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Glenn IS, Hall LN, Khalid MM, Ott M, Shoichet BK. Colloidal aggregation confounds cell-based Covid-19 antiviral screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.564435. [PMID: 37961552 PMCID: PMC10634915 DOI: 10.1101/2023.10.27.564435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Colloidal aggregation is one of the largest contributors to false-positives in early drug discovery and chemical biology. Much work has focused on its impact on pure-protein screens; here we consider aggregations role in cell-based infectivity assays in Covid-19 drug repurposing. We began by investigating the potential aggregation of 41 drug candidates reported as SARs-CoV-2 entry inhibitors. Of these, 17 formed colloidal-particles by dynamic light scattering and exhibited detergent-dependent enzyme inhibition. To evaluate antiviral efficacy of the drugs in cells we used spike pseudotyped lentivirus and pre-saturation of the colloids with BSA. The antiviral potency of the aggregators was diminished by at least 10-fold and often entirely eliminated in the presence of BSA, suggesting antiviral activity can be attributed to the non-specific nature of the colloids. In confocal microscopy, the aggregates induced fluorescent puncta of labeled spike protein, consistent with sequestration of the protein on the colloidal particles. Addition of either non-ionic detergent or of BSA disrupted these puncta. These observations suggest that colloidal aggregation is common among cell-based anti-viral drug repurposing, and perhaps cell-based assays more broadly, and offers rapid counter-screens to detect and eliminate these artifacts, allowing the community invest resources in compounds with true potential as a Covid-19 therapeutic.
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Affiliation(s)
- Isabella S Glenn
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Lauren N Hall
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Mir M Khalid
- Gladstone Institutes, San Francisco, California, United States
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California, United States
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
- Chan Zuckerberg Biohub, San Francisco, California, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
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Zahra N, Iqbal J, Arif M, Abbasi BA, Sher H, Nawaz AF, Yaseen T, Ydyrys A, Sharifi-Rad J, Calina D. A comprehensive review on traditional uses, phytochemistry and pharmacological properties of Paeonia emodi Wall. ex Royle: current landscape and future perspectives. Chin Med 2023; 18:23. [PMID: 36859262 PMCID: PMC9979516 DOI: 10.1186/s13020-023-00727-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/10/2023] [Indexed: 03/03/2023] Open
Abstract
Paeonia emodi Wall. ex Royle is commonly known as Himalayan paeony has great importance as a food and medicine. The practice of Paeonia emodi Wall. ex Royle is very ancient and it is conventionally used for a wide range of illnesses in the folk system of medicine because of its wide beneficial phytochemical profile. The main purpose of the current review was the synthesis of recent data on botany, ethnopharmacology, phytochemistry and potential pharmacological mechanisms of action of Paeonia emodi Wall. ex Royle, thus offering new prospects for the development of new adjuvant natural therapies. Using scientific databases such as PubMed/MedLine, Scopus, Web of Science, ScienceDirect, Google Scholar, Springer, and Wiley, a comprehensive literature search was performed for Paeonia emodi Wall. ex Royle. For searching, we used the next MeSH terms: "Biological Product/isolation and purification", "Biological Products/pharmacology", "Drug Discovery/methods", "Ethnopharmacology, Medicine", "Traditional/methods", "Paeonia/chemistry", "Plant Extracts/pharmacology", "Phytochemicals/chemistry", "Phytochemicals/pharmacology", "Plants, Medicinal". The results of the most recent studies were analyzed and the most important data were summarized in tables and figures. Phytochemical research of Paeonia emodi Wall. ex Royle has led to the isolation of triterpenes, monoterpenes, phenolic acids, fatty acids, organic compounds, steroids, free radicals and some other classes of primary metabolites. In addition, diverse pharmacological activities like antibacterial, antifungal, anticoagulant, airway relaxant lipoxygenase and beta-glucuronidase inhibiting activity, radical scavenging activity, phytotoxic and insecticidal activities have been reported for Paeonia emodi Wall. ex Royle. Different bioactive compounds of Paeonia emodi Wall. ex Royle has proven their therapeutic potential in modern pharmacological and biomedical research to cure numerous gastrointestinal and nervous disorders. In future, further in vitro and in vivo therapeutic studies are required to identify new mechanisms of action, pharmacokinetics studies, and new pharmaceutical formulations for target transport and possible interaction with allopathic drugs. Also, new research regarding quality evaluation, toxicity and safety data in humans is needed.
