicity of the shortlisted proteins was assessed through diverse prediction algorithm, culminating in the identification of five promising vaccination contenders, based on probability scores. We discerned B-cell, helper T-lymphocyte, and cytotoxic T-lymphocyte epitopes. Two proteins with the most favorable epitope were harnessed to construct a multi-subunit vaccine, through judicious linker integration. Employing the I-TASSER software, three-dimensional models of the constituent proteins was obtained and was validated using diverse tools like ProSA, VERIFY3D, and ERRAT. The modelled proteins underwent Molecular Dynamics (MD) simulation in a solvent environment to evaluate the stability of the multi-subunit vaccine. Furthermore, we conducted molecular docking through the ClusPro web server to elucidate potential interactions with Toll-like receptors (TLR2 and TLR4). Docking scores revealed a pronounced affinity of the multi-subunit vaccine for TLR2. Significantly, 100 ns MD simulation of the protein-receptor complex unveiled a persistent hydrogen bond linkage between the ARG63 residue of the sub-unit vaccine and the GLU32 residue of the TLR2 receptor. These findings collectively advocate the potential efficacy of the first multi-subunit vaccine from the potential hypothetical proteins of P. falciparum. Supplementary Information The online version contains supplementary material available at 10.1007/s12639-024-01696-w.
Collapse
Affiliation(s)
- Prajna Ritaparna
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha 751024 India
- National Innovation Foundation, India, KIIT-TBI, Bhubaneswar, Odisha 751024 India
| | - Muskan Ray
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha 751024 India
| | - Ajit Kumar Dhal
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha 751024 India
| | | |
Collapse
|
13
|
Nguyen TL, Kim H. Discovering peptides and computational investigations of a multiepitope vaccine target Mycobacterium tuberculosis. Synth Syst Biotechnol 2024; 9:391-405. [PMID: 38585591 PMCID: PMC10997871 DOI: 10.1016/j.synbio.2024.03.010] [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: 01/31/2024] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 04/09/2024] Open
Abstract
Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), a prevalent airborne infectious disease. Despite the availability of the Bacille Calmette-Guerin vaccine, its global efficacy remains modest, and tuberculosis persists as a significant global public health threat. Addressing this challenge and advancing towards the End MTB Strategy, we developed a multiepitope vaccine (MEV) based on immunoinformatics and computational approaches. Immunoinformatics screening of MBT protein identified immune-dominant epitopes based on Major Histocompatibility Complex (MHC) allele binding, immunogenicity, antigenicity, allergenicity, toxicity, and cytokine inducibility. Selected epitopes were integrated into an MEV construct with adjuvant and linkers, forming a fully immunogenic vaccine candidate. Comprehensive analyses encompassed the evaluation of immunological and physicochemical properties, determination of tertiary structure, molecular docking with Toll-Like Receptors (TLR), molecular dynamics (MD) simulations for all atoms, and immune simulations. Our MEV comprises 534 amino acids, featuring 6 cytotoxic T lymphocyte, 8 helper T lymphocyte, and 7 linear B lymphocyte epitopes, demonstrating high antigenicity and stability. Notably, molecular docking studies and triplicate MD simulations revealed enhanced interactions and stability of MEV with the TLR4 complex compared to TLR2. In addition, the immune simulation indicated the capacity to effectively induce elevated levels of antibodies and cytokines, emphasizing the vaccine's robust immunogenic response. This study presents a promising MEV against TB, exhibiting favorable immunological and physicochemical attributes. The findings provide theoretical support for TB vaccine development. Our study aligns with the global initiative of the End MTB Strategy, emphasizing its potential impact on addressing persistent challenges in TB control.
Collapse
Affiliation(s)
- Truc Ly Nguyen
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- eGnome, Inc., Seoul, 05836, Republic of Korea
| |
Collapse
|
14
|
McCoy KM, Ackerman ME, Grigoryan G. A comparison of antibody-antigen complex sequence-to-structure prediction methods and their systematic biases. Protein Sci 2024; 33:e5127. [PMID: 39167052 PMCID: PMC11337930 DOI: 10.1002/pro.5127] [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: 03/15/2024] [Revised: 06/24/2024] [Accepted: 07/14/2024] [Indexed: 08/23/2024]
Abstract
The ability to accurately predict antibody-antigen complex structures from their sequences could greatly advance our understanding of the immune system and would aid in the development of novel antibody therapeutics. There have been considerable recent advancements in predicting protein-protein interactions (PPIs) fueled by progress in machine learning (ML). To understand the current state of the field, we compare six representative methods for predicting antibody-antigen complexes from sequence, including two deep learning approaches trained to predict PPIs in general (AlphaFold-Multimer and RoseTTAFold), two composite methods that initially predict antibody and antigen structures separately and dock them (using antibody-mode ClusPro), local refinement in Rosetta (SnugDock) of globally docked poses from ClusPro, and a pipeline combining homology modeling with rigid-body docking informed by ML-based epitope and paratope prediction (AbAdapt). We find that AlphaFold-Multimer outperformed other methods, although the absolute performance leaves considerable room for improvement. AlphaFold-Multimer models of lower quality display significant structural biases at the level of tertiary motifs (TERMs) toward having fewer structural matches in non-antibody-containing structures from the Protein Data Bank (PDB). Specifically, better models exhibit more common PDB-like TERMs at the antibody-antigen interface than worse ones. Importantly, the clear relationship between performance and the commonness of interfacial TERMs suggests that the scarcity of interfacial geometry data in the structural database may currently limit the application of ML to the prediction of antibody-antigen interactions.
Collapse
Affiliation(s)
- Katherine Maia McCoy
- Molecular and Cell Biology Graduate ProgramDartmouth CollegeHanoverNew HampshireUSA
| | - Margaret E. Ackerman
- Molecular and Cell Biology Graduate ProgramDartmouth CollegeHanoverNew HampshireUSA
- Thayer School of EngineeringDartmouth CollegeHanoverNew HampshireUSA
| | - Gevorg Grigoryan
- Molecular and Cell Biology Graduate ProgramDartmouth CollegeHanoverNew HampshireUSA
- Department of Computer ScienceDartmouth CollegeHanoverNew HampshireUSA
| |
Collapse
|
15
|
Singha S, Nath N, Sarma V, Barman K, Sharma GC, Saikia L, Baruah S. Identification of Immunodominant Epitopes of Dengue Virus 2 Envelope and NS1 Proteins: Evaluating the Diagnostic Potential of a Synthetic Peptide. Mol Diagn Ther 2024; 28:633-643. [PMID: 38980575 DOI: 10.1007/s40291-024-00728-8] [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] [Accepted: 06/23/2024] [Indexed: 07/10/2024]
Abstract
BACKGROUND AND OBJECTIVE Dengue is a major infectious disease with potential for outbreaks and epidemics. A specific and sensitive diagnosis is a prerequisite for clinical management of the disease. We designed our study to identify epitopes on the Dengue virus (DENV) envelope (E) and non-structural protein 1 (NS1) with potential for diagnosis. METHODS Serology and immunoinformatic approaches were employed. We collected DENV-positive, DENV-negative and Japanese encephalitis virus-positive samples from collaborating hospitals in 2019 and 2022-2023. Seropositive peptides in 15-18 mer peptide arrays of E and NS1 proteins of DENV2 were determined by an indirect enzyme-linked immunosorbent assay. B-cell linear and conformational epitopes were predicted using BepiPred2.0 and ElliPro, respectively. A consensus recombinant peptide was designed, synthesised and evaluated for its diagnostic potential using patient sera. RESULTS Eight peptides of E protein and six peptides of NS1 protein were identified to be the most frequently recognised by Dengue-positive patients. These peptide sequences were compared with B-cell epitope regions and found to be overlapped with predicted B-cell linear and conformational epitopes. EP11 and NSP15 showed a 100% amino acid sequence overlap with B-cell epitopes. EP1 and NSP15 had 14 whereas EP28, EP31, EP60 16, NSP12 and NSP32 had more than 15 interacting interface residues with a neutralising antibody, suggesting a strength of interaction. Interestingly, potential epitopes identified were localised on the surface of proteins as visualised by PyMOL. Validation with a recombined synthetic peptide yielded 92.3% sensitivity and 91.42% specificity. CONCLUSIONS Immunodominant regions identified by serology and computationally predicted epitopes overlapped, thereby showing the robustness of the methodology and the peptide designed for diagnosis.
Collapse
Affiliation(s)
- Sushmita Singha
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur Assam, 784028, India
| | - Neena Nath
- Gauhati Medical College and Hospital, Bhangagarh, Guwahati, Assam, India
| | - Vaishali Sarma
- Gauhati Medical College and Hospital, Bhangagarh, Guwahati, Assam, India
| | - Kangkana Barman
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur Assam, 784028, India
| | - Gurumayum Chourajit Sharma
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur Assam, 784028, India
| | - Lahari Saikia
- Gauhati Medical College and Hospital, Bhangagarh, Guwahati, Assam, India
| | - Shashi Baruah
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur Assam, 784028, India.
| |
Collapse
|
16
|
Nguyen TL, Kim H. Integrating immunoinformatics and computational epitope prediction for a vaccine candidate against respiratory syncytial virus. Infect Dis Model 2024; 9:763-774. [PMID: 38708060 PMCID: PMC11068479 DOI: 10.1016/j.idm.2024.04.005] [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: 02/12/2024] [Revised: 04/04/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024] Open
Abstract
Respiratory syncytial virus (RSV) poses a significant global health threat, especially affecting infants and the elderly. Addressing this, the present study proposes an innovative approach to vaccine design, utilizing immunoinformatics and computational strategies. We analyzed RSV's structural proteins across both subtypes A and B, identifying potential helper T lymphocyte, cytotoxic T lymphocyte, and linear B lymphocyte epitopes. Criteria such as antigenicity, allergenicity, toxicity, and cytokine-inducing potential were rigorously examined. Additionally, we evaluated the conservancy of these epitopes and their population coverage across various RSV strains. The comprehensive analysis identified six major histocompatibility complex class I (MHC-I) binding, five MHC-II binding, and three B-cell epitopes. These were integrated with suitable linkers and adjuvants to form the vaccine. Further, molecular docking and molecular dynamics simulations demonstrated stable interactions between the vaccine candidate and human Toll-like receptors (TLR4 and TLR5), with a notable preference for TLR4. Immune simulation analysis underscored the vaccine's potential to elicit a strong immune response. This study presents a promising RSV vaccine candidate and offers theoretical support, marking a significant advancement in vaccine development efforts. However, the promising in silico findings need to be further validated through additional in vivo studies.
Collapse
Affiliation(s)
- Truc Ly Nguyen
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- eGnome, Inc., Seoul, 05836, Republic of Korea
| |
Collapse
|
17
|
Asadinezhad M, Pakzad I, Asadollahi P, Ghafourian S, Kalani BS. Proteomics Exploration of Brucella melitensis to Design an Innovative Multi-Epitope mRNA Vaccine. Bioinform Biol Insights 2024; 18:11779322241272404. [PMID: 39220468 PMCID: PMC11365029 DOI: 10.1177/11779322241272404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 07/09/2024] [Indexed: 09/04/2024] Open
Abstract
Brucellosis is a chronic and debilitating disease in humans, causing great economic losses in the livestock industry. Making an effective vaccine is one of the most important concerns for this disease. The new mRNA vaccine technology due to its accuracy and high efficiency has given promising results in various diseases. The objective of this research was to create a novel mRNA vaccine with multiple epitopes targeting Brucella melitensis. Seventeen antigenic proteins and their appropriate epitopes were selected with immunoinformatic tools and surveyed in terms of toxicity, allergenicity, and homology. Then, their presentation and identification by MHC cells and other immune cells were checked with valid tools such as molecular docking, and a multi-epitope protein was modeled, and after optimization, mRNA was analyzed in terms of structure and stability. Ultimately, the immune system's reaction to this novel vaccine was evaluated and the results disclosed that the designed mRNA construct can be an effective and promising vaccine that requires laboratory and clinical trials.
