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Hashempour A, Khodadad N, Bemani P, Ghasemi Y, Akbarinia S, Bordbari R, Tabatabaei AH, Falahi S. Design of multivalent-epitope vaccine models directed toward the world's population against HIV-Gag polyprotein: Reverse vaccinology and immunoinformatics. PLoS One 2024; 19:e0306559. [PMID: 39331650 DOI: 10.1371/journal.pone.0306559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/18/2024] [Indexed: 09/29/2024] Open
Abstract
Significant progress has been made in HIV-1 research; however, researchers have not yet achieved the objective of eradicating HIV-1 infection. Accordingly, in this study, eucaryotic and procaryotic in silico vaccines were developed for HIV-Gag polyproteins from 100 major HIV subtypes and CRFs using immunoinformatic techniques to simulate immune responses in mice and humans. The epitopes located in the conserved domains of the Gag polyprotein were evaluated for allergenicity, antigenicity, immunogenicity, toxicity, homology, topology, and IFN-γ induction. Adjuvants, linkers, CTLs, HTLs, and BCL epitopes were incorporated into the vaccine models. Strong binding affinities were detected between HLA/MHC alleles, TLR-2, TLR-3, TLR-4, TLR-7, and TLR-9, and vaccine models. Immunological simulation showed that innate and adaptive immune cells elicited active and consistent responses. The human vaccine model was matched with approximately 93.91% of the human population. The strong binding of the vaccine to MHC/HLA and TLR molecules was confirmed through molecular dynamic stimulation. Codon optimization ensured the successful translation of the designed constructs into human cells and E. coli hosts. We believe that the HIV-1 Gag vaccine formulated in our research can reduce the challenges faced in developing an HIV-1 vaccine. Nevertheless, experimental verification is necessary to confirm the effectiveness of these vaccines in these models.
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Affiliation(s)
- Ava Hashempour
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nastaran Khodadad
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Peyman Bemani
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shokufeh Akbarinia
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Bordbari
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Hossein Tabatabaei
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shahab Falahi
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
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Ghassabi F, Hashempour A, Dehghani B, Hasanshahi Z, Khodadad N, Behizadeh F, Davarpanah MA. Frequency of Fusion Inhibitor Resistance Mutations Among Therapy-Naïve HIV Patients. AIDS Res Hum Retroviruses 2024; 40:471-481. [PMID: 38553905 DOI: 10.1089/aid.2023.0102] [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: 04/17/2024] Open
Abstract
Glycoprotein 41 (gp41) of the human immunodeficiency virus type 1 (HIV-1) protein plays a critical role in membrane fusion. Gp41 binds to proteins in the plasma membrane of CD4+ T cells, particularly the T-cell antigen receptor (TCR). These findings indicate that gp41 is involved in the assembly of HIV-1 at the plasma membrane of T cells and affects the stimulation of the TCR. To control HIV-1, new inhibitors were introduced to target the gp41 protein. However, mutations in this region might reduce their efficacy. The Gp41 region was amplified from the sera of 30 patients using nested polymerase chain reaction. The sequences were analyzed by bioinformatics tools to identify mutations and gp41 structural features. Subtyping and the interaction between fusion inhibitors and gp41 proteins were also examined. As the first report from Iran, docking analysis between fusion inhibitors and Iranian gp41 proteins showed that mutations in gp41 could not reduce the efficacy of the fusion inhibitors. Most of the patients were infected with CRF35-AD. Several post-modification positions, including glycosylation and phosphorylation sites, were identified in the gp41 protein. Our findings revealed no known multinational drug resistance to gp41 inhibitors; thus, fusion inhibitors can effectively inhibit HIV in Iranian patients. In addition, the present study introduced a new gp41 region (36-44 aa), which considerably influences the interactions between gp41 inhibitors and the gp41 protein. This region may play a pivotal role in suppressing gp41 inhibitors in CFR35-AD. Furthermore, gp41 can be considered a good target for subtyping analysis via the phylogenetic method.