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Affiliation(s)
- Nida Zahra
- Department of Biotechnology, University of Mianwali, Mianwali, 42200 Pakistan
| | - Javed Iqbal
- Department of Botany, Bacha Khan University, Charsadda, Khyber Pakhtunkhwa Pakistan
| | - Muhammad Arif
- Department of Biotechnology, University of Mianwali, Mianwali, 42200 Pakistan
| | - Banzeer Ahsan Abbasi
- Department of Botany, Rawalpindi Women University, 6th Road, Satellite Town, Rawalpindi, 46300 Pakistan
| | - Hassan Sher
- Center for Plant Sciences and Biodiversity, University of Swat, Kanju, 19201 Pakistan
| | - Ayesha Fazal Nawaz
- National Institute of Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Park Road, Islamabad, Pakistan
| | - Tabassum Yaseen
- Department of Botany, Bacha Khan University, Charsadda, Khyber Pakhtunkhwa Pakistan
| | - Alibek Ydyrys
- Biomedical Research Centre, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, 050040 Almaty, Kazakhstan
- The Elliott School of International Affairs, George Washington University, 1957 E St NW, Washington, DC 20052 USA
| | | | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
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3
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Asgharian P, Quispe C, Herrera-Bravo J, Sabernavaei M, Hosseini K, Forouhandeh H, Ebrahimi T, Sharafi-Badr P, Tarhriz V, Soofiyani SR, Helon P, Rajkovic J, Durna Daştan S, Docea AO, Sharifi-Rad J, Calina D, Koch W, Cho WC. Pharmacological effects and therapeutic potential of natural compounds in neuropsychiatric disorders: An update. Front Pharmacol 2022; 13:926607. [PMID: 36188551 PMCID: PMC9521271 DOI: 10.3389/fphar.2022.926607] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Neuropsychiatric diseases are a group of disorders that cause significant morbidity and disability. The symptoms of psychiatric disorders include anxiety, depression, eating disorders, autism spectrum disorders (ASD), attention-deficit/hyperactivity disorder, and conduct disorder. Various medicinal plants are frequently used as therapeutics in traditional medicine in different parts of the world. Nowadays, using medicinal plants as an alternative medication has been considered due to their biological safety. Despite the wide range of medications, many patients are unable to tolerate the side effects and eventually lose their response. By considering the therapeutic advantages of medicinal plants in the case of side effects, patients may prefer to use them instead of chemical drugs. Today, the use of medicinal plants in traditional medicine is diverse and increasing, and these plants are a precious heritage for humanity. Investigation about traditional medicine continues, and several studies have indicated the basic pharmacology and clinical efficacy of herbal medicine. In this article, we discuss five of the most important and common psychiatric illnesses investigated in various studies along with conventional therapies and their pharmacological therapies. For this comprehensive review, data were obtained from electronic databases such as MedLine/PubMed, Science Direct, Web of Science, EMBASE, DynaMed Plus, ScienceDirect, and TRIP database. Preclinical pharmacology studies have confirmed that some bioactive compounds may have beneficial therapeutic effects in some common psychiatric disorders. The mechanisms of action of the analyzed biocompounds are presented in detail. The bioactive compounds analyzed in this review are promising phytochemicals for adjuvant and complementary drug candidates in the pharmacotherapy of neuropsychiatric diseases. Although comparative studies have been carefully reviewed in the preclinical pharmacology field, no clinical studies have been found to confirm the efficacy of herbal medicines compared to FDA-approved medicines for the treatment of mental disorders. Therefore, future clinical studies are needed to accelerate the potential use of natural compounds in the management of these diseases.