Collapse
Affiliation(s)
- Maryam Asadinezhad
- Students Research Committee, Ilam University of Medical Sciences, Ilam, Iran
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Iraj Pakzad
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Parisa Asadollahi
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Sobhan Ghafourian
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Behrooz Sadeghi Kalani
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
- Department of Medical Microbiology, School of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| |
Collapse
|
18
|
Douradinha B. Computational strategies in Klebsiella pneumoniae vaccine design: navigating the landscape of in silico insights. Biotechnol Adv 2024; 76:108437. [PMID: 39216613 DOI: 10.1016/j.biotechadv.2024.108437] [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: 05/28/2024] [Revised: 07/07/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
The emergence of multidrug-resistant Klebsiella pneumoniae poses a grave threat to global public health, necessitating urgent strategies for vaccine development. In this context, computational tools have emerged as indispensable assets, offering unprecedented insights into klebsiellal biology and facilitating the design of effective vaccines. Here, a review of the application of computational methods in the development of K. pneumoniae vaccines is presented, elucidating the transformative impact of in silico approaches. Through a systematic exploration of bioinformatics, structural biology, and immunoinformatics techniques, the complex landscape of K. pneumoniae pathogenesis and antigenicity was unravelled. Key insights into virulence factors, antigen discovery, and immune response mechanisms are discussed, highlighting the pivotal role of computational tools in accelerating vaccine development efforts. Advancements in epitope prediction, antigen selection, and vaccine design optimisation are examined, highlighting the potential of in silico approaches to update vaccine development pipelines. Furthermore, challenges and future directions in leveraging computational tools to combat K. pneumoniae are discussed, emphasizing the importance of multidisciplinary collaboration and data integration. This review provides a comprehensive overview of the current state of computational contributions to K. pneumoniae vaccine development, offering insights into innovative strategies for addressing this urgent global health challenge.
Collapse
|
19
|
Mursaleen S, Sarfraz A, Shehroz M, Zaman A, Rahman FU, Moura AA, Sheheryar S, Aziz S, Ullah R, Iqbal Z, Nishan U, Shah M, Sun W. Genome-level therapeutic targets identification and chimeric Vaccine designing against the Blastomyces dermatitidis. Heliyon 2024; 10:e36153. [PMID: 39224264 PMCID: PMC11367477 DOI: 10.1016/j.heliyon.2024.e36153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 08/11/2024] [Indexed: 09/04/2024] Open
Abstract
Blastomyces dermatitidis is a thermally dimorphic fungus that can cause serious and sometimes fatal infections, including blastomycosis. After spore inhalation, a pulmonary infection develops, which can be asymptomatic and have lethal effects, such as acute respiratory distress syndrome. Its most common extra-pulmonary sites are the central nervous system, bones, skin, and genito-urinary systems. Currently, no vaccine has been approved by the FDA to prevent this infection. In the study, a peptide-based vaccine was developed against blastomycosis by using subtractive proteomics and reverse vaccinology approaches. It focuses on mining the whole genome of B. dermatitidis, identifying potential therapeutic targets, and pinpointing potential epitopes for both B- and T-cells that are immunogenic, non-allergenic, non-toxic, and highly antigenic. Multi-epitope constructs were generated by incorporating appropriate linker sequences. A linker (EAAAK) was also added to incorporate an adjuvant sequence to increase immunological potential. The addition of adjuvants and linkers ultimately resulted in the formation of a vaccine construct in which the number of amino acids was 243 and the molecular weight was 26.18 kDa. The designed antigenic and non-allergenic vaccine constructs showed suitable physicochemical properties. The vaccine's structures were predicted, and further analysis verified their interactions with the human TLR-4 receptor through protein-protein docking. Additionally, MD simulation showed a potent interaction between prioritized vaccine-receptor complexes. Immune simulation predicted that the final vaccine injections resulted in significant immune responses for the T- and B-cell immune responses. Moreover, in silico cloning ensured a high expression possibility of the lead vaccine in the E. coli (K12) vector. This study offers an initiative for the development of effective vaccines against B. dermatitidis; however, it is necessary to validate the designed vaccine's immunogenicity experimentally.
Collapse
Affiliation(s)
- Sawvara Mursaleen
- Department of Biochemistry, Bahauddin Zakariya University, Multan-66000, Pakistan
| | - Asifa Sarfraz
- Department of Biochemistry, Bahauddin Zakariya University, Multan-66000, Pakistan
| | - Muhammad Shehroz
- Department of Bioinformatics, Kohsar University Murree, Murree-47150, Pakistan
| | - Aqal Zaman
- Department of Microbiology & Molecular Genetics, Bahauddin Zakariya University, Multan-66000, Pakistan
| | - Faiz U Rahman
- Department of Zoology, Shangla Campus, University of Swat, Khyber Pakhtunkhwa, Pakistan
| | - Arlindo A. Moura
- Department of Animal Science, Federal University of Ceara, Fortaleza, Brazil
| | - Sheheryar Sheheryar
- Department of Animal Science, Federal University of Ceara, Fortaleza, Brazil
| | - Shahid Aziz
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451-970, Brazil
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University Riyadh Saudi Arabia, Kingdom of Saudi Arabia
| | - Zafar Iqbal
- Department of Surgery, College of Medicine, King Saud University P.O. Box 7805, Riyadh, 11472, Kingdom of Saudi Arabia
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan-66000, Pakistan
| | - Wenwen Sun
- Department of Intensive Care Unit, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 213004, China
| |
Collapse
|
20
|
Aftab A, Sil S, Nath S, Basu A, Basu S. Intrinsic Disorder and Other Malleable Arsenals of Evolved Protein Multifunctionality. J Mol Evol 2024:10.1007/s00239-024-10196-7. [PMID: 39214891 DOI: 10.1007/s00239-024-10196-7] [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: 03/20/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
Microscopic evolution at the functional biomolecular level is an ongoing process. Leveraging functional and high-throughput assays, along with computational data mining, has led to a remarkable expansion of our understanding of multifunctional protein (and gene) families over the past few decades. Various molecular and intermolecular mechanisms are now known that collectively meet the cumulative multifunctional demands in higher organisms along an evolutionary path. This multitasking ability is attributed to a certain degree of intrinsic or adapted flexibility at the structure-function level. Evolutionary diversification of structure-function relationships in proteins highlights the functional importance of intrinsically disordered proteins/regions (IDPs/IDRs) which are highly dynamic biological soft matter. Multifunctionality is favorably supported by the fluid-like shapes of IDPs/IDRs, enabling them to undergo disorder-to-order transitions upon binding to different molecular partners. Other new malleable members of the protein superfamily, such as those involved in fold-switching, also undergo structural transitions. This new insight diverges from all traditional notions of functional singularity in enzyme classes and emphasizes a far more complex, multi-layered diversification of protein functionality. However, a thorough review in this line, focusing on flexibility and function-driven structural transitions related to evolved multifunctionality in proteins, is currently missing. This review attempts to address this gap while broadening the scope of multifunctionality beyond single protein sequences. It argues that protein intrinsic disorder is likely the most striking mechanism for expressing multifunctionality in proteins. A phenomenological analogy has also been drawn to illustrate the increasingly complex nature of modern digital life, driven by the need for multitasking, particularly involving media.
Collapse
Affiliation(s)
- Asifa Aftab
- Department of Zoology, Asutosh College, (affiliated with University of Calcutta), Kolkata, 700026, India
| | - Souradeep Sil
- Department of Genetics, Osmania University, Hyderabad, 500007, India
| | - Seema Nath
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Anirneya Basu
- Department of Microbiology, Asutosh College (Affiliated With University of Calcutta), Kolkata, 700026, India
| | - Sankar Basu
- Department of Microbiology, Asutosh College (Affiliated With University of Calcutta), Kolkata, 700026, India.
| |
Collapse
|
21
|
Zeng L, Zhu Y, Cui X, Chi J, Uddin A, Zhou Z, Song X, Dai M, Cristofanilli M, Kalinsky K, Wan Y. Tuning Immune-Cold Tumor by Suppressing USP10/B7-H4 Proteolytic Axis Reinvigorates Therapeutic Efficacy of ADCs. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400757. [PMID: 39206932 DOI: 10.1002/advs.202400757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 08/04/2024] [Indexed: 09/04/2024]
Abstract
Tuning immune-cold tumor hot has largely attracted attention to improve cancer treatment, including immunotherapy and antibody-drug conjugates (ADCs). Utilizing multiomic analyses and experimental validation, this work identifies a pivotal role for the USP10/B7-H4 proteolytic axis in mediating the interplay between tumor immune responses and ADC efficacy, particularly for sacituzumab govitecan (SG) in treating triple negative breast cancers (TNBCs). Mechanistically, the inhibition of autocrine motility factor receptor (AMFR)-mediated ubiquitylation of B7-H4 by the deubiquitinase USP10 leads to the stabilization of B7-H4, which suppresses tumor immune activity and reduces SG treatment effectiveness. Pharmacological inhibition of USP10 promotes the degradation of B7-H4, enhancing tumor immunogenicity and consequently improving the tumor-killing efficacy of SG. In preclinical TNBC models, suppression of USP10/B7-H4 proteolytic axis is effective in increasing SG killing efficacy and reducing tumor growth, especially for the tumors with the USP10high/B7-H7high signature. Collectively, these findings uncover a novel strategy for targeting the immunosuppressive molecule B7-H4 for cancer therapy.
Collapse
Affiliation(s)
- Lidan Zeng
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yueming Zhu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Xin Cui
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Junlong Chi
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- DGP graduate program, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Amad Uddin
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Zhuan Zhou
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xinxin Song
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Mingji Dai
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Chemistry, College of Arts and Science, Emory University, Atlanta, GA, 30322, USA
| | | | - Kevin Kalinsky
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yong Wan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| |
Collapse
|
22
|
Gomes DEB, Yang B, Vanella R, Nash MA, Bernardi RC. Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions. J Am Chem Soc 2024; 146:23842-23853. [PMID: 39146039 DOI: 10.1021/jacs.4c05869] [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: 08/17/2024]
Abstract
Understanding binding epitopes involved in protein-protein interactions and accurately determining their structure are long-standing goals with broad applicability in industry and biomedicine. Although various experimental methods for binding epitope determination exist, these approaches are typically low throughput and cost-intensive. Computational methods have potential to accelerate epitope predictions; however, recently developed artificial intelligence (AI)-based methods frequently fail to predict epitopes of synthetic binding domains with few natural homologues. Here we have developed an integrated method employing generalized-correlation-based dynamic network analysis on multiple molecular dynamics (MD) trajectories, initiated from AlphaFold2Multimer structures, to unravel the structure and binding epitope of the therapeutic PD-L1:Affibody complex. Both AlphaFold2 and conventional molecular dynamics trajectory analysis were ineffective in distinguishing between two proposed binding models, parallel and perpendicular. However, our integrated approach, utilizing dynamic network analysis, demonstrated that the perpendicular mode was significantly more stable. These predictions were validated using a suite of experimental epitope mapping protocols, including cross-linking mass spectrometry and next-generation sequencing-based deep mutational scanning. Conversely, AlphaFold3 failed to predict a structure bound in the perpendicular pose, highlighting the necessity for exploratory research in the search for binding epitopes and challenging the notion that AI-generated protein structures can be accepted without scrutiny. Our research underscores the potential of employing dynamic network analysis to enhance AI-based structure predictions for more accurate identification of protein-protein interaction interfaces.
