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Broni E, Ashley C, Adams J, Manu H, Aikins E, Okom M, Miller WA, Wilson MD, Kwofie SK. Cheminformatics-Based Study Identifies Potential Ebola VP40 Inhibitors. Int J Mol Sci 2023; 24:ijms24076298. [PMID: 37047270 PMCID: PMC10094735 DOI: 10.3390/ijms24076298] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
The Ebola virus (EBOV) is still highly infectious and causes severe hemorrhagic fevers in primates. However, there are no regulatorily approved drugs against the Ebola virus disease (EVD). The highly virulent and lethal nature of EVD highlights the need to develop therapeutic agents. Viral protein 40 kDa (VP40), the most abundantly expressed protein during infection, coordinates the assembly, budding, and release of viral particles into the host cell. It also regulates viral transcription and RNA replication. This study sought to identify small molecules that could potentially inhibit the VP40 protein by targeting the N-terminal domain using an in silico approach. The statistical quality of AutoDock Vina’s capacity to discriminate between inhibitors and decoys was determined, and an area under the curve of the receiver operating characteristic (AUC-ROC) curve of 0.791 was obtained. A total of 29,519 natural-product-derived compounds from Chinese and African sources as well as 2738 approved drugs were successfully screened against VP40. Using a threshold of −8 kcal/mol, a total of 7, 11, 163, and 30 compounds from the AfroDb, Northern African Natural Products Database (NANPDB), traditional Chinese medicine (TCM), and approved drugs libraries, respectively, were obtained after molecular docking. A biological activity prediction of the lead compounds suggested their potential antiviral properties. In addition, random-forest- and support-vector-machine-based algorithms predicted the compounds to be anti-Ebola with IC50 values in the micromolar range (less than 25 μM). A total of 42 natural-product-derived compounds were identified as potential EBOV inhibitors with desirable ADMET profiles, comprising 1, 2, and 39 compounds from NANPDB (2-hydroxyseneganolide), AfroDb (ZINC000034518176 and ZINC000095485942), and TCM, respectively. A total of 23 approved drugs, including doramectin, glecaprevir, velpatasvir, ledipasvir, avermectin B1, nafarelin acetate, danoprevir, eltrombopag, lanatoside C, and glycyrrhizin, among others, were also predicted to have potential anti-EBOV activity and can be further explored so that they may be repurposed for EVD treatment. Molecular dynamics simulations coupled with molecular mechanics Poisson–Boltzmann surface area calculations corroborated the stability and good binding affinities of the complexes (−46.97 to −118.9 kJ/mol). The potential lead compounds may have the potential to be developed as anti-EBOV drugs after experimental testing.
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Affiliation(s)
- Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Carolyn Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Joseph Adams
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
| | - Hammond Manu
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Ebenezer Aikins
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Mary Okom
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology and Neuroscience, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence: (W.A.M.III); (S.K.K.); Tel.: +1(708)-2168451 (W.A.M.III); +23-320-3797922 (S.K.K.)
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana
- Correspondence: (W.A.M.III); (S.K.K.); Tel.: +1(708)-2168451 (W.A.M.III); +23-320-3797922 (S.K.K.)
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Zhang Y, Zhong X, Xi Z, Li Y, Xu H. Antiviral Potential of the Genus Panax: An updated review on their effects and underlying mechanism of action. J Ginseng Res 2023; 47:183-192. [PMID: 36926608 PMCID: PMC10014226 DOI: 10.1016/j.jgr.2022.11.003] [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: 07/04/2022] [Revised: 10/18/2022] [Accepted: 11/03/2022] [Indexed: 11/18/2022] Open
Abstract
Viral infections are known as one of the major factors causing death. Ginseng is a medicinal plant that demonstrated a wide range of antiviral potential, and saponins are the major bioactive ingredients in the genus Panax with vast therapeutic potential. Studies focusing on the antiviral activity of the genus Panax plant-derived agents (extracts and saponins) and their mechanisms were identified and summarized, including contributions mainly from January 2016 until January 2022. P. ginseng, P. notoginseng, and P. quinquefolius were included in the review as valuable medicinal herbs against infections with 14 types of viruses. Reports from 9 extracts and 12 bioactive saponins were included, with 6 types of protopanaxadiol (PPD) ginsenosides and 6 types of protopanaxatriol (PPT) ginsenosides. The mechanisms mainly involved the inhibition of viral attachment and replication, the modulation of immune response by regulating signaling pathways, including the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway, cystathionine γ-lyase (CSE)/hydrogen sulfide (H2S) pathway, phosphoinositide-dependent kinase-1 (PDK1)/ protein kinase B (Akt) signaling pathway, c-Jun N-terminal kinase (JNK)/activator protein-1 (AP-1) pathway, and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway. This review includes detailed information about the mentioned antiviral effects of the genus Panax extracts and saponins in vitro and in vivo, and in human clinical trials, which provides a scientific basis for ginseng as an adjunctive therapeutic drug or nutraceutical.