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Affiliation(s)
- Parina Asgharian
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Cristina Quispe
- Facultad de Ciencias de la Salud, Universidad Arturo Prat, Iquique, Chile
| | - Jesús Herrera-Bravo
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomas, Santo Tomas, Chile
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Mahsa Sabernavaei
- Department of Pharmacognosy and Pharmaceutical Biotechnology, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran
| | - Kamran Hosseini
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Haleh Forouhandeh
- Infectious and Tropical Diseases Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tahereh Ebrahimi
- Infectious and Tropical Diseases Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Paria Sharafi-Badr
- Department of Pharmacognosy, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahideh Tarhriz
- Infectious and Tropical Diseases Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
- *Correspondence: Vahideh Tarhriz, ; Saiedeh Razi Soofiyani, ; Jovana Rajkovic, ; Javad Sharifi-Rad, ; Daniela Calina, ; Wojciech Koch, ; William C. Cho,
| | - Saiedeh Razi Soofiyani
- Infectious and Tropical Diseases Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
- Clinical Research Development Unit of Sina Educational, Research and Treatment Center, Tabriz University of Medical Sciences, Tabriz, Iran
- *Correspondence: Vahideh Tarhriz, ; Saiedeh Razi Soofiyani, ; Jovana Rajkovic, ; Javad Sharifi-Rad, ; Daniela Calina, ; Wojciech Koch, ; William C. Cho,
| | - Paweł Helon
- Branch in Sandomierz, Jan Kochanowski University of Kielce, Sandomierz, Poland
| | - Jovana Rajkovic
- Medical Faculty, Institute of Pharmacology, Clinical Pharmacology and Toxicology, University of Belgrade, Belgrade, Serbia
- *Correspondence: Vahideh Tarhriz, ; Saiedeh Razi Soofiyani, ; Jovana Rajkovic, ; Javad Sharifi-Rad, ; Daniela Calina, ; Wojciech Koch, ; William C. Cho,
| | - Sevgi Durna Daştan
- Department of Biology, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
- Beekeeping Development Application and Research Center, Sivas Cumhuriyet University, Sivas, Turkey
| | - Anca Oana Docea
- Department of Toxicology, University of Medicine and Pharmacy of Craiova, Craiova, Romania
| | - Javad Sharifi-Rad
- Facultad de Medicina, Universidad del Azuay, Cuenca, Ecuador
- *Correspondence: Vahideh Tarhriz, ; Saiedeh Razi Soofiyani, ; Jovana Rajkovic, ; Javad Sharifi-Rad, ; Daniela Calina, ; Wojciech Koch, ; William C. Cho,
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, Craiova, Romania
- *Correspondence: Vahideh Tarhriz, ; Saiedeh Razi Soofiyani, ; Jovana Rajkovic, ; Javad Sharifi-Rad, ; Daniela Calina, ; Wojciech Koch, ; William C. Cho,
| | - Wojciech Koch
- Department of Food and Nutrition, Medical University of Lublin, Lublin, Poland
- *Correspondence: Vahideh Tarhriz, ; Saiedeh Razi Soofiyani, ; Jovana Rajkovic, ; Javad Sharifi-Rad, ; Daniela Calina, ; Wojciech Koch, ; William C. Cho,
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong SAR, China
- *Correspondence: Vahideh Tarhriz, ; Saiedeh Razi Soofiyani, ; Jovana Rajkovic, ; Javad Sharifi-Rad, ; Daniela Calina, ; Wojciech Koch, ; William C. Cho,
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Ali ES, Akter S, Ramproshad S, Mondal B, Riaz TA, Islam MT, Khan IN, Docea AO, Calina D, Sharifi-Rad J, Cho WC. Targeting Ras-ERK cascade by bioactive natural products for potential treatment of cancer: an updated overview. Cancer Cell Int 2022; 22:246. [PMID: 35941592 PMCID: PMC9358858 DOI: 10.1186/s12935-022-02666-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/27/2022] [Indexed: 12/11/2022] Open
Abstract
MAPK (mitogen-activated protein kinase) or ERK (extracellular-signal-regulated kinase) pathway is an important link in the transition from extracellular signals to intracellular responses. Because of genetic and epigenetic changes, signaling cascades are altered in a variety of diseases, including cancer. Extant studies on the homeostatic and pathologic behavior of MAPK signaling have been conducted; however, much remains to be explored in preclinical and clinical research in terms of regulation and action models. MAPK has implications for cancer therapy response, more specifically in response to experimental MAPK suppression, compensatory mechanisms are activated. The current study investigates MAPK as a very complex cell signaling pathway that plays roles in cancer treatment response, cellular normal conduit maintenance, and compensatory pathway activation. Most MAPK inhibitors, unfortunately, cause resistance by activating compensatory feedback loops in tumor cells and tumor microenvironment components. As a result, innovative combinatorial treatments for cancer management must be applied to limit the likelihood of alternate pathway initiation as a possibility for generating novel therapeutics based on incorporation in translational research. We summarize current knowledge about the implications of ERK (MAPK) in cancer, as well as bioactive products from plants, microbial organisms or marine organisms, as well as the correlation with their chemical structures, which modulate this pathway for the treatment of different types of cancer.