Collapse
Affiliation(s)
- Diego E B Gomes
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
| | - Byeongseon Yang
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Basel 4058, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Rosario Vanella
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Basel 4058, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Basel 4058, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Rafael C Bernardi
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
| |
Collapse
|
23
|
Berkowitz N, MacMillan A, Simmons MB, Shinde U, Purdy GE. Structural modeling and characterization of the Mycobacterium tuberculosis MmpL3 C-terminal domain. FEBS Lett 2024. [PMID: 39198717 DOI: 10.1002/1873-3468.15007] [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: 03/21/2024] [Revised: 07/29/2024] [Accepted: 08/05/2024] [Indexed: 09/01/2024]
Abstract
The Mycobacterium tuberculosis (Mtb) cell envelope provides a protective barrier against the immune response and antibiotics. The mycobacterial membrane protein large (MmpL) family of proteins export cell envelope lipids and siderophores; therefore, these proteins are important for the basic biology and pathogenicity of Mtb. In particular, MmpL3 is essential and a known drug target. Despite interest in MmpL3, the structural data in the field are incomplete. Utilizing homology modeling, AlphaFold, and biophysical techniques, we characterized the cytoplasmic C-terminal domain (CTD) of MmpL3 to better understand its structure and function. Our in silico models of the MmpL11TB and MmpL3TB CTD reveal notable features including a long unstructured linker that connects the globular domain to the last transmembrane (TM) in each transporter, charged lysine and arginine residues facing the membrane, and a C-terminal alpha helix. Our predicted overall structure enables a better understanding of these transporters.
Collapse
Affiliation(s)
- Naomi Berkowitz
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Allison MacMillan
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Marit B Simmons
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Ujwal Shinde
- Biophysics Core Facility, Oregon Health & Science University, Portland, OR, USA
| | - Georgiana E Purdy
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| |
Collapse
|
24
|
Sasovsky DJ, Angelina E, Leiva LC, Bal de Kier Joffé E, Lomonte B, Bustillo S. Comparative in vitro and in silico analysis of the ability of basic Asp49 phospholipase A 2 and Lys49-phospholipase A 2-like myotoxins from Bothrops diporus venom to inhibit the metastatic potential of murine mammary tumor cells and endothelial cell tubulogenesis. Chem Biol Interact 2024; 402:111217. [PMID: 39197813 DOI: 10.1016/j.cbi.2024.111217] [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: 04/10/2024] [Revised: 05/08/2024] [Accepted: 08/26/2024] [Indexed: 09/01/2024]
Abstract
Snake venoms are a complex mixture of proteins and polypeptides that represent a valuable source of potential molecular tools for understanding physiological processes for the development of new drugs. In this study two major PLA2s, named PLA2-I (Asp49) and PLA2-II (Lys49), isolated from the venom of Bothrops diporus from Northeastern Argentina, have shown cytotoxic effects on LM3 murine mammary tumor cells, with PLA2-II-like exhibiting a stronger effect compared to PLA2-I. At sub-cytotoxic levels, both PLA2s inhibited adhesion, migration, and invasion of these adenocarcinoma cells. Moreover, these toxins hindered tubulogenesis in endothelial cells, implicating a potential role in inhibiting tumor angiogenesis. All these inhibitory effects were more pronounced for the catalytically-inactive toxin. Additionally, in silico studies strongly suggest that this PLA2-II-like myotoxin could effectively block fibronectin binding to the integrin receptor, offering a dual advantage over PLA2-I in interacting with the αVβ3 integrin. In conclusion, this study reports for the first time, integrating both in vitro and in silico approaches, a comparative analysis of the antimetastatic and antiangiogenic potential effects of two isoforms, an Asp49 PLA2-I and a Lys49 PLA2-II-like, both isolated from Bothrops diporus venom.
Collapse
Affiliation(s)
- Daniela J Sasovsky
- Grupo de Investigaciones Biológicas y Moleculares (GIByM) IQUIBA-NEA-CONICET. Facultad de Ciencias Exactas y Naturales y Agrimensura. Universidad Nacional del Nordeste. Argentina
| | - Emilio Angelina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Argentina; IQUIBA-NEA-CONICET, Argentina
| | - Laura C Leiva
- Grupo de Investigaciones Biológicas y Moleculares (GIByM) IQUIBA-NEA-CONICET. Facultad de Ciencias Exactas y Naturales y Agrimensura. Universidad Nacional del Nordeste. Argentina
| | - Elisa Bal de Kier Joffé
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Oncología Angel H Roffo, Área Investigación. Argentina
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica
| | - Soledad Bustillo
- Grupo de Investigaciones Biológicas y Moleculares (GIByM) IQUIBA-NEA-CONICET. Facultad de Ciencias Exactas y Naturales y Agrimensura. Universidad Nacional del Nordeste. Argentina.
| |
Collapse
|
25
|
Cui M, Ji X, Guan F, Su G, Du L. Design of a Helicobacter pylori multi-epitope vaccine based on immunoinformatics. Front Immunol 2024; 15:1432968. [PMID: 39247202 PMCID: PMC11377293 DOI: 10.3389/fimmu.2024.1432968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/07/2024] [Indexed: 09/10/2024] Open
Abstract
Helicobacter pylori (H. pylori) is an infectious bacterium that colonizes the stomach of approximately half of the global population. It has been classified as a Group I carcinogen by the World Health Organization due to its strong association with an increased incidence of gastric cancer and exacerbation of stomach diseases. The primary treatment for H. pylori infection currently involves triple or quadruple therapy, primarily consisting of antibiotics and proton pump inhibitors. However, the increasing prevalence of antibiotic resistance poses significant challenges to this approach, underscoring the urgent need for an effective vaccine. In this study, a novel multi-epitope H. pylori vaccine was designed using immunoinformatics. The vaccine contains epitopes derived from nine essential proteins. Software tools and online servers were utilized to predict, evaluate, and analyze the physiochemical properties, secondary and tertiary structures, and immunogenicity of the candidate vaccine. These comprehensive assessments ultimately led to the formulation of an optimal design scheme for the vaccine. Through constructing a novel multi-epitope vaccine based on immunoinformatics, this study offers promising prospects and great potential for the prevention of H. pylori infection. This study also provides a reference strategy to develop multi-epitope vaccines for other pathogens.
Collapse
Affiliation(s)
- Man Cui
- Research and Development Centre, Beijing Zhifei Lvzhu Biopharmaceutical Co., Ltd., Beijing, China
- Beijing Bacterial Vaccine Engineering Research Centre, Beijing, China
| | - Xiaohui Ji
- Research and Development Centre, Beijing Zhifei Lvzhu Biopharmaceutical Co., Ltd., Beijing, China
- Beijing Bacterial Vaccine Engineering Research Centre, Beijing, China
| | - Fengtao Guan
- Research and Development Centre, Beijing Zhifei Lvzhu Biopharmaceutical Co., Ltd., Beijing, China
- Beijing Bacterial Vaccine Engineering Research Centre, Beijing, China
| | - Guimin Su
- Research and Development Centre, Beijing Zhifei Lvzhu Biopharmaceutical Co., Ltd., Beijing, China
- Beijing Bacterial Vaccine Engineering Research Centre, Beijing, China
| | - Lin Du
- Research and Development Centre, Beijing Zhifei Lvzhu Biopharmaceutical Co., Ltd., Beijing, China
- Beijing Bacterial Vaccine Engineering Research Centre, Beijing, China
| |
Collapse
|
26
|
Abid A, Khalid A, Suleman M, Akbar H, Hafeez MA, Khan JA, Rashid MI. Humoral and cellular immunity in response to an in silico-designed multi-epitope recombinant protein of Theileria annulata. Front Immunol 2024; 15:1400308. [PMID: 39234242 PMCID: PMC11371685 DOI: 10.3389/fimmu.2024.1400308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/24/2024] [Indexed: 09/06/2024] Open
Abstract
Tropical theileriosis is a lymphoproliferative disease caused by Theileria annulata and is transmitted by Ixodid ticks of the genus Hyalomma. It causes significant losses in livestock, especially in exotic cattle. The existing methods for controlling it, chemotherapeutic agents and a vaccine based on an attenuated schizont stage parasite, have several limitations. A promising solution to control this disease is the use of molecular vaccines based on potential immunogenic proteins of T. annulata. For this purpose, we selected five antigenic sequences of T. annulata, i.e. SPAG-1, Tams, TaSP, spm2, and Ta9. These were subjected to epitope prediction for cytotoxic T lymphocytes, B-cells, and helper T lymphocytes. CTL and B-cell epitopes with a higher score whereas those of HTL with a lower score, were selected for the construct. A single protein was constructed using specific linkers and evaluated for high antigenicity and low allergenicity. The construct was acidic, hydrophobic, and thermostable in nature. Secondary and tertiary structures of this construct were drawn using the PSIPRED and RaptorX servers, respectively. A Ramachandran plot showed a high percentage of residues in this construct in favorable, allowed, and general regions. Molecular docking studies suggested that the complex was stable and our construct could potentially be a good candidate for immunization trials. Furthermore, we successfully cloned it into the pET-28a plasmid and transformed it into the BL21 strain. A restriction analysis was performed to confirm the transformation of our plasmid. After expression and purification, recombinant protein of 49 kDa was confirmed by western blotting. An ELISA detected increased specific antibody levels in the sera of the immunized animals compared with the control group, and flow cytometric analysis showed a stronger cell-mediated immune response. We believe our multi-epitope recombinant protein has the potential for the large-scale application for disease prevention globally in the bovine population. This study will act as a model for similar parasitic challenges.
Collapse
Affiliation(s)
- Asadullah Abid
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Ambreen Khalid
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Suleman
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Haroon Akbar
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Mian Abdul Hafeez
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Jawaria Ali Khan
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Imran Rashid
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| |
Collapse
|
27
|
Choi ES, Hnath B, Sha CM, Dokholyan NV. Unveiling the double-edged sword: SOD1 trimers possess tissue-selective toxicity and bind septin-7 in motor neuron-like cells. Structure 2024:S0969-2126(24)00319-8. [PMID: 39208794 DOI: 10.1016/j.str.2024.08.002] [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: 04/11/2024] [Revised: 06/10/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024]
Abstract
Misfolded species of superoxide dismutase 1 (SOD1) are associated with increased death in amyotrophic lateral sclerosis (ALS) models compared to insoluble protein aggregates. The mechanism by which structurally independent SOD1 trimers cause cellular toxicity is unknown but may drive disease pathology. Here, we uncovered the SOD1 trimer interactome-a map of potential tissue-selective protein-binding partners in the brain, spinal cord, and skeletal muscle. We identified binding partners and key pathways associated with SOD1 trimers and found that trimers may affect normal cellular functions such as dendritic spine morphogenesis and synaptic function in the central nervous system and cellular metabolism in skeletal muscle. We discovered SOD1 trimer-selective enrichment of genes. We performed detailed computational and biochemical characterization of SOD1 trimer protein binding for septin-7. Our investigation highlights key proteins and pathways within distinct tissues, revealing a plausible intersection of genetic and pathophysiological mechanisms in ALS through interactions involving SOD1 trimers.
