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Chen Q, Nie X, Huang W, Wang C, Lai R, Lu Q, He Q, Yu X. Unlocking the potential of chicken liver byproducts: Identification of antioxidant peptides through in silico approaches and anti-aging effects of a selected peptide in Caenorhabditis elegans. Int J Biol Macromol 2024; 272:132833. [PMID: 38834112 DOI: 10.1016/j.ijbiomac.2024.132833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/28/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024]
Abstract
Chicken meat processing generates a substantial number of byproducts, which are either underutilized or improperly disposed. In this study, we employed in silico approaches to identify antioxidant peptides in chicken liver byproducts. Notably, the peptide WYR exhibited remarkable 2,2-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) radical scavenging activity with an IC50 of 0.13 ± 0.01 mg/mL and demonstrated stability under various conditions, including thermal, pH, NaCl, and simulated gastrointestinal digestion. Molecular docking analysis revealed significant hydrogen bonding interactions, while molecular dynamics showed differential stability with ABTS and 2,2-Diphenyl-1-picrylhydrazyl (DPPH). WYR exhibited improved stress resistance, decreased levels of reactive oxygen species (ROS), elevated the activities of superoxide dismutase (SOD) and catalase (CAT), and modulated the expression of crucial genes through the insulin/insulin-like growth factor (IIS) signaling pathway, mitogen-activated protein kinase (MAPK), and heat shock transcription factor-1 (HSF-1) pathways. These effects collectively contributed to the extension of Caenorhabditis elegans' lifespan. This study not only provides an effective method for antioxidant peptide analysis but also highlights the potential for enhancing the utilization of poultry byproducts.
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Affiliation(s)
- Qianzi Chen
- Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Xuekui Nie
- Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Wangxiang Huang
- Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Chen Wang
- Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Ren Lai
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, China
| | - Qiumin Lu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, China
| | - Qiyi He
- Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Science, Chongqing Normal University, Chongqing 401331, China.
| | - Xiaodong Yu
- Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Science, Chongqing Normal University, Chongqing 401331, China.
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Rahman S, Chiou CC, Ahmad S, Islam ZU, Tanaka T, Alouffi A, Chen CC, Almutairi MM, Ali A. Subtractive Proteomics and Reverse-Vaccinology Approaches for Novel Drug Target Identification and Chimeric Vaccine Development against Bartonella henselae Strain Houston-1. Bioengineering (Basel) 2024; 11:505. [PMID: 38790371 PMCID: PMC11118080 DOI: 10.3390/bioengineering11050505] [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: 04/09/2024] [Revised: 05/03/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Bartonella henselae is a Gram-negative bacterium causing a variety of clinical symptoms, ranging from cat-scratch disease to severe systemic infections, and it is primarily transmitted by infected fleas. Its status as an emerging zoonotic pathogen and its capacity to persist within host erythrocytes and endothelial cells emphasize its clinical significance. Despite progress in understanding its pathogenesis, limited knowledge exists about the virulence factors and regulatory mechanisms specific to the B. henselae strain Houston-1. Exploring these aspects is crucial for targeted therapeutic strategies against this versatile pathogen. Using reverse-vaccinology-based subtractive proteomics, this research aimed to identify the most antigenic proteins for formulating a multi-epitope vaccine against the B. henselae strain Houston-1. One crucial virulent and antigenic protein, the PAS domain-containing sensor histidine kinase protein, was identified. Subsequently, the identification of B-cell and T-cell epitopes for the specified protein was carried out and the evaluated epitopes were checked for their antigenicity, allergenicity, solubility, MHC binding capability, and toxicity. The filtered epitopes were merged using linkers and an adjuvant to create a multi-epitope vaccine construct. The structure was then refined, with 92.3% of amino acids falling within the allowed regions. Docking of the human receptor (TLR4) with the vaccine construct was performed and demonstrated a binding energy of -1047.2 Kcal/mol with more interactions. Molecular dynamic simulations confirmed the stability of this docked complex, emphasizing the conformation and interactions between the molecules. Further experimental validation is necessary to evaluate its effectiveness against B. henselae.