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Affiliation(s)
- Farzaneh Ghassabi
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ava Hashempour
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Behzad Dehghani
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Hasanshahi
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nastaran Khodadad
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farideh Behizadeh
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohamad Ali Davarpanah
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
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Rizwan M, Cheng K, Gang Y, Hou Y, Wang C. Immunomodulatory Effects of Vitamin D and Zinc on Viral Infection. Biol Trace Elem Res 2024:10.1007/s12011-024-04139-y. [PMID: 38451442 DOI: 10.1007/s12011-024-04139-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
Several nutrients are crucial in enhancing the immune system and preserving the structural integrity of bodily tissue barriers. Vitamin D (VD) and zinc (Zn) have received considerable interest due to their immunomodulatory properties and ability to enhance the body's immune defenses. Due to their antiviral, anti-inflammatory, antioxidative, and immunomodulatory properties, the two nutritional powerhouses VD and Zn are crucial for innate and adaptive immunity. As observed with COVID-19, deficiencies in these micronutrients impair immune responses, increasing susceptibility to viral infections and severe disease. Ensuring an adequate intake of VD and Zn emerges as a promising strategy for fortifying the immune system. Ongoing clinical trials are actively investigating their potential therapeutic advantages. Beyond the immediate context of the pandemic, these micronutrients offer valuable tools for enhancing immunity and overall well-being, especially in the face of future viral threats. This analysis emphasizes the enduring significance of VD and Zn as both treatment and preventive measures against potential viral challenges beyond the current health crisis. The overview delves into the immunomodulatory potential of VD and Zn in combating viral infections, with particular attention to their effects on animals. It provides a comprehensive summary of current research findings regarding their individual and synergistic impacts on immune function, underlining their potential in treating and preventing viral infections. Overall, this overview underscores the need for further research to understand how VD and Zn can modulate the immune response in combatting viral diseases in animals.
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Affiliation(s)
- Muhammad Rizwan
- College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China
| | - Ke Cheng
- College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China
| | - Yang Gang
- College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China
| | - Yuntao Hou
- College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China
| | - Chunfang Wang
- College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China.
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Nabi-Afjadi M, Karami H, Goudarzi K, Alipourfard I, Bahreini E. The effect of vitamin D, magnesium and zinc supplements on interferon signaling pathways and their relationship to control SARS-CoV-2 infection. Clin Mol Allergy 2021; 19:21. [PMID: 34749737 PMCID: PMC8573303 DOI: 10.1186/s12948-021-00161-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/12/2021] [Indexed: 01/08/2023] Open
Abstract
The concern of today's communities is to find a way to prevent or treat COVID-19 and reduce its symptoms in the patients. However, the genetic mutations and more resistant strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerge; the designed vaccines and adjuvant therapies would potentially control the symptoms and severity of COVID-19. The most important complication of this viral infection is acute respiratory distress syndrome, which occurs due to the infiltration of leukocytes into the alveoli and the raised cytokine storm. Interferons, as a cytokine family in the host, play an important role in the immune-related antiviral defense and have been considered in the treatment protocols of COVID-19. In addition, it has been indicated that some nutrients, including vitamin D, magnesium and zinc are essential in the modulation of the immune system and interferon (IFN) signaling pathway. Several recent studies have investigated the treatment effect of vitamin D on COVID-19 and reported the association between optimal levels of this vitamin and reduced disease risk. In the present study, the synergistic action of vitamin D, magnesium and zinc in IFN signaling is discussed as a treatment option for COVID-19 involvement.
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Affiliation(s)
- Mohsen Nabi-Afjadi
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Hadis Karami
- Department of Molecular Cell Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Kaveh Goudarzi
- Nursing Department, Islamic Azad University, Khorasgan Branch, Isfahan, Iran
| | - Iraj Alipourfard
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Bankowa 9, 40-007, Katowice, Poland
| | - Elham Bahreini
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, P.O. Box: 1449614525, Tehran, Iran.
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The Regulatory Network of Sturgeon Chondroitin Sulfate on Colorectal Cancer Inhibition by Transcriptomic and Proteomic Analysis. Int J Mol Sci 2021; 22:ijms22179395. [PMID: 34502301 PMCID: PMC8430666 DOI: 10.3390/ijms22179395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/11/2022] Open
Abstract
Chondroitin sulfate (CS) is a food-derived bioactive substance with multiple biological functions, which exists in animal cartilage and/or bone. Sturgeon, a type of cartilaginous fish, is rich in CS. Our recent study demonstrated the effect of sturgeon chondroitin sulfate (SCS) on reducing colorectal cancer cell proliferation and tumor formation. However, the molecular mechanisms of its anticancer activity remain unknown. In this study, the cell proliferation assay and flow cytometric analysis were used to examine the cell viability and apoptosis of colon cancer cell HT-29 cells and normal colonic epithelial cell NCM460 cells. Transcriptomic and proteomic studies were used to identify the main targets of SCS. SCS showed little effect on the genes/proteins expression profile of NCM460 cells but more sensitive to HT-29, in which 188 genes and 10 proteins were differentially expressed after SCS treatment. Enrichment analysis of those genes/proteins showed that the majority of them are involved in DNA replication, cell cycle progression and apoptosis. Quantitative RT-PCR and Western blot were used to determine essential genes/proteins and networks targeted by SCS to exert inhibiting the development of colorectal cancer function. This study provided great insights into developing food-derived novel therapeutics for colorectal cancer treatment.