Collapse
Affiliation(s)
- Esther Sue Choi
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA; Medical Scientist Training Program, Penn State College of Medicine, Hershey, PA, USA
| | - Brianna Hnath
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA; Department of Biomedical Engineering, Penn State University, University Park, PA, USA
| | - Congzhou Mike Sha
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA; Medical Scientist Training Program, Penn State College of Medicine, Hershey, PA, USA
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA; Department of Biomedical Engineering, Penn State University, University Park, PA, USA; Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA; Department of Chemistry, Penn State University, University Park, PA, USA.
| |
Collapse
|
28
|
Deb A, Nagpal S, Yadav RK, Thakur H, Nair D, Krishnan V, Vrati S. Japanese encephalitis virus NS5 protein interacts with nucleolin to enhance the virus replication. J Virol 2024; 98:e0085824. [PMID: 39078257 PMCID: PMC11334521 DOI: 10.1128/jvi.00858-24] [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: 05/16/2024] [Accepted: 06/29/2024] [Indexed: 07/31/2024] Open
Abstract
Japanese encephalitis virus (JEV) is an arthropod-borne, plus-strand flavivirus causing viral encephalitis in humans with a high case fatality rate. The JEV non-structural protein 5 (NS5) with the RNA-dependent RNA polymerase activity interacts with the viral and host proteins to constitute the replication complex. We have identified the multifunctional protein Nucleolin (NCL) as one of the several NS5-interacting host proteins. We demonstrate the interaction and colocalization of JEV NS5 with NCL in the virus-infected HeLa cells. The siRNA-mediated knockdown of NCL indicated that it was required for efficient viral replication. Importantly, JEV grew to higher titers in cells over-expressing exogenous NCL, demonstrating its pro-viral role. We demonstrated that NS5 interacted with the RRM and GAR domains of NCL. We show that the NCL-binding aptamer AS1411 containing the G-quadruplex (GQ) structure and the GQ ligand BRACO-19 caused significant inhibition of JEV replication. The antiviral effect of AS1411 and BRACO-19 could be overcome in HeLa cells by the overexpression of exogenous NCL. We demonstrated that the synthetic RNAs derived from the 3'-NCR of JEV genomic RNA containing the GQ sequence could bind NCL in vitro. The replication complex binding to the 3'-NCR is required for the viral RNA synthesis. It is likely that NCL present in the replication complex destabilizes the GQ structures in the genomic RNA, thus facilitating the movement of the replication complex resulting in efficient virus replication.IMPORTANCEJapanese encephalitis virus (JEV) is endemic in most parts of South-East Asia and the Western Pacific region, causing epidemics of encephalitis with a high case fatality rate. While a tissue culture-derived JEV vaccine is available, no antiviral therapy exists. The JEV NS5 protein has RNA-dependent RNA polymerase activity. Together with several host and viral proteins, it constitutes the replication complex necessary for virus replication. Understanding the interaction of NS5 with the host proteins could help design novel antivirals. We identified Nucleolin (NCL) as a crucial host protein interactor of JEV NS5 having a pro-viral role in virus replication. The NS5-interacting NCL binds to the G-quadruplex (GQ) structure sequence in the 3'-NCR of JEV RNA. This may smoothen the movement of the replication complex along the genomic RNA, thereby facilitating the virus replication. This study is the first report on how NCL, a host protein, helps in JEV replication through GQ-binding.
Collapse
Affiliation(s)
- Arundhati Deb
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Shilpi Nagpal
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Rajnesh Kumari Yadav
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Harsh Thakur
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Deepak Nair
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Vengadesan Krishnan
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Sudhanshu Vrati
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| |
Collapse
|
29
|
Xu Y, Zhu F, Zhou Z, Ma S, Zhang P, Tan C, Luo Y, Qin R, Chen J, Pan P. A novel mRNA multi-epitope vaccine of Acinetobacter baumannii based on multi-target protein design in immunoinformatic approach. BMC Genomics 2024; 25:791. [PMID: 39160492 PMCID: PMC11334330 DOI: 10.1186/s12864-024-10691-7] [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: 05/13/2024] [Accepted: 08/06/2024] [Indexed: 08/21/2024] Open
Abstract
Acinetobacter baumannii is a gram-negative bacillus prevalent in nature, capable of thriving under various environmental conditions. As an opportunistic pathogen, it frequently causes nosocomial infections such as urinary tract infections, bacteremia, and pneumonia, contributing to increased morbidity and mortality in clinical settings. Consequently, developing novel vaccines against Acinetobacter baumannii is of utmost importance. In our study, we identified 10 highly conserved antigenic proteins from the NCBI and UniProt databases for epitope mapping. We subsequently screened and selected 8 CTL, HTL, and LBL epitopes, integrating them into three distinct vaccines constructed with adjuvants. Following comprehensive evaluations of immunological and physicochemical parameters, we conducted molecular docking and molecular dynamics simulations to assess the efficacy and stability of these vaccines. Our findings indicate that all three multi-epitope mRNA vaccines designed against Acinetobacter baumannii are promising; however, further animal studies are required to confirm their reliability and effectiveness.
Collapse
Affiliation(s)
- Yizhong Xu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fei Zhu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ziyou Zhou
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shiyang Ma
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Peipei Zhang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Caixia Tan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuying Luo
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Rongliu Qin
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jie Chen
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China.
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China.
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Pinhua Pan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China.
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China.
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.
| |
Collapse
|
30
|
Yang Y, Li G, Pang K, Cao W, Zhang Z, Li X. Deciphering 3'UTR Mediated Gene Regulation Using Interpretable Deep Representation Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2407013. [PMID: 39159140 DOI: 10.1002/advs.202407013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/23/2024] [Indexed: 08/21/2024]
Abstract
The 3' untranslated regions (3'UTRs) of messenger RNAs contain many important cis-regulatory elements that are under functional and evolutionary constraints. It is hypothesized that these constraints are similar to grammars and syntaxes in human languages and can be modeled by advanced natural language techniques such as Transformers, which has been very effective in modeling complex protein sequence and structures. Here 3UTRBERT is described, which implements an attention-based language model, i.e., Bidirectional Encoder Representations from Transformers (BERT). 3UTRBERT is pre-trained on aggregated 3'UTR sequences of human mRNAs in a task-agnostic manner; the pre-trained model is then fine-tuned for specific downstream tasks such as identifying RBP binding sites, m6A RNA modification sites, and predicting RNA sub-cellular localizations. Benchmark results show that 3UTRBERT generally outperformed other contemporary methods in each of these tasks. More importantly, the self-attention mechanism within 3UTRBERT allows direct visualization of the semantic relationship between sequence elements and effectively identifies regions with important regulatory potential. It is expected that 3UTRBERT model can serve as the foundational tool to analyze various sequence labeling tasks within the 3'UTR fields, thus enhancing the decipherability of post-transcriptional regulatory mechanisms.
Collapse
Affiliation(s)
- Yuning Yang
- School of Information Science and Technology, Northeast Normal University, Changchun, Jilin, 130117, China
| | - Gen Li
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Kuan Pang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Wuxinhao Cao
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Zhaolei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun, Jilin, 130012, China
| |
Collapse
|
31
|
Han R, Zhu T, Kong Z, Zhang X, Wang D, Liu J. Understanding and manipulating the recognition of necrosis-inducing secreted protein 1 (NIS1) by BRI1-associated receptor kinase 1 (BAK1). Int J Biol Macromol 2024; 278:134821. [PMID: 39154678 DOI: 10.1016/j.ijbiomac.2024.134821] [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: 02/17/2024] [Revised: 08/07/2024] [Accepted: 08/15/2024] [Indexed: 08/20/2024]
Abstract
Necrosis-inducing secreted protein 1 (NIS1) is a core effector of Ascomycota and Basidiomycota fungi. They inhibit the immune responses of host plants mainly through interaction with the multi-functional coreceptor BRI1-associated receptor kinase 1 (BAK1). However, the structural mechanism of the NIS1 family and how they are recognized by BAK1 are unknown. Herein, we report the first crystal structure of the NIS1 family protein, the Magnaporthe oryzae NIS1 (MoNIS1), analyze the recognition mechanism of NIS1s by BAK1, and explore regulation of the NIS1-BAK1 interaction by a chemical compound. MoNIS1 exists as a β barrel formed by eight β strands, a folding mode that has not been reported. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) assay suggested that β4-β5 loop and β5 strand of MoNIS1 participate in OsBAK1 interaction, which was supported by further single-point mutational assays. For OsBAK1, HDX-MS assay suggested four regions involved in MoNIS1 interaction. Additionally, we identified a compound that blocks MoNIS1-OsBAK1 interaction in vitro and inhibits the virulence of M. oryzae on rice. Collectively, we determined the first structure of NIS1 family effectors, presented the recognition mechanism of NIS1 by BAK1, and showed that blocking NIS1-BAK1 interaction could be a new target for fungicide development.
Collapse
Affiliation(s)
- Rui Han
- Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Tongtong Zhu
- Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhiwei Kong
- Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xin Zhang
- Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Dongli Wang
- Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Junfeng Liu
- State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
32
|
Adhish M, Manjubala I. Probing the effects of single point mutations in the GKWWRPS motif on the PNAIG motif within Loop 2 of sclerostin (SOST) using in-silico techniques. Comput Biol Chem 2024; 112:108173. [PMID: 39182248 DOI: 10.1016/j.compbiolchem.2024.108173] [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: 05/29/2024] [Revised: 08/06/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
Sclerostin (SOST), a Wnt signaling pathway inhibitor, is involved in the pathogenesis of skeletal disorders. This study investigated the impact of the GKWWRPS motif on the PNAIG motif in Loop 2 of SOST, which is accountable for the interactions with the LRP6 protein that triggers the down-regulation of the Wnt signaling pathway. Single amino acid mutations on the GKWWRPS motif, hypothesized to have a probable stabilization effect towards the PNAIG motif, led to a significant reduction in the primary interactions between the SOST and LRP6 proteins. Protein-protein docking and molecular dynamic studies were conducted to investigate the role of the motif. The study found that a solitary mutation in the GKWWRPS motif significantly reduced the primary interactions between SOST and LRP6 proteins, except for probable cold-spot residues. The study's findings establish the GKWWRPS motif as a promising target for therapeutic interventions. Based on the obtained results, it can be inferred that alterations implemented within the GKWWRPS motif could lead to the destabilization of the PNAIG motif, which would directly modulate the interactions between the SOST and LRP6 proteins. The present investigation thus presents novel opportunities in the field of anti-sclerostin interventions.
Collapse
Affiliation(s)
- Mazumder Adhish
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - I Manjubala
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
| |
Collapse
|
33
|
Chen S, De Zutter N, Meijer A, Gistelinck K, Wytynck P, Verbeke I, Osterne VJS, Kondeti S, De Meyer T, Audenaert K, Van Damme EJM. Overexpression of the ribosome-inactivating protein OsRIP1 modulates the jasmonate signaling pathway in rice. FRONTIERS IN PLANT SCIENCE 2024; 15:1385477. [PMID: 39206039 PMCID: PMC11349648 DOI: 10.3389/fpls.2024.1385477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 07/24/2024] [Indexed: 09/04/2024]
Abstract
Ribosome-inactivating proteins (RIPs) are plant enzymes that target the rRNA. The cytoplasmic RIP, called OsRIP1, plays a crucial role in regulating jasmonate, a key plant hormone. Understanding the role of OsRIP1 can provide insights into enhancing stress tolerance and optimizing growth of rice. Transcription profiling by mRNA sequencing was employed to measure the changes in gene expression in rice plants in response to MeJA treatment. Compared to wild type (WT) plants, OsRIP1 overexpressing rice plants showed a lower increase in mRNA transcripts for genes related to jasmonate responses when exposed to MeJA treatment for 3 h. After 24 h of MeJA exposure, the mRNA transcripts associated with the gibberellin pathway occurred in lower levels in OsRIP1 overexpressing plants compared to WT plants. We hypothesize that the mechanism underlying OsRIP1 antagonization of MeJA-induced shoot growth inhibition involves cytokinin-mediated leaf senescence and positive regulation of cell cycle processes, probably via OsRIP1 interaction with 40S ribosomal protein S5 and α-tubulin. Moreover, the photosystem II 10kDa polypeptide was identified to favorably bind to OsRIP1, and its involvement may be attributed to the reduction of photosynthesis in OsRIP1-overexpressing plants subjected to MeJA at the early timepoint (3 h).