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Affiliation(s)
- Sudais Rahman
- Department of Zoology, Abdul Wali Khan University, Mardan 23200, Khyber Pakhtunkhwa, Pakistan;
| | - Chien-Chun Chiou
- Department of Dermatology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 600, Taiwan;
| | - Shabir Ahmad
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, Brazil;
| | - Zia Ul Islam
- Department of Biotechnology, Abdul Wali Khan University, Mardan 23200, Khyber Pakhtunkhwa, Pakistan
| | - Tetsuya Tanaka
- Laboratory of Infectious Diseases, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
| | - Abdulaziz Alouffi
- King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia
| | - Chien-Chin Chen
- Department of Pathology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 600, Taiwan
- Department of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan 717, Taiwan
- Ph.D. Program in Translational Medicine, Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Mashal M. Almutairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Abid Ali
- Department of Zoology, Abdul Wali Khan University, Mardan 23200, Khyber Pakhtunkhwa, Pakistan;
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Ghaffar SA, Tahir H, Muhammad S, Shahid M, Naqqash T, Faisal M, Albekairi TH, Alshammari A, Albekairi NA, Manzoor I. Designing of a multi-epitopes based vaccine against Haemophilius parainfluenzae and its validation through integrated computational approaches. Front Immunol 2024; 15:1380732. [PMID: 38690283 PMCID: PMC11058264 DOI: 10.3389/fimmu.2024.1380732] [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: 02/02/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
Haemophilus parainfluenzae is a Gram-negative opportunist pathogen within the mucus of the nose and mouth without significant symptoms and has an ability to cause various infections ranging from ear, eye, and sinus to pneumonia. A concerning development is the increasing resistance of H. parainfluenzae to beta-lactam antibiotics, with the potential to cause dental infections or abscesses. The principal objective of this investigation is to utilize bioinformatics and immuno-informatic methodologies in the development of a candidate multi-epitope Vaccine. The investigation focuses on identifying potential epitopes for both B cells (B lymphocytes) and T cells (helper T lymphocytes and cytotoxic T lymphocytes) based on high non-toxic and non-allergenic characteristics. The selection process involves identifying human leukocyte antigen alleles demonstrating strong associations with recognized antigenic and overlapping epitopes. Notably, the chosen alleles aim to provide coverage for 90% of the global population. Multi-epitope constructs were designed by using suitable linker sequences. To enhance the immunological potential, an adjuvant sequence was incorporated using the EAAAK linker. The final vaccine construct, comprising 344 amino acids, was achieved after the addition of adjuvants and linkers. This multi-epitope Vaccine demonstrates notable antigenicity and possesses favorable physiochemical characteristics. The three-dimensional conformation underwent modeling and refinement, validated through in-silico methods. Additionally, a protein-protein molecular docking analysis was conducted to predict effective binding poses between the multi-epitope Vaccine and the Toll-like receptor 4 protein. The Molecular Dynamics (MD) investigation of the docked TLR4-vaccine complex demonstrated consistent stability over the simulation period, primarily attributed to electrostatic energy. The docked complex displayed minimal deformation and enhanced rigidity in the motion of residues during the dynamic simulation. Furthermore, codon translational optimization and computational cloning was performed to ensure the reliability and proper expression of the multi-Epitope Vaccine. It is crucial to emphasize that despite these computational validations, experimental research in the laboratory is imperative to demonstrate the immunogenicity and protective efficacy of the developed vaccine. This would involve practical assessments to ascertain the real-world effectiveness of the multi-epitope Vaccine.
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Affiliation(s)
- Sana Abdul Ghaffar
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Haneen Tahir
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Sher Muhammad
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Tahir Naqqash
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | | | - Thamer H. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Norah A. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Irfan Manzoor
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
- Department of Biology, Indiana University, Bloomington, IN, United States
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Jamil F, Aslam L, Ali H, Shoukat K, Rasheed MA, Raza S, Ibrahim M. An In silico study of derivative of Newcastle disease virus epitopes based vaccine against Hemagglutunin neuraminidase protein. J Anim Sci 2022; 101:skac375. [PMID: 36371806 PMCID: PMC9883717 DOI: 10.1093/jas/skac375] [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: 07/26/2022] [Accepted: 11/11/2022] [Indexed: 11/14/2022] Open
Abstract
The causative agent of Newcastle disease (ND) is Newcastle disease virus. It belongs to avian species of Orthoavulavirus, Avulavirinae subfamily and if left untreated it may cause epidemic in poultry. Many vaccines have been made against Newcastle disease based on inactivated and attenuated viruses but become useless due to the genetic changes in the virus. We have recently reported epitope based vaccine by using immunoinformatics approaches. The vaccine was previously constructed against Hemagglutunin neuraminidase protein of Newcastle disease virus. Here we extended our work to develop several chimera of the proposed vaccine to design a new multi-epitope vaccine by shuffling the cytotoxic T lymphocytes (CTL) segments of the vaccine. Total 5040 constructs have been analyzed by shuffling 7 CTL epitopes. Highest antigenic multi-epitope construct was selected for the further study. Our new multi-epitope vaccine (MEV) construct contains 259 amino acids and is immunogenic, more antigenic and non-allergen. The refinement of the structure of MEV construct was performed. Molecular docking analyses showed its maximum binding with avian Toll-like 4 receptor. Subsequently, immune simulations showed its predicted ability to induce the host primary and secondary responses. Study suggests that our new multi-epitope vaccine chimera is more effective and stable protein against Newcastle disease virus strains in Pakistan. However, further studies are required to validate the vaccine through In vitro and In vivo studies.