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Affiliation(s)
- Eunus S Ali
- College of Medicine and Public Health, Flinders University, Bedford Park, 5042, Australia
| | - Shamima Akter
- Department of Bioinformatics and Computational Biology, George Mason University, Fairfax, VA, 22030, USA
| | - Sarker Ramproshad
- Department of Pharmacy, Ranada Prasad Shaha University, Narayanganj, 1400, Bangladesh
| | - Banani Mondal
- Department of Pharmacy, Ranada Prasad Shaha University, Narayanganj, 1400, Bangladesh
| | - Thoufiqul Alam Riaz
- Department of Pharmacology and Institute of New Drug Development, Jeonbuk National University Medical School, Jeonju, 54907, Republic of Korea
| | - Muhammad Torequl Islam
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Ishaq N Khan
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, 25100, Pakistan
| | - Anca Oana Docea
- Department of Toxicology, University of Medicine and Pharmacy of Craiova, 200349, Craiova, Romania
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349, Craiova, Romania.
| | | | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong.
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Thuy PT, Son NT. Thermodynamic and kinetic studies on antioxidant capacity of amentoflavone: a DFT (density functional theory) computational approach. Free Radic Res 2022; 56:526-535. [PMID: 36370431 DOI: 10.1080/10715762.2022.2146584] [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: 11/13/2022]
Abstract
Density functional theory (DFT) at the theoretical M06-2X/6-311G(d,p) level was used to assess thermodynamics and kinetics in the antioxidative action of amentoflavone (AF). The antioxidative HAT pathway (H-atom transfer) is assigned to this compound in gas, but the SPL-ET (sequential proton loss-electron transfer) is the main route in polar solvents methanol and water. In all four mediums gas, benzene, methanol, and water, 4‴-OH is the most active site in free radical quenching with the lowest BDE (bond dissociation enthalpy) values of 81.8-84.8 kcal/mol, as well as it exerted the PA (proton affinity) values of 29.8-33.0 kcal/mol in methanol and water. Regarding kinetics, when interacted with •OOH and •NO2 in gas and methanol, 4‴-OH group is also responsible for the lowest ΔG# values (Gibbs free energy of activation), and the highest rate constant K values. Acidic assessment also indicated that 4‴-OH is associated with the strongest acidity (the lowest pKa). Two favorable oriented 4‴-OH and 7-OH groups further exhibited antioxidative activity since they prevented metal ions Zn2+ and Fe2+ from participating in free radical producing processes, in which the most stable complex [FeAF(H2O)4] generated the lowest IE value of -206.2 kcal/mol, and Egap value of 3.491 kcal/mol, but the highest MIA values of 184.6 kcal/mol in methanol.
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Affiliation(s)
- Phan Thi Thuy
- Department of Chemistry, College of Education, Vinh University, Vinh, Vietnam
| | - Ninh The Son
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST), Caugiay, Vietnam
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Šamec D, Karalija E, Dahija S, Hassan STS. Biflavonoids: Important Contributions to the Health Benefits of Ginkgo ( Ginkgo biloba L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11101381. [PMID: 35631806 PMCID: PMC9143338 DOI: 10.3390/plants11101381] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 05/03/2023]
Abstract
Ginkgo (Ginkgo biloba L.) is one of the most distinctive plants, characterized by excellent resistance to various environmental conditions. It is used as an ornamental plant and is recognized as a medicinal plant in both traditional and Western medicine. Its bioactive potential is associated with the presence of flavonoids and terpene trilactones, but many other compounds may also have synergistic effects. Flavonoid dimers-biflavonoids-are important constituents of ginkgophytopharmaceuticals. Currently, the presence of 13 biflavonoids has been reported in ginkgo, of which amentoflavone, bilobetin, sciadopitysin, ginkgetin and isoginkgetin are the most common. Their role in plants remains unknown, but their bioactivity and potential role in the management of human health are better investigated. In this review, we have provided an overview of the chemistry, diversity and biological factors that influence the presence of biflavonoids in ginkgo, as well as their bioactive and health-related properties. We have focused on their antioxidant, anticancer, antiviral, antibacterial, antifungal and anti-inflammatory activities as well as their potential role in the treatment of cardiovascular, metabolic and neurodegenerative diseases. We also highlighted their potential toxicity and pointed out further research directions.