Collapse
Affiliation(s)
- Simin Chen
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Noémie De Zutter
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Anikó Meijer
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Koen Gistelinck
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Pieter Wytynck
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Isabel Verbeke
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Vinicius J. S. Osterne
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Subramanyam Kondeti
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Tim De Meyer
- Department of Data Analysis & Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Els J. M. Van Damme
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| |
Collapse
|
34
|
Mittal S, Prajapati KP, Ansari M, Joshi K, Mishra N, Mahato OP, Anand BG, Kar K. Cu(II) Specifically Disassembles Insulin Amyloid Nanostructures via Direct Interaction with Cross-β Fibrils. NANO LETTERS 2024; 24:9784-9792. [PMID: 38990555 DOI: 10.1021/acs.nanolett.4c00113] [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: 07/12/2024]
Abstract
In this work, we demonstrate direct evidence of the antiamyloid potential of Cu(II) ions against amyloid formation of insulin. The Cu(II) ions were found to efficiently disassemble the preformed amyloid nanostructures into soluble species and suppress monomer fibrillation under aggregation-prone conditions. The direct interaction of Cu(II) ions with the cross-β structure of amyloid fibrils causes substantial disruption of both the interchain and intrachain interactions, predominantly the H-bonds and hydrophobic contacts. Further, the Cu(II) ions show a strong affinity for the aggregation-prone conformers of the protein and inhibit their spontaneous self-assembly. These results reveal the possible molecular mechanism for the antiamyloidogenic potential of Cu(II) which could be important for the development of metal-ion specific therapeutic strategies against amyloid linked complications.
Collapse
Affiliation(s)
- Shikha Mittal
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Kailash Prasad Prajapati
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Masihuzzaman Ansari
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Kajal Joshi
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Nishant Mishra
- Biomolecular Self-Assembly Lab, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Om Prakash Mahato
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Bibin Gnanadhason Anand
- Biomolecular Self-Assembly Lab, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Karunakar Kar
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
35
|
Seong K, Wei W, Vega B, Dee A, Ramirez-Bernardino G, Kumar R, Parra L, Krasileva K. Engineering the plant intracellular immune receptor Sr50 to restore recognition of the AvrSr50 escape mutant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.07.607039. [PMID: 39149390 PMCID: PMC11326300 DOI: 10.1101/2024.08.07.607039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Sr50, an intracellular nucleotide-binding leucine-rich repeat receptor (NLR), confers resistance of wheat against stem rust caused by the fungal pathogen Puccinia graminis f. sp. tritici. The receptor recognizes the pathogen effector AvrSr50 through its C-terminal leucine-rich repeat domain, initiating a localized cell death immune response. However, this immunity is compromised by mutations in the effector, as in the escape mutant AvrSr50QCMJC, which evades Sr50 detection. In this study, we employed iterative computational structural analyses and site-directed mutagenesis for rational engineering of Sr50 to gain recognition of AvrSr50QCMJC. Following an initial structural hypothesis driven by molecular docking, we identified the Sr50K711D single mutant, which induces an intermediate immune response against AvrSr50QCMJC without losing recognition against AvrSr50. Increasing gene expression with a stronger promoter enabled the mutant to elicit a robust response, indicating weak effector recognition can be complemented by enhanced receptor expression. Further structural refinements led to the creation of five double mutants and two triple mutants with dual recognition of AvrSr50 and AvrSr50QCMJC with greater immune response intensities than Sr50K711D against the escape mutant. All effective mutations against AvrSr50QCMJC required the K711D substitution, indicating that multiple solutions exist for gain of recognition, but the path to reach these mutations may be confined. Furthermore, this single substitution alters the prediction of AlphaFold 2, allowing it to model the complex structure of Sr50K711D and AvrSr50 that match our final structural hypothesis. Collectively, our study outlines a framework for rational engineering of NLR systems to overcome pathogen escape mutations and provides datasets for future computational models for NLR resurrection.
Collapse
Affiliation(s)
- Kyungyong Seong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Wei Wei
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Brandon Vega
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Amanda Dee
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | | | - Rakesh Kumar
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Lorena Parra
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Ksenia Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94704
| |
Collapse
|
36
|
Silverman I, Gerber M, Shaykevich A, Stein Y, Siegman A, Goel S, Maitra R. Structural modifications and kinetic effects of KRAS interactions with HRAS and NRAS: an in silico comparative analysis of KRAS mutants. Front Mol Biosci 2024; 11:1436976. [PMID: 39184150 PMCID: PMC11342451 DOI: 10.3389/fmolb.2024.1436976] [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: 05/22/2024] [Accepted: 06/25/2024] [Indexed: 08/27/2024] Open
Abstract
The RAS genes which code for KRAS, HRAS, and NRAS are three of the most frequently mutated oncogenes responsible for cancer deaths. Tumorigenesis is one of the most significant outcomes of deregulation of RAS GTPases. Although the structures have been extensively studied, there is still more to be discovered about the actual binding conformations of the three isoforms, especially when mutated, to design an inhibitory drug. Recent studies have identified important interactions between the three isoforms that affect the oncogenic strength of the others when they are mutated. In this study, we utilize molecular dynamics simulations to examine the modifications of the structural property, mechanism, and kinetic energy of KRAS when interacting individually and with HRAS and NRAS. Notably, we found that WT-KRAS' orientation when bound to WT-HRAS vs. WT-NRAS is rotated 180°, with mutants demonstrating a similar binding pattern. The binding sites of the isoforms with KRAS share similarities with those involved in the GDP/GTP active site and site of KRAS dimerization. Thus, the isoform interaction can serve as an inhibitory method of KRAS actions. This study advances the understanding of inhibiting RAS-driven cancers through a novel isoform interaction approach only recently discovered, which has been proven to be an effective alternate therapeutic approach. We developed a blueprint of the interaction which would be beneficial in the development of KRAS mutant-specific and pan-KRAS mutant inhibitory drugs that mimic the isoform interactions. Our results support the direct interaction inhibition mechanism of mutant KRAS when bound to WT-HRAS and WT-NRAS by the isoforms' hypervariable region binding to the G-domain of KRAS. Furthermore, our results support the approach of reducing the effects of oncogenic KRAS by altering the concentration of the isoforms or a drug alternative based on the overall structural and kinetic stability, as well as the binding strength of the mutant-isoform complexes.
Collapse
Affiliation(s)
- Isaac Silverman
- Department of Biology, Yeshiva University, New York, NY, United States
| | - Michael Gerber
- Department of Biology, Yeshiva University, New York, NY, United States
| | - Aaron Shaykevich
- Department of Biology, Yeshiva University, New York, NY, United States
| | - Yitzchak Stein
- Department of Biology, Yeshiva University, New York, NY, United States
| | - Alexander Siegman
- Department of Biology, Yeshiva University, New York, NY, United States
| | - Sanjay Goel
- Department of Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Radhashree Maitra
- Department of Biology, Yeshiva University, New York, NY, United States
| |
Collapse
|
37
|
Yang G, Ding C, Yang X, Jiang J, He S, Shao Y, Zhang E, Fan X, Zhou X, Huang L, Xinyu Zhang C, Sun J, Wang Y, Zang L, Zheng M, Ma J. NDRG1 enhances the sensitivity to Cetuximab by promoting Stat1 ubiquitylation in colorectal cancer. J Adv Res 2024:S2090-1232(24)00319-9. [PMID: 39128702 DOI: 10.1016/j.jare.2024.07.035] [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: 02/25/2024] [Revised: 05/16/2024] [Accepted: 07/29/2024] [Indexed: 08/13/2024] Open
Abstract
INTRODUCTION Cetuximab (CTX) is an effective targeted drug for the treatment of metastatic colorectal cancer, but it is effective only in patients with wild-type KRAS genes. Even in this subset of patients, the sensitivity of CTX in patients with right hemi-colon cancer is much lower than that in patients with left hemi-colon cancer. This significantly limits its clinical application. Therefore, further elucidation of the underlying molecular mechanisms is needed. N-myc downstream-regulated gene 1 (NDRG1) plays an important role in solid tumor invasion and metastasis, but whether it can influence CTX sensitivity has not been thoroughly investigated. OBJECTIVE Our study aimed to identify a novel mechanism by which NDRG1 affects CTX sensitivity. METHODS Through mass spectrometry analysis of our previously constructed CTX-resistant RKO and HCT116 cells, we found that the signal transducer and activator of transcription-1 (Stat1) might be a potential target of NDRG1. By knocking out NDRG1 or/and Stat1 genes, we then applied the loss-of-function experiments to explore the regulatory relationship between NDRG1 and Stat1 and their roles in the cell cycle, epithelial-mesenchymal transition (EMT), and the sensitivity to CTX in these two colorectal cancer (CRC) cells. Finally, we used the nude-mouse transplanted tumor model and human CRC samples to verify the expression of NDRG1 and Stat1 and their impact on CTX sensitivity in vivo. RESULTS Stat1 was upregulated in CTX-resistant cells, whereas NDRG1 was downregulated. Mechanically, NDRG1 was inversely correlated with Stat1 expression. It suppressed CRC cell proliferation, migration, and invasion, and promoted apoptosis and epithelial-mesenchymal transition (EMT) by inhibiting Stat1. In addition, NDRG1 directly interacted with Stat1 and promoted Smurf1-induced Stat1 ubiquitination. Importantly, this novel NDRG1-dependent regulatory loop also enhanced CTX sensitivity both in vitro and in vivo. CONCLUSION Our study revealed that NDRG1 enhanced the sensitivity to Cetuximab by inhibiting Stat1 expression and promoting its ubiquitination in colorectal cancer, elucidating NDRG1 might be a potential therapeutic target for refractory CTX-resistant CRC tumors. But its clinical value still needs to be validated in a larger sample size as well as a different genetic background.
