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Aleebrahim-Dehkordi E, Ghoshouni H, Koochaki P, Esmaili-Dehkordi M, Aleebrahim E, Chichagi F, Jafari A, Hanaei S, Heidari-Soureshjani E, Rezaei N. Targeting the vital non-structural proteins (NSP12, NSP7, NSP8 and NSP3) from SARS-CoV-2 and inhibition of RNA polymerase by natural bioactive compound naringenin as a promising drug candidate against COVID-19. J Mol Struct 2023; 1287:135642. [PMID: 37131962 PMCID: PMC10131750 DOI: 10.1016/j.molstruc.2023.135642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/04/2023]
Abstract
The prevalence of SARS-CoV-2-induced respiratory infections is now a major challenge worldwide. There is currently no specific antiviral drug to prevent or treat this disease. Infection with COVID-19 seriously needs to find effective therapeutic agents. In the present study, naringenin, as a potential inhibitor candidate for RNA Polymerase SARS-CoV-2 was compared with remdesivir (FDA-approved drug) and GS-441,524 (Derivative of the drug remdesivir) by screening with wild-type and mutant SARS-CoV-2 NSP12 (NSP7-NSP8) and NSP3 interfaces, then complexes were simulated by molecular dynamics (MD) simulations to gain their stabilities. The docking results displayed scores of -3.45 kcal/mol and -4.32 kcal/mol against NSP12 and NSP3, respectively. Our results showed that naringenin had ΔG values more negative than the ΔG values of Remdesivir (RDV) and GS-441,524. Hence, naringenin was considered to be a potential inhibitor. Also, the number of hydrogen bonds of naringenin with NSP3 and later NSP12 are more than Remdesivir and its derivative. In this research, Mean root mean square deviation (RMSD) values of NSP3 and NSP12with naringenin ligand (5.55±1.58 nm to 3.45±0.56 nm and 0.238±0.01 to 0.242±0.021 nm, respectively showed stability in the presence of ligand. The root mean square fluctuations (RMSF) values of NSP3 and NSP12 amino acid units in the presence of naringenin in were 1.5 ± 0.31 nm and 0.118±0.058, respectively. Pharmacokinetic properties and prediction of absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of naringenin and RDV showed that these two compounds had no potential cytotoxicity.
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Affiliation(s)
- Elahe Aleebrahim-Dehkordi
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Nutritional Health Team (NHT), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Hamed Ghoshouni
- Medical student, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Pooneh Koochaki
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Elham Aleebrahim
- PhD Student in Food Sciences and Engineering, Islamic Azad University, Tehran North Branch, Tehran, Iran
| | - Fatemeh Chichagi
- Research Development Center, Sina Hospital, Tehran University of Medical Science, Tehran, Iran
| | - Ali Jafari
- Nutritional Health Team (NHT), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Student Research Committee, Department of Nutrition, School of Health, Golestan University of Medical Sciences, Gorgan, Iran
- Golestan Research Center of Gastroenterology and Hepatology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Sara Hanaei
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Ehsan Heidari-Soureshjani
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box. 115, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Nima Rezaei
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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Aleebrahim-Dehkordi E, Koochaki P, Samami E, Ghoshouni H, Ghadimi DJ, Shadnoush F, Saberianpour S, Rafieian-Kopaei M. Possible Therapeutic Targets from Derivatives of Natural Marine Products Based on PI3K/AKT Dependent Inhibitors in Viral Infection COVID-19. Cell Physiol Biochem 2022; 56:707-729. [PMID: 36537138 DOI: 10.33594/000000595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2022] [Indexed: 12/24/2022] Open
Abstract
Natural resources have long played a prominent part in conventional treatments as a parental source due to their multifaceted functions and lesser side effects. The diversity of marine products is a significant source of possible bioactive chemical compounds with a wide range of potential medicinal applications. Marine organisms produce natural compounds and new drugs with unique properties are produced from these compounds. A lot of bioactive compounds with medicinal properties are extracted from marine invertebrates, including Peptides, Alkaloids, Terpenoids, Steroids. Thus, it can be concluded that marine ecosystems are endowed with natural resources that have a wide range of medicinal properties, and it is important to examine the therapeutic and pharmacological capabilities of these molecules. So, finding particular inhibitors of the COVID-19 in natural compounds will be extremely important. Natural ingredients, in this light, could be a valuable resource in the progression of COVID-19 therapeutic options. Controlling the immunological response in COVID-19 patients may be possible by addressing the PI3K/Akt pathway and regulating T cell responses. T cell effector activity can be improved by preventing anti-viral exhaustion by suppressing PI3K and Akt during the early anti-viral response. The diversity of marine life is a significant supply of potentially bioactive chemical compounds with a broad range of medicinal uses. In this study, some biologically active compounds from marine organisms capable of inhibiting PI3K/AKT and the possible therapeutic targets from these compounds in viral infection COVID-19 have been addressed.
