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Xiang Y, Zhai G, Li Y, Wang M, Chen X, Wang R, Xie H, Zhang W, Ge G, Zhang Q, Xu Y, Caflisch A, Xu J, Chen H, Chen L. Ginkgolic acids inhibit SARS-CoV-2 and its variants by blocking the spike protein/ACE2 interplay. Int J Biol Macromol 2023; 226:780-792. [PMID: 36521705 PMCID: PMC9743696 DOI: 10.1016/j.ijbiomac.2022.12.057] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Targeting the interaction between the spike protein receptor binding domain (S-RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and angiotensin-converting enzyme 2 (ACE2) is a potential therapeutic strategy for treating coronavirus disease 2019 (COVID-19). However, we still lack small-molecule drug candidates for this target due to the missing knowledge in the hot spots for the protein-protein interaction. Here, we used NanoBiT technology to identify three Ginkgolic acids from an in-house traditional Chinese medicine (TCM) library, and they interfere with the S-RBD/ACE2 interplay. Our pseudovirus assay showed that one of the compounds, Ginkgolic acid C17:1 (GA171), significantly inhibits the entry of original SARS-CoV-2 and its variants into the ACE2-overexpressed HEK293T cells. We investigated and proposed the binding sites of GA171 on S-RBD by combining molecular docking and molecular dynamics simulations. Site-directed mutagenesis and surface plasmon resonance revealed that GA171 specifically binds to the pocket near R403 and Y505, critical residues of S-RBD for S-RBD interacting with ACE2. Thus, we provide structural insights into developing new small-molecule inhibitors and vaccines against the proposed S-RBD binding site.
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Affiliation(s)
- Yusen Xiang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guanglei Zhai
- Shanghai HighsLab Therapeutics. Inc., Shanghai 201203, China
| | - Yaozong Li
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland,Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Mengge Wang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xixiang Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China,Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Ruyu Wang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hang Xie
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Weidong Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China,Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qian Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jianrong Xu
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China,Shanghai Universities Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China,Corresponding authors
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China,Corresponding authors
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China,Corresponding authors
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Pharmacological Activities of Ginkgolic Acids in Relation to Autophagy. Pharmaceuticals (Basel) 2022; 15:ph15121469. [PMID: 36558920 PMCID: PMC9785683 DOI: 10.3390/ph15121469] [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: 10/10/2022] [Revised: 11/14/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Plant-derived natural compounds are widely used as alternative medicine in healthcare throughout the world. Ginkgolic acids, the phenolic compounds isolated from the leaves and seeds of Ginkgo biloba, are among the chemicals that have been explored the most. Ginkgolic acids exhibit cytotoxic activity against a vast number of human cancers in various preclinical models in vitro and in vivo. Additionally, the pharmacological activities of ginkgolic acids are also involved in antidiabetic, anti-bacteria, anti-virus, anti-fibrosis, and reno/neuroprotection. Autophagy as a highly conserved self-cleaning process that plays a crucial role in maintaining cellular and tissue homeostasis and has been proven to serve as a protective mechanism in the pathogenesis of many diseases, including neurodegenerative diseases, cancer, and infectious diseases. In this review, we surveyed the pharmacological activities of the major three forms of ginkgolic acids (C13:0, C15:1, and C17:1) that are linked to autophagic activity and the mechanisms to which these compounds may participate. A growing body of studies in last decade suggests that ginkgolic acids may represent promising chemical compounds in future drug development and an alternative remedy in humans.
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The Mechanism of Action of Ginkgolic Acid (15:1) against Gram-Positive Bacteria Involves Cross Talk with Iron Homeostasis. Microbiol Spectr 2022; 10:e0099121. [PMID: 35019708 PMCID: PMC8754111 DOI: 10.1128/spectrum.00991-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
With the increasing reports of community-acquired and nosocomial infection caused by multidrug-resistant Gram-positive pathogens, there is an urgent need to develop new antimicrobial agents with novel antibacterial mechanisms. Here, we investigated the antibacterial activity of the natural product ginkgolic acid (GA) (15:1), derived from Ginkgo biloba, and its potential mode of action against the Gram-positive bacteria Enterococcus faecalis and Staphylococcus aureus. The MIC values of GA (15:1) against clinical E. faecalis and S. aureus isolates from China were ≤4 and ≤8 μg/mL, respectively, from our test results. Moreover, GA (15:1) displayed high efficiency in biofilm formation inhibition and bactericidal activity against E. faecalis and S. aureus. During its inhibition of the planktonic bacteria, the antibacterial activity of GA (15:1) was significantly improved under the condition of abolishing iron homeostasis. When iron homeostasis was abolished, inhibition of planktonic bacteria by GA (15:1) was significantly improved. This phenomenon can be interpreted as showing that iron homeostasis disruption facilitated the disruption of the functions of ribosome and protein synthesis by GA (15:1), resulting in inhibition of bacterial growth and cell death. Genetic mutation of ferric uptake regulator (Fur) led to GA (15:1) tolerance in in vitro-induced resistant derivatives, while overexpression of Fur led to increased GA (15:1) susceptibility. Additionally, GA (15:1) significantly decreased the bacterial loads of S. aureus strain USA300 in the lung tissues of mice in a pneumonic murine model. Conclusively, this study revealed an antimicrobial mechanism of GA (15:1) involving cross talk with iron homeostasis against Gram-positive pathogens. In the future, the natural product GA (15:1) might be applied to combat infections caused by Gram-positive pathogens. IMPORTANCE The increasing emergence of infectious diseases associated with multidrug-resistant Gram-positive pathogens has raised the urgent need to develop novel antibiotics. GA (15:1) is a natural product derived from Ginkgo biloba and possesses a wide range of bioactivities, including antimicrobial activity. However, its antibacterial mechanisms remain unclear. Our current study found that the function of ferric uptake regulator (Fur) was highly correlated with the antimicrobial activity of GA (15:1) against E. faecalis and that the antibacterial activity of GA (15:1) could be strengthened by the disruption of iron homeostasis. This study provided important insight into the mode of action of GA (15:1) against Gram-positive bacteria and suggested that GA (15:1) holds the potential to be an antimicrobial treatment option for infection caused by multidrug-resistant Gram-positive pathogens.