Collapse
Affiliation(s)
- Guang Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chengsheng Ding
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiang Jiang
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shiyuan He
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanfei Shao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Enkui Zhang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaodong Fan
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xueliang Zhou
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ling Huang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cindy Xinyu Zhang
- Faculty of Science, University of Alberta, 1-560 Enterprise Square,10230 Jasper Avenue, Edmonton, Canada
| | - Jing Sun
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Wang
- Department of Gynecology and Obstetrics, Inner Mongolia Medical UniversityAffiliated Hospital, 1 Tongdao North Street, Hohhot, China.
| | - Lu Zang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Minhua Zheng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Junjun Ma
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
38
|
Baral J, Bhattacharje G, Dash S, Samanta D, Hinde E, Rouiller I, Das AK. In silico and in vitro characterization of the mycobacterial protein Ku to unravel its role in non-homologous end-joining DNA repair. Int J Biol Macromol 2024; 278:134584. [PMID: 39122073 DOI: 10.1016/j.ijbiomac.2024.134584] [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: 06/08/2023] [Revised: 06/06/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Non-homologous end-joining (NHEJ) stands as a pivotal DNA repair pathway crucial for the survival and persistence of Mycobacterium tuberculosis (Mtb) during its dormant, non-replicating phase, a key aspect of its long-term resilience. Mycobacterial NHEJ is a remarkably simple two-component system comprising the rate-limiting DNA binding protein Ku (mKu) and Ligase D. To elucidate mKu's role in NHEJ, we conducted a series of in silico and in vitro experiments. Molecular dynamics simulations and in vitro assays revealed that mKu's DNA binding stabilizes both the protein and DNA, while also shielding DNA ends from exonuclease degradation. Surface plasmon resonance (SPR) and electrophoretic mobility shift assays (EMSA) demonstrated mKu's robust affinity for linear double-stranded DNA (dsDNA), showing positive cooperativity for DNA substrates of 40 base pairs or longer, and its ability to slide along DNA strands. Moreover, analytical ultracentrifugation, size exclusion chromatography, and negative stain electron microscopy (EM) unveiled mKu's unique propensity to form higher-order oligomers exclusively with DNA, suggesting a potential role in mycobacterial NHEJ synapsis. This comprehensive characterization sheds new light on mKu's function within the Mtb NHEJ repair pathway. Targeting this pathway may thus impede the pathogen's ability to persist in its latent state within the host for prolonged periods.
Collapse
Affiliation(s)
- Joydeep Baral
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, India; School of Physics, University of Melbourne, Victoria, Australia; Department of Biochemistry and Pharmacology, University of Melbourne, Victoria, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia; ARC Centre for Cryo-electron Microscopy of Membrane Proteins, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Gourab Bhattacharje
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Sagarika Dash
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Dibyendu Samanta
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Elizabeth Hinde
- School of Physics, University of Melbourne, Victoria, Australia.
| | - Isabelle Rouiller
- Department of Biochemistry and Pharmacology, University of Melbourne, Victoria, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia; ARC Centre for Cryo-electron Microscopy of Membrane Proteins, The University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Amit Kumar Das
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, India.
| |
Collapse
|
39
|
Fatima T, Mubasher MM, Rehman HM, Niyazi S, Alanzi AR, Kalsoom M, Khalid S, Bashir H. Computational modeling study of IL-15-NGR peptide fusion protein: a targeted therapeutics for hepatocellular carcinoma. AMB Express 2024; 14:91. [PMID: 39133343 PMCID: PMC11319546 DOI: 10.1186/s13568-024-01747-8] [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: 05/30/2024] [Accepted: 07/25/2024] [Indexed: 08/13/2024] Open
Abstract
The primary challenge to improving existing cancer treatment is to develop drugs that specifically target tumor cell. NGR peptide is tumor homing peptide that selectively target cancer cells while interleukin 15 is a pleiotropic cytokine with anticancer properties. This study computationally engineered a IL15-NGR fusion peptide by linking the homing peptide NGR with the targeting peptide IL-15. After evaluating and validating the chimeric peptide, we docked it to the IL-15Rα/IL-15Rβ/γc heterodimer receptor, examining the interactions and binding energy and lastly, molecular dynamics simulations were performed. The secondary and tertiary structures, along with physicochemical properties of the designed IL-15-NGR chimeric protein, were predicted using GOR IV, trRosetta and ProtParam online servers respectively. The quality and 3D structure validation were confirmed via ProSA-web and SAVES 6.0 analysis which predicted an ERRAT score of 96.72%, with 97.6% of residues in the Ramachandran plot, validating its structure. Finally, Docking, MD simulations and interaction analysis were performed using ClusPro 2.0 and GROMACS and PDBsum, which exhibited significant hydrogen bonding and salt bridges, confirming the formation of a stable docked complex. These results were further corroborated by simulation analysis, which demonstrated a stable and dynamic behavior of the docked complex in a biological environment. The predicted high expression value of fusion protein was 0.844 in E.coli using SOLUPROT tool. These findings suggest efficient expression of the IL15-NGR fusion protein if its gene is inserted into E. coli and indicates its potential as a safe and effective anticancer treatment, paving the way for targeted therapeutic interventions.
Collapse
Affiliation(s)
- Tehreem Fatima
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, 87-West canal, Bank Road, Lahore, 53700, Pakistan
| | | | - Hafiz Muhammad Rehman
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, 87-West canal, Bank Road, Lahore, 53700, Pakistan.
- University Institute of Medical Lab Technology, Faculty of Allied health sciences, The University of Lahore, Lahore, 54590, Pakistan.
| | - Sakina Niyazi
- School of Biotechnology, IFTM University, Moradabad, 244102, India
| | - Abdullah R Alanzi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Maria Kalsoom
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, 87-West canal, Bank Road, Lahore, 53700, Pakistan
| | - Sania Khalid
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, 87-West canal, Bank Road, Lahore, 53700, Pakistan
| | - Hamid Bashir
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, 87-West canal, Bank Road, Lahore, 53700, Pakistan.
| |
Collapse
|
40
|
Wang K, Chen X, Lin P, Wu J, Huang Q, Chen Z, Tian J, Wang H, Tian Y, Shi M, Qian M, Hui B, Zhu Y, Li L, Yao R, Bian H, Zhu P, Chen R, Chen L. CD147-K148me2-Driven Tumor Cell-Macrophage Crosstalk Provokes NSCLC Immunosuppression via the CCL5/CCR5 Axis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400611. [PMID: 38873823 PMCID: PMC11304266 DOI: 10.1002/advs.202400611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/15/2024] [Indexed: 06/15/2024]
Abstract
Immunosuppression is a major hallmark of tumor progression in non-small cell lung cancer (NSCLC). Cluster of differentiation 147 (CD147), an important pro-tumorigenic factor, is closely linked to NSCLC immunosuppression. However, the role of CD147 di-methylation in the immunosuppressive tumor microenvironment (TME) remains unclear. Here, di-methylation of CD147 at Lys148 (CD147-K148me2) is identified as a common post-translational modification (PTM) in NSCLC that is significantly associated with unsatisfying survival outcomes among NSCLC sufferers, especially those in the advanced stages of the disease. The methyltransferase NSD2 catalyzes CD147 to generate CD147-K148me2. Further analysis demonstrates that CD147-K148me2 reestablishes the immunosuppressive TME and promotes NSCLC progression. Mechanistically, this modification promotes the interaction between cyclophilin A (CyPA) and CD147, and in turn, increases CCL5 gene transcription by activating p38-ZBTB32 signaling, leading to increased NSCLC cell-derived CCL5 secretion. Subsequently, CD147-K148me2-mediated CCL5 upregulation facilitates M2-like tumor-associated macrophage (TAM) infiltration in NSCLC tissues via CCL5/CCR5 axis-dependent intercellular crosstalk between tumor cells and macrophages, which is inhibited by blocking CD147-K148me2 with the targeted antibody 12C8. Overall, this study reveals the role of CD147-K148me2-driven intercellular crosstalk in the development of NSCLC immunosuppression, and provides a potential interventional strategy for PTM-targeted NSCLC therapy.
Collapse
Affiliation(s)
- Ke Wang
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Xiaohong Chen
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Peng Lin
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Jiao Wu
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Qiang Huang
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
- School of MedicineShanghai UniversityShanghai200444China
| | - Zhi‐Nan Chen
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Jiale Tian
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Hao Wang
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Ye Tian
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Mingyan Shi
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Meirui Qian
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Bengang Hui
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
- Department of Thoracic Surgery of Tangdu HospitalFourth Military Medical UniversityXi'an710038China
| | - Yumeng Zhu
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Ling Li
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Rui Yao
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Huijie Bian
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Ping Zhu
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Ruo Chen
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing HospitalFourth Military Medical UniversityXi'an710032China
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
| | - Liang Chen
- State Key Laboratory of New Targets Discovery and Drug Development for Major DiseasesChina
- School of MedicineShanghai UniversityShanghai200444China
| |
Collapse
|
41
|
Ahmed I, Muzammal M, Khan MA, Ullah H, Farid A, Yasin M, Khan J, Alam K, Mir A. Identification of Four Novel Candidate Genes for Non-syndromic Intellectual Disability in Pakistani Families. Biochem Genet 2024; 62:2571-2586. [PMID: 37985543 DOI: 10.1007/s10528-023-10556-w] [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: 07/03/2023] [Accepted: 10/21/2023] [Indexed: 11/22/2023]
Abstract
Intellectual disability, a genetically and clinically varied disorder and is a significant health problem, particularly in less developed countries due to larger family size and high ratio of consanguineous marriages. In the current genetic study, we investigate and find the novel disease causative factors in the four Pakistani families with severe type of non-syndromic intellectual disability. For genetic analysis whole-exome sequencing (WES) and Sanger sequencing was performed. I-TASSER and Cluspro tools were used for Protein modeling and Protein-protein docking. Sanger sequencing confirms the segregation of novel homozygous variants in all the families i.e., c.245 T > C; p.Leu82Pro in SLC50A1 gene in family 1, missense variant c.1037G > A; p.Arg346His in TARS2 gene in family 2, in family 3 and 4, nonsense mutation c.234G > A; p.Trp78Term and missense mutation c.2200G > A; p.Asp734Asn in TBC1D3 and ANAPC2 gene, respectively. In silico functional studies have found the drastic effect of these mutations on protein structure and its interaction properties. Substituted amino acids were highly conserved and present on highly conserved region throughout the species. The discovery of pathogenic variants in SLC50A1, TARS2, TBC1D1 and ANAPC2 shows that the specific pathways connected with these genes may be important in cognitive impairment. The decisive role of pathogenic variants in these genes cannot be determined with certainty due to lack of functional data. However, exome sequencing and segregation analysis of all filtered variants revealed that the currently reported variants were the only variations from the respective families that segregated with the phenotype in the family.
Collapse
Affiliation(s)
- Iftikhar Ahmed
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, 29050, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Muzammal
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, 29050, Khyber Pakhtunkhwa, Pakistan
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, 29050, Khyber Pakhtunkhwa, Pakistan
| | - Hafiz Ullah
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, 29050, Khyber Pakhtunkhwa, Pakistan
| | - Arshad Farid
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, 29050, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Yasin
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, 29050, Khyber Pakhtunkhwa, Pakistan
| | - Jabbar Khan
- Institue of Biological Science, Gomal University, Dera Ismail Khan, 29050, Khyber Pakhtunkhwa, Pakistan
| | - Khurshid Alam
- Departement of Clinical Pharmacy, School Pf Pharmaceutical Sciences, Univesiti Sains Malaysia (USM), 11800, Gelugor, Penang, Malaysia
| | - Asif Mir
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan.
| |
Collapse
|
42
|
Ogire E, Perrin-Cocon L, Figl M, Kundlacz C, Jacquemin C, Hubert S, Aublin-Gex A, Toesca J, Ramière C, Vidalain PO, Mathieu C, Lotteau V, Diaz O. Dengue Virus dependence on glucokinase activity and glycolysis Confers Sensitivity to NAD(H) biosynthesis inhibitors. Antiviral Res 2024; 228:105939. [PMID: 38909960 DOI: 10.1016/j.antiviral.2024.105939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/20/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Abstract
Viruses have developed sophisticated strategies to control metabolic activity of infected cells in order to supply replication machinery with energy and metabolites. Dengue virus (DENV), a mosquito-borne flavivirus responsible for dengue fever, is no exception. Previous reports have documented DENV interactions with metabolic pathways and shown in particular that glycolysis is increased in DENV-infected cells. However, underlying molecular mechanisms are still poorly characterized and dependence of DENV on this pathway has not been investigated in details yet. Here, we identified an interaction between the non-structural protein 3 (NS3) of DENV and glucokinase regulator protein (GCKR), a host protein that inhibits the liver-specific hexokinase GCK. NS3 expression was found to increase glucose consumption and lactate secretion in hepatic cell line expressing GCK. Interestingly, we observed that GCKR interaction with GCK decreases DENV replication, indicating the dependence of DENV to GCK activity and supporting the role of NS3 as an inhibitor of GCKR function. Accordingly, in the same cells, DENV replication both induces and depends on glycolysis. By targeting NAD(H) biosynthesis with the antimetabolite 6-Amino-Nicotinamide (6-AN), we decreased cellular glycolytic activity and inhibited DENV replication in hepatic cells. Infection of primary organotypic liver cultures (OLiC) from hamsters was also inhibited by 6-AN. Altogether, our results show that DENV has evolved strategies to control glycolysis in the liver, which could account for hepatic dysfunctions associated to infection. Besides, our findings suggest that lowering intracellular availability of NAD(H) could be a valuable therapeutic strategy to control glycolysis and inhibit DENV replication in the liver.