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Affiliation(s)
- Farrukh Jamil
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Laiba Aslam
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Hira Ali
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Kainaat Shoukat
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Muhammad Asif Rasheed
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Sohail Raza
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Ibrahim
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
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Regulation of Host Immune Response against Enterobacter cloacae Proteins via Computational mRNA Vaccine Design through Transcriptional Modification. Microorganisms 2022; 10:microorganisms10081621. [PMID: 36014038 PMCID: PMC9415879 DOI: 10.3390/microorganisms10081621] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 12/13/2022] Open
Abstract
Enterobacter cloacae is mainly responsible for sepsis, urethritis, and respiratory tract infections. These bacteria may affect the transcription of the host and particularly their immune system by producing changes in their epigenetics. In the present study, four proteins of Enterobacter cloacae were used to predict the epitopes for the construction of an mRNA vaccine against Enterobacter cloacae infections. In order to generate cellular and humoral responses, various immunoinformatic-based approaches were used for developing the vaccine. The molecular docking analysis was performed for predicting the interaction among the chosen epitopes and corresponding MHC alleles. The vaccine was developed by combining epitopes (thirty-three total), which include the adjuvant Toll-like receptor-4 (TLR4). The constructed vaccine was analyzed and predicted to cover 99.2% of the global population. Additionally, in silico immunological modeling of the vaccination was also carried out. When it enters the cytoplasm of the human (host), the codon is optimized to generate the translated mRNA efficiently. Moreover, the peptide structures were analyzed and docked with TLR-3 and TLR-4. A dynamic simulation predicted the stability of the binding complex. The assumed construct was considered to be a potential candidate for a vaccine against Enterobacter cloacae infections. Hence, the proposed construct is suitable for in vitro analyses to validate its effectiveness.
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Bai S, Jiang H, Song Y, Zhu Y, Qin M, He C, Du G, Sun X. Aluminum nanoparticles deliver a dual-epitope peptide for enhanced anti-tumor immunotherapy. J Control Release 2022; 344:134-146. [PMID: 35217098 DOI: 10.1016/j.jconrel.2022.02.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/15/2022] [Accepted: 02/20/2022] [Indexed: 12/24/2022]
Abstract
Tumor peptide vaccines contain only key amino acid sequences of tumor neoantigens, and therefore can provide precise activation of immune responses. Recent research has found that short peptide vaccines restricted to MHC-I epitopes are insufficient to activate effective CD8+ T cell responses for tumor elimination, and assistance from CD4+ T cell immunity could significantly improve the therapeutic outcome. Herein, we proposed an innovative peptide vaccine strategy to simultaneously activate CD8+ and CD4+ T cell responses by combining MHC-I and MHC-II epitopes into one long peptide antigen. To further strengthen the anti-tumor immune response induced by this dual-epitope peptide, we engineered a PEG derivative (PpASE) stabilized aluminum nanoparticle for delivering the synthetic long peptides (ANLs). The synthesized nanovaccine with a diameter of ~100 nm showed good stability and enhanced antigen uptake by antigen-presenting cells (APCs). As a result, ANLs promoted the presentation of MHC-I epitope in APCs and induced stronger activation and proliferation of CD8+ T cells as compared to aluminum nanoparticle loaded with MHC-I epitope restricted peptides (ANSs). After subcutaneous vaccination, the developed nanovaccine significantly inhibited tumor growth and prolonged mouse survival in both B16-OVA and B16F10 tumor models. Finally, ANLs were also able to elevate the maturation level of human dendritic cells (DCs), showing a great possibility of clinical translation.
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Affiliation(s)
- Shuting Bai
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, No.17, Block 3, Southern Renmin Road, Chengdu 610041, China
| | - Hao Jiang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, No.17, Block 3, Southern Renmin Road, Chengdu 610041, China
| | - Yuanshuai Song
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, No.17, Block 3, Southern Renmin Road, Chengdu 610041, China
| | - Yining Zhu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, No.17, Block 3, Southern Renmin Road, Chengdu 610041, China
| | - Ming Qin
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, No.17, Block 3, Southern Renmin Road, Chengdu 610041, China
| | - Chunting He
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, No.17, Block 3, Southern Renmin Road, Chengdu 610041, China
| | - Guangsheng Du
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, No.17, Block 3, Southern Renmin Road, Chengdu 610041, China
| | - Xun Sun
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, No.17, Block 3, Southern Renmin Road, Chengdu 610041, China.
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