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Patel JJ, Martindale RG, McClave SA. Relevant Nutrition Therapy in COVID-19 and the Constraints on Its Delivery by a Unique Disease Process. Nutr Clin Pract 2020; 35:792-799. [PMID: 32786117 PMCID: PMC7436662 DOI: 10.1002/ncp.10566] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Worldwide, as of July 2020, >13.2 million people have been infected by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The spectrum of coronavirus disease 2019 (COVID-19) ranges from mild illness to critical illness in 5% of cases. The population infected with SARS-CoV-2 requiring an intensive care unit admission often requires nutrition therapy as part of supportive care. Although the various societal guidelines for critical care nutrition meet most needs for the patient with COVID-19, numerous factors, which impact the application of those guideline recommendations, need to be considered. Since the SARS-CoV-2 virus is highly contagious, several key principles should be considered when caring for all patients with COVID-19 to ensure the safety of all healthcare personnel involved. Management strategies should cluster care, making all attempts to bundle patient care to limit exposure. Healthcare providers should be protected, and the spread of SARS-CoV-2 should be limited by minimizing procedures and other interventions that lead to aerosolization, avoiding droplet exposure through hand hygiene and use of personal protective equipment (PPE). PPE should be preserved by decreasing the number of individuals providing direct patient care and by limiting the number of patient interactions. Enteral nutrition (EN) is tolerated by the majority of patients with COVID-19, but a relatively low threshold for conversion to parenteral nutrition should be maintained if increased exposure to the virus is required to continue EN. This article offers relevant and practical recommendations on how to optimize nutrition therapy in critically ill patients with COVID-19.
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Affiliation(s)
- Jayshil J. Patel
- Division of Pulmonary & Critical Care MedicineMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Robert G. Martindale
- Division of Gastrointestinal and General SurgeryOregon Health Sciences UniversityPortlandOregonUSA
| | - Stephen A. McClave
- Division of GastroenterologyHepatologyand NutritionUniversity of LouisvilleLouisvilleKentuckyUSA
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Martindale R, Patel JJ, Taylor B, Arabi YM, Warren M, McClave SA. Nutrition Therapy in Critically Ill Patients With Coronavirus Disease 2019. JPEN J Parenter Enteral Nutr 2020; 44:1174-1184. [PMID: 32462719 PMCID: PMC7283713 DOI: 10.1002/jpen.1930] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/13/2020] [Accepted: 05/19/2020] [Indexed: 02/06/2023]
Abstract
In the midst of a coronavirus disease 2019 (COVID-19) pandemic, a paucity of data precludes derivation of COVID-19-specific recommendations for nutrition therapy. Until more data are available, focus must be centered on principles of critical care nutrition modified for the constraints of this disease process, ie, COVID-19-relevant recommendations. Delivery of nutrition therapy must include strategies to reduce exposure and spread of disease by providing clustered care, adequate protection of healthcare providers, and preservation of personal protective equipment. Enteral nutrition (EN) should be initiated early after admission to the intensive care unit (ICU) using a standard isosmolar polymeric formula, starting at trophic doses and advancing as tolerated, while monitoring for gastrointestinal intolerance, hemodynamic instability, and metabolic derangements. Intragastric EN may be provided safely, even with use of prone-positioning and extracorporeal membrane oxygenation. Clinicians should have a lower threshold for switching to parenteral nutrition in cases of intolerance, high risk of aspiration, or escalating vasopressor support. Although data extrapolated from experience in acute respiratory distress syndrome warrants use of fiber additives and probiotic organisms, the lack of benefit precludes a recommendation for micronutrient supplementation. Practices that increase exposure or contamination of equipment, such as monitoring gastric residual volumes, indirect calorimetry to calculate requirements, endoscopy or fluoroscopy to achieve enteral access, or transport out of the ICU for additional imaging, should be avoided. At all times, strategies for nutrition therapy need to be assessed on a risk/benefit basis, paying attention to risk for both the patient and the healthcare provider.
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Affiliation(s)
- Robert Martindale
- Department of SurgeryOregon Health and Science UniversityPortlandOregonUSA
| | - Jayshil J. Patel
- Division of Pulmonary & Critical Care MedicineMedical College of WisconsinMilwaukeeWisconsinUSA
| | | | - Yaseen M. Arabi
- King Abdullah International Medical Research CenterKing Saud Din Abdulaziz University for Health SciencesRiyadhSaudi Arabia
| | - Malissa Warren
- Department of SurgeryOregon Health and Science University and Portland VA Health Care CenterPortlandOregonUSA
| | - Stephen A. McClave
- Division of Gastroenterology Hepatology and NutritionSchool of MedicineUniversity of LouisvilleLouisvilleKentuckyUSA
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