Collapse
Affiliation(s)
- Eva Ogire
- CIRI, Centre International de Recherche en Infectiologie, NeuroInvasion TROpism and VIRal Encephalitis Team, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, F-69007, Lyon, France
| | - Laure Perrin-Cocon
- CIRI, Centre International de Recherche en Infectiologie, VIRal Infection Metabolism and Immunity Team, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, F-69007, Lyon, France
| | - Marianne Figl
- CIRI, Centre International de Recherche en Infectiologie, VIRal Infection Metabolism and Immunity Team, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, F-69007, Lyon, France
| | - Cindy Kundlacz
- CIRI, Centre International de Recherche en Infectiologie, VIRal Infection Metabolism and Immunity Team, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, F-69007, Lyon, France
| | - Clémence Jacquemin
- CIRI, Centre International de Recherche en Infectiologie, VIRal Infection Metabolism and Immunity Team, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, F-69007, Lyon, France
| | - Sophie Hubert
- CIRI, Centre International de Recherche en Infectiologie, VIRal Infection Metabolism and Immunity Team, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, F-69007, Lyon, France
| | - Anne Aublin-Gex
- CIRI, Centre International de Recherche en Infectiologie, VIRal Infection Metabolism and Immunity Team, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, F-69007, Lyon, France
| | - Johan Toesca
- CIRI, Centre International de Recherche en Infectiologie, VIRal Infection Metabolism and Immunity Team, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, F-69007, Lyon, France
| | - Christophe Ramière
- CIRI, Centre International de Recherche en Infectiologie, VIRal Infection Metabolism and Immunity Team, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, F-69007, Lyon, France; Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Pierre-Olivier Vidalain
- CIRI, Centre International de Recherche en Infectiologie, VIRal Infection Metabolism and Immunity Team, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, F-69007, Lyon, France
| | - Cyrille Mathieu
- CIRI, Centre International de Recherche en Infectiologie, NeuroInvasion TROpism and VIRal Encephalitis Team, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, F-69007, Lyon, France
| | - Vincent Lotteau
- CIRI, Centre International de Recherche en Infectiologie, VIRal Infection Metabolism and Immunity Team, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, F-69007, Lyon, France; Laboratoire P4-Jean Mérieux, INSERM, Lyon, France
| | - Olivier Diaz
- CIRI, Centre International de Recherche en Infectiologie, VIRal Infection Metabolism and Immunity Team, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, F-69007, Lyon, France.
| |
Collapse
|
43
|
Mashhadi Kholerdi A, Moradian F, Mehralitabar H. In vitro study of the expression of autophagy genes ATG101, mTOR and AMPK in breast cancer with treatment of lactoferrin and in silico study of their communication networks and protein interactions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 190:19-27. [PMID: 38782098 DOI: 10.1016/j.pbiomolbio.2024.05.003] [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: 12/20/2023] [Revised: 04/20/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Autophagy is a new window of science that has been noticed due to the importance of specific therapies in cancer. In this study, the effect of lactoferrin (Lf) on the expression level of ATG101, mTOR and AMPK genes in breast cancer cell line MCF7, as well as the interaction between lactoferrin protein and their protein were investigated. The expression level of the genes was measured using a real-time PCR method. PDB, UniProt, KEGG, and STRING databases and ClusPro webserver and PyMol software were used in silico study. The results showed that the expression level of the ATG101 gene in treatment with concentrations of 100, 400, 600, and 800 μg/ml Lf decreased by 0.05, 0.13, 0.54 and 0.77, respectively. The expression level of the mTOR gene in treatment with concentrations of 100, 400, 600, and 800 μg/ml Lf decreased by 0.07, 0.05, 0.13, and 0.49 times respectively. The level of the AMPK gene expression in treatment with concentrations of 100, 400, 600, and 800 μg/ml Lf decreased by 0.05, 0.01, 0.06, and 0.03, respectively. Virtualization of the interaction of Lf protein with ATG101, mTOR and AMPK proteins by Pymol software showed that the N lobe region of Lf interacted with the HORMA domain of ATG101 protein, the fat domain of mTOR protein, and the CTD domain of AMPK protein. Although Lf was not able to increase the expression of autophagy-inducing genes, it may be able to induce autophagy through protein interaction by activating or inhibiting proteins related to autophagy regulation.
Collapse
Affiliation(s)
- Atefeh Mashhadi Kholerdi
- Department of Basic Sciences, Sari Agricultural Sciences and Natural Resources University, Sari, Mazandaran, Iran
| | - Fatemeh Moradian
- Department of Basic Sciences, Sari Agricultural Sciences and Natural Resources University, Sari, Mazandaran, Iran.
| | | |
Collapse
|
44
|
Aiman S, Ali Y, Malik A, Alkholief M, Ahmad A, Akhtar S, Ali S, Khan A, Li C, Shams S. Immunoinformatic-guided novel mRNA vaccine designing to elicit immunogenic responses against the endemic Monkeypox virus. J Biomol Struct Dyn 2024; 42:6292-6306. [PMID: 37424185 DOI: 10.1080/07391102.2023.2233627] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
Monkeypox virus (MPXV) is an orthopoxvirus, causing zoonotic infections in humans with smallpox-like symptoms. The WHO reported MPXV cases in May 2022 and the outbreak caused significant morbidity threats to immunocompromised individuals and children. Currently, no clinically validated therapies are available against MPXV infections. The present study is based on immunoinformatics approaches to design mRNA-based novel vaccine models against MPXV. Three proteins were prioritized based on high antigenicity, low allergenicity, and toxicity values to predict T- and B-cell epitopes. Lead T- and B-cell epitopes were used to design vaccine constructs, linked with epitope-specific linkers and adjuvant to enhance immune responses. Additional sequences, including Kozak sequence, MITD sequence, tPA sequence, Goblin 5', 3' UTRs, and a poly(A) tail were added to design stable and highly immunogenic mRNA vaccine construct. High-quality structures were predicted by molecular modeling and 3D-structural validation of the vaccine construct. Population coverage and epitope-conservancy speculated broader protection of designed vaccine model against multiple MPXV infectious strains. MPXV-V4 was eventually prioritized based on its physicochemical and immunological parameters and docking scores. Molecular dynamics and immune simulations analyses predicted significant structural stability and binding affinity of the top-ranked vaccine model with immune receptors to elicit cellular and humoral immunogenic responses against the MPXV. The pursuance of experimental and clinical follow-up of these prioritized constructs may lay the groundwork to develop safe and effective vaccine against MPXV.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Yasir Ali
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Musaed Alkholief
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abbas Ahmad
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Suhail Akhtar
- A.T. Still University of Health Sciences, Kirksville, MO, USA
| | - Sajid Ali
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| |
Collapse
|
45
|
Cho Y, Sukhan ZP, Lee WK, Kho KH. Structural and functional characterization of Hdh-HSBP1 and its involvement in heat stress and early development in Pacific abalone, Haliotis discus hannai. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109660. [PMID: 38830519 DOI: 10.1016/j.fsi.2024.109660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/05/2024]
Abstract
Heat shock factor binding protein 1 (HSBP1) is known to regulate the activity of heat shock factor 1 (HSF1) and the early development of organisms. To understand the involvement of HSBP1 in the heat shock response and embryonic and larval development of Pacific abalone (Haliotis discus hannai), the Hdh-HSBP1 gene was sequenced from the digestive gland (DG) tissue. The full-length sequence of Hdh-HSBP1 encompassed 738 nucleotides, encoding an 8.42 kDa protein consisting of 75 deduced amino acids. The protein contains an HSBP1 domain and a coiled-coil domain, which are conserved features in the HSBP1 protein family. Protein-protein molecular docking revealed that the coiled-coil region of Hdh-HSBP1 binds to the coiled-coil region of Hdh-HSF1. Tissue expression analysis demonstrated that the highest Hdh-HSBP1 expression occurred in the DG, whereas seasonal expression analysis revealed that this gene was most highly expressed in summer. In heat-stressed abalone, the highest expression of Hdh-HSBP1 occurred at 30 °C. Moreover, time-series analysis revealed that the expression of this gene began to increase significantly at 6 h post-heat stress, with higher expression observed at 12 h and 24 h post-heat stress. Furthermore, Hdh-HSBP1 mRNA expression showed a link to ROS production. Additionally, the expression of Hdh-HSBP1 showed significantly higher expression in the early stages of embryonic development in Pacific abalone. These results suggest that Hdh-HSBP1 plays a crucial role in the stress physiology of Pacific abalone by interacting with Hdh-HSF1, as well as its embryonic development.
Collapse
Affiliation(s)
- Yusin Cho
- Department of Fisheries Science, Chonnam National University, Yeosu, South Korea
| | - Zahid Parvez Sukhan
- Department of Fisheries Science, Chonnam National University, Yeosu, South Korea
| | - Won-Kyo Lee
- Department of Fisheries Science, Chonnam National University, Yeosu, South Korea
| | - Kang Hee Kho
- Department of Fisheries Science, Chonnam National University, Yeosu, South Korea.
| |
Collapse
|
46
|
Darawshi O, Yassin O, Shmuel M, Wek RC, Mahdizadeh SJ, Eriksson LA, Hatzoglou M, Tirosh B. Phosphorylation of GCN2 by mTOR confers adaptation to conditions of hyper-mTOR activation under stress. J Biol Chem 2024; 300:107575. [PMID: 39013537 PMCID: PMC11362803 DOI: 10.1016/j.jbc.2024.107575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/18/2024] Open
Abstract
Adaptation to the shortage in free amino acids (AA) is mediated by 2 pathways, the integrated stress response (ISR) and the mechanistic target of rapamycin (mTOR). In response to reduced levels, primarily of leucine or arginine, mTOR in its complex 1 configuration (mTORC1) is suppressed leading to a decrease in translation initiation and elongation. The eIF2α kinase general control nonderepressible 2 (GCN2) is activated by uncharged tRNAs, leading to induction of the ISR in response to a broader range of AA shortage. ISR confers a reduced translation initiation, while promoting the selective synthesis of stress proteins, such as ATF4. To efficiently adapt to AA starvation, the 2 pathways are cross-regulated at multiple levels. Here we identified a new mechanism of ISR/mTORC1 crosstalk that optimizes survival under AA starvation, when mTORC1 is forced to remain active. mTORC1 activation during acute AA shortage, augmented ATF4 expression in a GCN2-dependent manner. Under these conditions, enhanced GCN2 activity was not dependent on tRNA sensing, inferring a different activation mechanism. We identified a labile physical interaction between GCN2 and mTOR that results in a phosphorylation of GCN2 on serine 230 by mTOR, which promotes GCN2 activity. When examined under prolonged AA starvation, GCN2 phosphorylation by mTOR promoted survival. Our data unveils an adaptive mechanism to AA starvation, when mTORC1 evades inhibition.