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Affiliation(s)
- Elahe Aleebrahim-Dehkordi
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran, .,Nutritional Health Team (NHT), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Pooneh Koochaki
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Elham Samami
- University of Florida Health Cancer Center, Gainesville, FL, USA.,University of Florida, College of Nursing, Gainesville, FL, USA
| | - Hamed Ghoshouni
- Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Delaram J Ghadimi
- Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Shirin Saberianpour
- Vascular and Endovascular Surgery Research Center, Mashhad University of Medical Science, Mashhad, Iran
| | - Mahmoud Rafieian-Kopaei
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran,
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Aleebrahim-Dehkordi E, Molavi B, Mokhtari M, Deravi N, Fathi M, Fazel T, Mohebalizadeh M, Koochaki P, Shobeiri P, Hasanpour-Dehkordi A. T helper type (Th1/Th2) responses to SARS-CoV-2 and influenza A (H1N1) virus: From cytokines produced to immune responses. Transpl Immunol 2022; 70:101495. [PMID: 34774738 PMCID: PMC8579696 DOI: 10.1016/j.trim.2021.101495] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 01/08/2023]
Abstract
Cytokines produced by T helper cells (Th cells) have essential roles in the body's defense against viruses. Type 1 T helper (Th1) cells are essential for the host defense toward intracellular pathogens while T helper type 2 (Th2) cells are considered to be critical for the helminthic parasites' elimination swine-origin influenza A (H1N1) virus, a disease led to an epidemic in 2009 and rapidly spread globally via human-to-human transmission. Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a global pandemic in 2020 and is a serious threat to the public health. Pulmonary immunopathology is the leading cause of death during influenza and SARS-CoV-2 epidemics and pandemics. Influenza and SARS-CoV-2 cause high levels of cytokines in the lung. Both inadequate levels and high levels of specific cytokines can have side effects. In this literature review article, we want to compare the Th1 and Th2 cells responses in SARS-CoV-2 and H1N1.
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Affiliation(s)
- Elahe Aleebrahim-Dehkordi
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
| | - Bahareh Molavi
- Department of Anesthesiology, Faculty of Paramedical, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Melika Mokhtari
- Dental Faculty, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Niloofar Deravi
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran; School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mobina Fathi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tara Fazel
- school of international campus, Guilan University of Medical Sciences, Rasht, Iran
| | - Mehdi Mohebalizadeh
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran
| | - Pooneh Koochaki
- Islamic Azad University, Tehran Medical Science Branch, faculty of medicine, Tehran, Iran
| | - Parnian Shobeiri
- School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran.; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran; Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Hasanpour-Dehkordi
- Social Determinants of Health Research Center, School of Allied Medical Sciences, Shahrekord University of Medical Sciences, Shahrekord, Iran..
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Koochaki P, Revicki D, Wilson H, Pokrzywinski R, Jordan R, Lucas J. 080 Women’s Experiences With Bremelanotide Administered, On Demand, for the Treatment of Hypoactive Sexual Desire Disorder. J Sex Med 2019. [DOI: 10.1016/j.jsxm.2019.03.521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Zinner N, Kobashi KC, Ebinger U, Viegas A, Egermark M, Quebe-Fehling E, Koochaki P. Darifenacin treatment for overactive bladder in patients who expressed dissatisfaction with prior extended-release antimuscarinic therapy. Int J Clin Pract 2008; 62:1664-74. [PMID: 18811599 PMCID: PMC2680263 DOI: 10.1111/j.1742-1241.2008.01893.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION AND OBJECTIVE Patient perception of overactive bladder (OAB) treatment outcomes can be a useful indicator of benefit and may help drive persistence on treatment, which is known to be poor in OAB. It remains unclear whether OAB patients dissatisfied with one antimuscarinic can achieve satisfaction with another and supporting data are limited. This study investigated patient-reported outcomes and clinical parameters during darifenacin treatment in OAB patients who expressed dissatisfaction with prior extended-release (ER) oxybutynin or tolterodine therapy (administered for >or= 1 week within the past year). METHODS This open-label study was conducted in darifenacin-naïve OAB patients. Patients received 7.5 mg darifenacin once daily with the possibility of up-titrating to 15 mg after 2 weeks, for up to 12 weeks. Efficacy parameters included the Patient's Perception of Bladder Condition (PPBC), patient satisfaction with treatment, micturition frequency and number of urgency and urge urinary incontinence (UUI) episodes. Adverse events (AEs) were also recorded. RESULTS In total, 497 patients were treated (84.1% women). Darifenacin treatment resulted in statistically significant improvements in PPBC scores, micturition frequency, urgency and UUI episodes from baseline at 12 weeks. The improvements were similar for patients previously treated with oxybutynin ER or tolterodine ER. More than 85% of patients expressed satisfaction with darifenacin. As noted in other studies, the most common AEs were dry mouth and constipation, but these infrequently resulted in treatment discontinuation, which was low overall. CONCLUSIONS In this study, PPBC score and OAB symptoms were significantly improved, and satisfaction was high during treatment with darifenacin (7.5/15 mg) in patients who were dissatisfied with the previous antimuscarinic treatment.
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Affiliation(s)
- N Zinner
- Western Clinical Research, Inc., Torrance, CA 90505, USA.
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