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Affiliation(s)
- Dunja Šamec
- Department of Food Technology, University North, Trga Dr. Žarka Dolinara 1, 48000 Koprivnica, Croatia
- Correspondence:
| | - Erna Karalija
- Department for Biology, Faculty of Science, University of Sarajevo, Zmaja od Bosne 33-35, 71000 Sarajevo, Bosnia and Herzegovina; (E.K.); (S.D.)
| | - Sabina Dahija
- Department for Biology, Faculty of Science, University of Sarajevo, Zmaja od Bosne 33-35, 71000 Sarajevo, Bosnia and Herzegovina; (E.K.); (S.D.)
| | - Sherif T. S. Hassan
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic;
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Activities and Molecular Mechanisms of Diterpenes, Diterpenoids, and Their Derivatives in Rheumatoid Arthritis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:4787643. [PMID: 35368757 PMCID: PMC8975657 DOI: 10.1155/2022/4787643] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/11/2021] [Accepted: 02/02/2022] [Indexed: 12/11/2022]
Abstract
Diterpenes and their derivatives have many biological activities, including anti-inflammatory and immunomodulatory effects. To date, several diterpenes, diterpenoids, and their laboratory-derived products have been demonstrated for antiarthritic activities. This study summarizes the literature about diterpenes and their derivatives acting against rheumatoid arthritis (RA) depending on the database reports until 31 August 2021. For this, we have conducted an extensive search in databases such as PubMed, Science Direct, Google Scholar, and Clinicaltrials.gov using specific relevant keywords. The search yielded 2708 published records, among which 48 have been included in this study. The findings offer several potential diterpenes and their derivatives as anti-RA in various test models. Among the diterpenes and their derivatives, andrographolide, triptolide, and tanshinone IIA have been found to exhibit anti-RA activity through diverse pathways. In addition, some important derivatives of triptolide and tanshinone IIA have also been shown to have anti-RA effects. Overall, findings suggest that these substances could reduce arthritis score, downregulate oxidative, proinflammatory, and inflammatory biomarkers, modulate various arthritis pathways, and improve joint destruction and clinical arthritic conditions, signs, symptoms, and physical functions in humans and numerous experimental animals, mainly through cytokine and chemokine as well as several physiological protein interaction pathways. Taken all together, diterpenes, diterpenoids, and their derivatives may be promising tools for RA management.
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Rafi MO, Al-Khafaji K, Sarker MT, Taskin-Tok T, Rana AS, Rahman MS. Design of a multi-epitope vaccine against SARS-CoV-2: immunoinformatic and computational methods. RSC Adv 2022; 12:4288-4310. [PMID: 35425433 PMCID: PMC8981096 DOI: 10.1039/d1ra06532g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/23/2022] [Indexed: 12/17/2022] Open
Abstract
A novel infectious agent, SARS-CoV-2, is responsible for causing the severe respiratory disease COVID-19 and death in humans. Spike glycoprotein plays a key role in viral particles entering host cells, mediating receptor recognition and membrane fusion, and are considered useful targets for antiviral vaccine candidates. Therefore, computational techniques can be used to design a safe, antigenic, immunogenic, and stable vaccine against this pathogen. Drawing upon the structure of the S glycoprotein, we are trying to develop a potent multi-epitope subunit vaccine against SARS-CoV-2. The vaccine was designed based on cytotoxic T-lymphocyte and helper T-lymphocyte epitopes with an N-terminal adjuvant via conducting immune filters and an extensive immunoinformatic investigation. The safety and immunogenicity of the designed vaccine were further evaluated via using various physicochemical, allergenic, and antigenic characteristics. Vaccine-target (toll-like receptors: TLR2 and TLR4) interactions, binding affinities, and dynamical stabilities were inspected through molecular docking and molecular dynamic (MD) simulation methods. Moreover, MD simulations for dimeric TLRs/vaccine in the membrane-aqueous environment were performed to understand the differential domain organization of TLRs/vaccine. Further, dynamical behaviors of vaccine/TLR systems were inspected via identifying the key residues (named HUB nodes) that control interaction stability and provide a clear molecular mechanism. The obtained results from molecular docking and MD simulation revealed a strong and stable interaction between vaccine and TLRs. The vaccine's ability to stimulate the immune response was assessed by using computational immune simulation. This predicted a significant level of cytotoxic T cell and helper T cell activation, as well as IgG, interleukin 2, and interferon-gamma production. This study shows that the designed vaccine is structurally and dynamically stable and can trigger an effective immune response against viral infections.
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Affiliation(s)
- Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Khattab Al-Khafaji
- Department of Medical Laboratory Technology, AL-Nisour University College Baghdad Iraq
| | - Md Takim Sarker
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Tugba Taskin-Tok
- Department of Bioinformatics and Computational Biology, Institute of Health Sciences, Gaziantep University Gaziantep 27310 Turkey
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University Gaziantep Turkey
| | - Abdus Samad Rana
- School of Biotechnology, Jiangnan University Wuxi 214122 PR China
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
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