Collapse
Affiliation(s)
- Odai Darawshi
- The School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Olaya Yassin
- The School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Miri Shmuel
- The School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - S Jalil Mahdizadeh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Boaz Tirosh
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, USA.
| |
Collapse
|
47
|
Araujo-Abad S, Rizzuti B, Soto-Conde L, Vidal M, Abian O, Velazquez-Campoy A, Neira JL, de Juan Romero C. Citrullinating enzyme PADI4 and transcriptional repressor RING1B bind in cancer cells. Int J Biol Macromol 2024; 274:133163. [PMID: 38878927 DOI: 10.1016/j.ijbiomac.2024.133163] [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: 04/23/2024] [Revised: 05/26/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024]
Abstract
Polycomb groups (PcGs) are transcriptional repressors, formed by a complex of several proteins, involved in multicellular development and cancer epigenetics. One of these proteins is the E3 ubiquitin-protein ligase RING1 (or RING1B), associated with the regulation of transcriptional repression and responsible for monoubiquitylation of the histone H2A. On the other hand, PADI4 is one of the human isoforms of a family of enzymes implicated in the conversion of arginine to citrulline, and it is also involved in the development of glioblastoma, among other types of cancers. In this work, we showed the association of PADI4 and RING1B in the nucleus and cytosol in several cancer cell lines by using immunofluorescence and proximity ligation assays. Furthermore, we demonstrated that binding was hampered in the presence of GSK484, an enzymatic PADI4 inhibitor, suggesting that RING1B could bind to the active site of PADI4, as confirmed by protein-protein docking simulations. In vitro and in silico findings showed that binding to PADI4 occurred for the isolated fragments corresponding to both the N-terminal (residues 1-221) and C-terminal (residues 228-336) regions of RING1B. Binding to PADI4 was also hampered by GSK484, as shown by isothermal titration calorimetry (ITC) experiments for the sole N-terminal region, and by both NMR and ITC for the C-terminal one. The dissociation constants between PADI4 and any of the two isolated RING1B fragments were in the low micromolar range (~2-10 μM), as measured by fluorescence and ITC. The interaction between RING1B and PADI4 might imply citrullination of the former, leading to several biological consequences, as well as being of potential therapeutic relevance for improving cancer treatment with the generation of new antigens.
Collapse
Affiliation(s)
- Salome Araujo-Abad
- Cancer Research Group, Faculty of Engineering and Applied Sciences, Universidad de Las Américas, 170124 Quito, Ecuador; IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain.
| | - Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy; Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | | | - Miguel Vidal
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Calle Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche (Alicante), Spain.
| |
Collapse
|
48
|
Koçkaya ES, Can H, Yaman Y, Kandemir Ç, Taşkın T, Karakavuk M, Değirmenci Döşkaya A, Döşkaya M, Pehlivan E, Şireli HD, Gürüz AY, Ün C. Newly developed peptide-ELISA successfully detected anti-IgG antibodies against Maedi-Visna virus in sheep. Vet Immunol Immunopathol 2024; 274:110806. [PMID: 39002364 DOI: 10.1016/j.vetimm.2024.110806] [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: 05/06/2024] [Revised: 06/13/2024] [Accepted: 07/05/2024] [Indexed: 07/15/2024]
Abstract
Maedi Visna Virus (MVV) is a retrovirus that can infect sheep. There is still no effective therapy or vaccine against this virus and timely diagnosis is important to combat the complications of the disease. In this study, we aimed to develop an ELISA using peptides derived from gag protein as antigen. For this purpose, B cell epitopes of gag protein were predicted and a docking analysis with the B cell receptor was performed to select peptides to be used in ELISA. After three soluble epitopes with the highest antigenicity were produced as peptides, the immunogenicity of each peptide was determined by ELISA using sheep serum samples categorized as MVV positive (n=24) and negative (n=13). Subsequently, in house ELISA using above mentioned immunogenic peptides as antigen was used to investigate MVV seroprevalence in sheep (n=88). According to the results, among three peptides, two of them strongly reacted with MVV positive serum samples and the mean absorbance values detected among positive and negative serum samples were statistically significant, indicating that these peptides were immunogenic (P=0.016 and P=0.038). The third peptide also reacted with positive serum samples but the mean absorbance value was not statistically significant and this peptide was considered non-immunogenic (P=0.175). The immunogenic two peptides showed the same high sensitivity and specificity values of 91.60 and 92.80 according to the commercial kit. Moreover, MVV seroprevalence detected by peptide-ELISAs using CKQGSKE and CRPQGKAGHKG peptides as antigen was 3.40 % and 4.5 %, respectively. As a result, it was shown that these peptides can be successfully used for serological diagnosis of MVV.
Collapse
Affiliation(s)
- Ecem Su Koçkaya
- Ege University Faculty of Science Department of Biology Molecular Biology Section, İzmir, Türkiye
| | - Hüseyin Can
- Ege University Faculty of Science Department of Biology Molecular Biology Section, İzmir, Türkiye; Ege University Vaccine Development Application and Research Center, İzmir, Türkiye.
| | - Yalçın Yaman
- Siirt University Faculty of Veterinary Medicine, Department of Genetics, Siirt, Türkiye
| | - Çağrı Kandemir
- Ege University Faculty of Agriculture, Department of Animal Science, İzmir, Türkiye
| | - Turgay Taşkın
- Ege University Faculty of Agriculture, Department of Animal Science, İzmir, Türkiye
| | - Muhammet Karakavuk
- Ege University Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University Ödemiş Vocational School, İzmir, Türkiye
| | - Aysu Değirmenci Döşkaya
- Ege University Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University Faculty of Medicine, Department of Parasitology, İzmir, Türkiye
| | - Mert Döşkaya
- Ege University Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University Faculty of Medicine, Department of Parasitology, İzmir, Türkiye
| | - Erkan Pehlivan
- Ankara University Faculty of Agriculture, Department of Animal Science, Ankara, Türkiye
| | - Halit Deniz Şireli
- Dicle University Faculty of Agriculture, Department of Animal Science, Diyarbakır, Türkiye
| | - Adnan Yüksel Gürüz
- Ege University Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University Faculty of Medicine, Department of Parasitology, İzmir, Türkiye
| | - Cemal Ün
- Ege University Faculty of Science Department of Biology Molecular Biology Section, İzmir, Türkiye; Ege University Vaccine Development Application and Research Center, İzmir, Türkiye
| |
Collapse
|
49
|
Moqbel Hassan Alzubaydi N, Oun Ali Z, Al-Asadi S, Al-Kahachi R. Design and characterization of a multi-epitope vaccine targeting Chlamydia abortus using immunoinformatics approach. J Biomol Struct Dyn 2024; 42:6660-6677. [PMID: 37774751 DOI: 10.1080/07391102.2023.2240891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/06/2023] [Indexed: 10/01/2023]
Abstract
Chlamydiosis is a widespread ailment affecting humans, livestock, and wildlife, caused by C. abortus, a member of the Chlamydia genus. This disease leads to reproductive disorders in bovines and poses a zoonotic risk, resulting in adverse outcomes such as abortion, stillbirths, weak offspring, endometritis, repeat breeding, and perinatal mortality. However, current chlamydiosis vaccines have limitations in terms of safety, efficacy, and stability, necessitating the development of effective and safe alternatives. In this study, our objective was to design a multi-epitope vaccine (MEV) targeting all strains of C. abortus using bioinformatics and immunoinformatics approaches. We identified highly antigenic and non-allergic proteins (yidC, yajC, secY, CAB503, and CAB746) using VaxiJen and AlgPred tools. Physicochemical analyses and secondary structure predictions confirmed protein stability through ProtParam and SOPMA methods. Furthermore, we employed IEDB-AR, NETMHCpan, and ToxinPred2 tools to predict cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B-cell epitopes, resulting in the identification of conserved epitopes for further analysis. The MEV construct, consisting of 545 amino acids, incorporated the adjuvant Beta defensin-3, along with 9 CTL epitopes and 21 HTL epitopes linked by EAAAK, KK, and AAY linkers. We assessed the safety and immunogenicity of the vaccine through comprehensive evaluations of antigenicity, toxicity, allergenicity, and physicochemical properties. Structural stability and quality were examined using 3D modeling via the ab initio approach with the Robetta platform. Molecular docking analysis explored the compatibility of the MEV with Toll-like receptor 9 (TLR9) using ClusPro, while molecular dynamics simulation with the DESMOND Maestro software predicted the stability and flexibility of the docked complex. Despite promising in silico findings, further wet lab investigations are crucial to validate the safety and efficacy of the MEV. Successful development and validation of this MEV hold significant potential in combatting chlamydiosis in both animal and human populations.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Zainab Oun Ali
- Department of Radiology Techniques, College of Health and Medical Techniques, Middle Technical University, Baghdad, Iraq
| | - Sura Al-Asadi
- Department of Laboratory Techniques, College of Health and Medical Techniques, Middle Technical University, Baghdad, Iraq
| | - Rusul Al-Kahachi
- Department of Scholarships and Cultural Relationship, Republic of Iraq Ministry of Higher Education and Scientific Research, Baghdad, Iraq
| |
Collapse
|
50
|
Zhou Y, Kang L, Xu R, Zhao D, Wang J, Wu J, Lin H, Ding Z, Zou Y. Mitochondrial outer membrane protein Samm50 protects against hypoxia-induced cardiac injury by interacting with Shmt2. Cell Signal 2024; 120:111219. [PMID: 38723737 DOI: 10.1016/j.cellsig.2024.111219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Cardiac remodeling is a critical process following myocardial infarction (MI), potentially leading to heart failure if untreated. The significance of mitochondrial homeostasis in MI remains insufficiently understood. Samm50 is an essential component of mitochondria. Our study aimed to investigate its role in hypoxia-induced cardiac injury and the underlying mechanisms. First, we observed that Samm50 was dynamically downregulated in mice with MI compared to the control mice. In vitro, Samm50 was also downregulated in oxygen-glucose-deprived neonatal rat cardiomyocytes and fibroblasts. Overexpression and knockdown of Samm50 mitigated and exacerbated cardiac apoptosis and fibrosis, while also improving and worsening mitochondrial homeostasis, respectively. Protein interactions with Samm50 during the protective process were identified via immune-coprecipitation/mass spectroscopy. Mechanistically, serine hydroxymethyltransferase 2 (Shmt2) interacted with Samm50, acting as a crucial element in the protective process by hindering the transfer of Bax from the cytoplasm to the mitochondria and subsequent activation of caspase-3. Inhibition of Shmt2 diminished the protective effect of Samm50 overexpression against cardiac injury. Finally, Samm50 overexpression in vivo mitigated cardiac remodeling and enhanced cardiac function in both acute and chronic MI. In conclusion, Samm50 overexpression mitigated hypoxia-induced cardiac remodeling by inhibiting apoptosis and fibrosis, with Shmt2 acting as a key regulator in this protective process. The Samm50/Shmt2 axis represents a newly discovered mitochondria-related pathway for mitigating hypoxia-induced cardiac injury.
Collapse
Affiliation(s)
- Yufei Zhou
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Le Kang
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ran Xu
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Di Zhao
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jienan Wang
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiaying Wu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Hong Lin
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhiwen Ding
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
| | - Yunzeng Zou
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| |
Collapse
|