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da Cunha LNOL, Tizziani T, Souza GB, Moreira MA, Neto JSS, Dos Santos CVD, de Carvalho MG, Dalmarco EM, Turqueti LB, Scotti MT, Scotti L, de Assis FF, Braga A, Sandjo LP. Natural Products with tandem Anti-inflammatory, Immunomodulatory and Anti-SARS-CoV/2 effects: A Drug Discovery Perspective against SARS-CoV-2. Curr Med Chem 2021; 29:2530-2564. [PMID: 34313197 DOI: 10.2174/0929867328666210726094955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/29/2021] [Accepted: 06/03/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND COVID-19 is still causing victims with long-term health consequences, mass deaths, and collapsing healthcare systems around the world. The disease has no efficient drugs. However, previous studies revealed that SARS-CoV-2 and SARS-CoV have 96% and 86.5% similarities in cysteine proteases (3CLpro) and papain-like protease (PLpro) sequences, respectively. This resemblance could be significant in the search for drug candidates with antiviral effects against SARS-CoV-2. OBJECTIVE This paper is a compilation of natural products that inhibit SARS-CoV 3CLpro and PLpro and, concomitantly, reduce inflammation and/or modulate the immune system as a perspective strategy for COVID-19 drug discovery. It also presents in silico studies performed on these selected natural products using SARS-CoV-2 3CLpro and PLpro as targets to propose a list of hit compounds. METHOD The plant metabolites were selected in the literature based on their biological activities on SARS-CoV proteins, inflammatory mediators, and immune response. The consensus docking analysis was performed using four different packages. RESULTS Seventy-nine compounds reported in the literature with inhibitory effects on SARS-CoV proteins were reported as anti-inflammatory agents. Fourteen of them showed in previous studies immunomodulatory effects. Five and six of these compounds showed significant in silico consensus as drug candidates that can inhibit PLpro and 3CLpro, respectively. Our findings corroborated recent results reported on anti-SARS-CoV-2 in the literature. CONCLUSION This study revealed that amentoflavone, rubranoside B, savinin, psoralidin, hirsutenone, and papyriflavonol A are good drug candidate for the search of antibiotics against COVID-19.
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Affiliation(s)
- Luana N O Leal da Cunha
- Programa de Pós-Graduação em Química, CFM, Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Tiago Tizziani
- Programa de Pós-Graduação em Química, CFM, Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Gabriella B Souza
- Programa de Pós-Graduação em Química, CFM, Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Monalisa A Moreira
- Programa de Pós-Graduação em Química, CFM, Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - José S S Neto
- Programa de Pós-Graduação em Química, CFM, Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Carlos V D Dos Santos
- Programa de Pós-Graduação em Química, CFM, Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Maryelle G de Carvalho
- Programa de Pós-Graduação em Química, CFM, Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Eduardo M Dalmarco
- Programa de Pós-Graduação em Farmácia, CCS, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Leonardo B Turqueti
- Programa de Pós-Graduação em Química, CFM, Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Marcus Tullius Scotti
- Program in Natural and Synthetic Bioactive Products Federal University of Paraíba Cidade Universitária-Castelo Branco III, João Pessoa, PB, Brazil
| | - Luciana Scotti
- Program in Natural and Synthetic Bioactive Products Federal University of Paraíba Cidade Universitária-Castelo Branco III, João Pessoa, PB, Brazil
| | - Francisco F de Assis
- Programa de Pós-Graduação em Química, CFM, Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Antonio Braga
- Programa de Pós-Graduação em Química, CFM, Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Louis Pergaud Sandjo
- Programa de Pós-Graduação em Química, CFM, Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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