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Key Words
- ARI, acute respiratory illness
- BG, black ginseng
- BVDV, bovine viral diarrhea virus
- CHB, chronic hepatitis B
- CSFV, classical swine fever virus
- CVBs, group B coxsackieviruses
- DAA, direct-acting antiviral therapies
- EBV, the Epstein-Barr virus
- EV, enterovirus
- EV71, human enterovirus 71
- GCRV, grass carp reovirus
- GSLS, Ginseng stem-leaf saponins
- HAART, highly active antiretroviral drug therapy
- HBV, hepatitis B virus
- HCV, Hepatitis C virus
- HIV-1, human immunodeficiency virus type 1
- HP, highly pathogenic
- HSV, herpes simplex virus
- HVJ, hemagglutinating virus of Japan
- IFN-1, type-I interferon
- JAK, janus kinase
- JNK, c-Jun N-terminal kinase
- KRG, Korean Red Ginseng
- KSHV, Kaposi's sarcoma-associated herpesvirus
- MHV-68, murine gammaherpesvirus 68
- NDV, Newcastle disease virus
- NK, natural killer
- PNAB, PEGylated nanoparticle albumin-bound
- PNR, P. notoginseng root water extract
- PPD, protopanaxadiol
- PPT, protopanaxatriol
- PRRSV, porcine reproductive and respiratory syndrome virus
- Panax ginseng
- RSV, respiratory syncytial virus
- RV, rotavirus
- STAT, signal transducer and activator of transcription
- antiviral activity
- ginseng
- ginsenosides
- mechanism of action
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Affiliation(s)
- Yibo Zhang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai, China
| | - Xuanlei Zhong
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai, China
| | - Zhichao Xi
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai, China
| | - Yang Li
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai, China
| | - Hongxi Xu
- Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Cho YK, Kim JE, Lee J. Korean Red Ginseng slows coreceptor switch in HIV-1 infected patients. J Ginseng Res 2023; 47:117-122. [PMID: 36644395 PMCID: PMC9834003 DOI: 10.1016/j.jgr.2022.06.003] [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: 05/23/2022] [Revised: 06/24/2022] [Accepted: 06/29/2022] [Indexed: 01/18/2023] Open
Abstract
Background Human immunodeficiency virus-1 (HIV-1) that binds to the coreceptor CCR5 (R5 viruses) can evolve into viruses that bind to the coreceptor CXCR4 (X4 viruses), with high viral replication rates governing this coreceptor switch. Korean Red Ginseng (KRG) treatment of HIV-1 infected patients has been found to slow the depletion of CD4+ T cells. This study assessed whether the KRG-associated slow depletion of CD4+ T cells was associated with coreceptor switching. Methods This study included 146 HIV-1-infected patients naïve to antiretroviral therapy (ART) and seven patients receiving ART. A total of 540 blood samples were obtained from these patients over 122 ± 129 months. Their env genes were amplified by nested PCR or RT-PCR and subjected to direct sequencing. Tropism was determined with a 10% false positive rate (FPR) cutoff. Results Of the 146 patients naïve to ART, 102 were KRG-naïve, and 44 had been treated with KRG. Evaluation of initial samples showed that coreceptor switch had occurred in 19 patients, later occurring in 38 additional patients. There was a significant correlation between the amount of KRG and FPR. Based on initial samples, the R5 maintenance period was extended 2.35-fold, with the coreceptor switch being delayed 2.42-fold in KRG-treated compared with KRG-naïve patients. The coreceptor switch occurred in 85% of a homogeneous cohort. The proportion of patients who maintained R5 for ≥10 years was significantly higher in long-term slow progressors than in typical progressors. Conclusion KRG therapy extends R5 maintenance period by increasing FPR, thereby slowing the coreceptor switch.
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Affiliation(s)
- Young-Keol Cho
- Corresponding author. Department of Microbiology, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea.
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Mesenchymal Stem Cells in Embryo-Maternal Communication under Healthy Conditions or Viral Infections: Lessons from a Bovine Model. Cells 2022; 11:cells11121858. [PMID: 35740987 PMCID: PMC9221285 DOI: 10.3390/cells11121858] [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: 05/05/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022] Open
Abstract
Bovine mesenchymal stem cells are a relevant cell population found in the maternal reproductive tract that exhibits the immunomodulation capacity required to prevent embryo rejection. The phenotypic plasticity showed by both endometrial mesenchymal stem cells (eMSC) and embryonic trophoblast through mesenchymal to epithelial transition and epithelial to mesenchymal transition, respectively, is essential for embryo implantation. Embryonic trophoblast maintains active crosstalk via EVs and soluble proteins with eMSC and peripheral blood MSC (pbMSC) to ensure the retention of eMSC in case of pregnancy and induce the chemotaxis of pbMSC, critical for successful implantation. Early pregnancy-related proteins and angiogenic markers are detected as cargo in EVs and the soluble fraction of the embryonic trophectoderm secretome. The pattern of protein secretion in trophectoderm-EVs changes depending on their epithelial or mesenchymal phenotype and due to the uptake of MSC EVs. However, the changes in this EV-mediated communication between maternal and embryonic MSC populations infected by viruses that cause abortions in cattle are poorly understood. They are critical in the investigation of reproductive viral pathologies.
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Yasri S, Wiwanitkit V. Usefulness of ginseng in management of dengue: a bioinformatics pathway interrelationship analysis. INTERNATIONAL JOURNAL OF PHYSIOLOGY, PATHOPHYSIOLOGY AND PHARMACOLOGY 2022; 14:114-117. [PMID: 35619663 PMCID: PMC9123470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 03/03/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE The function of traditional herbs in tropical illness therapy is interesting. Many researches are currently being conducted on the effects of traditional herbs on a number of tropical ailments, including dengue fever. METHODS In this short paper, we used network pharmacology to determine a shared biological pathway for the pharmacological impact of ginseng, a traditional Asian herb, and the pathophysiological process of dengue fever, a serious tropical vector-borne disease. RESULTS Using interrelationship analysis, the authors were able to discover the common pathway via the vimentin node. CONCLUSION It's possible that ginseng could help in dengue fever therapy.
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Affiliation(s)
| | - Viroj Wiwanitkit
- Dr DY Patil UiversityPune, India
- Joseph Ayobabalola UniversityIkeji-Arakeji, Nigeria
- Hainan Medical UniversityHaikou, China
- Faculty of Medicine, University of NisNis, Serbia
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