1
|
Lü Z, Dai X, Xu J, Liu Z, Guo Y, Gao Z, Meng F. Medicinal chemistry strategies toward broad-spectrum antiviral agents to prevent next pandemics. Eur J Med Chem 2024; 271:116442. [PMID: 38685143 DOI: 10.1016/j.ejmech.2024.116442] [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] [Received: 12/04/2023] [Revised: 04/02/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
The pandemic and tremendous impact of severe acute respiratory syndrome coronavirus 2 alert us, despite great achievements in prevention and control of infectious diseases, we still lack universal and powerful antiviral strategies to rapidly respond to the potential threat of serious infectious disease. Various highly contagious and pathogenic viruses, as well as other unknown viruses may appear or reappear in human society at any time, causing a catastrophic epidemic. Developing broad-spectrum antiviral drugs with high security and efficiency is of great significance for timely meeting public health emergency and protecting the lives and health of the people. Hence, in this review, we summarized diverse broad-spectrum antiviral targets and corresponding agents from a medicinal chemistry prospective, compared the pharmacological advantages and disadvantages of different targets, listed representative agents, showed their structures, pharmacodynamics and pharmacokinetics characteristics, and conducted a critical discussion on their development potential, in the hope of providing up-to-date guidance for the development of broad-spectrum antivirals and perspectives for applications of antiviral therapy.
Collapse
Affiliation(s)
- Zirui Lü
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Xiandong Dai
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Jianjie Xu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Yongbiao Guo
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Zhenhua Gao
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Fanhua Meng
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China.
| |
Collapse
|
2
|
Kim T, Jung W, Cho S, Kim G, Yun H, Chae J. Predicting lung exposure of intramuscular niclosamide as an antiviral agent: Power-law based pharmacokinetic modeling. Clin Transl Sci 2024; 17:e13833. [PMID: 38797873 PMCID: PMC11128490 DOI: 10.1111/cts.13833] [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: 02/29/2024] [Revised: 04/28/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
Niclosamide, a potent anthelmintic agent, has emerged as a candidate against COVID-19 in recent studies. Its formulation has been investigated extensively to address challenges related to systemic exposure. In this study, niclosamide was formulated as a long-acting intramuscular injection to achieve systemic exposure in the lungs for combating the virus. To establish the dose-exposure relationship, a hamster model was selected, given its utility in previous COVID-19 infection studies. Pharmacokinetic (PK) analysis was performed using NONMEM and PsN. Hamsters were administered doses of 55, 96, 128, and 240 mg/kg with each group comprising five animals. Two types of PK models were developed, linear models incorporating partition coefficients and power-law distributed models, to characterize the relationship between drug concentrations in the plasma and lungs of the hamsters. Numerical and visual diagnostics, including basic goodness-of-fit and visual predictive checks, were employed to assess the models. The power-law-based PK model not only demonstrated superior numerical performance compared with the linear model but also exhibited better agreement in visual diagnostic evaluations. This phenomenon was attributed to the nonlinear relationship between drug concentrations in the plasma and lungs, reflecting kinetic heterogeneity. Dose optimization, based on predicting lung exposure, was conducted iteratively across different drug doses, with the minimum effective dose estimated to be ~1115 mg/kg. The development of a power-law-based PK model proved successful and effectively captured the nonlinearities observed in this study. This method is expected to be applicable for investigating the drug disposition of specific formulations in the lungs.
Collapse
Affiliation(s)
- Taeheon Kim
- Life Science Institute, Daewoong PharmaceuticalYonginSouth Korea
| | - Woojin Jung
- College of PharmacyChungnam National UniversityDaejeonSouth Korea
| | - Sangeun Cho
- Life Science Institute, Daewoong PharmaceuticalYonginSouth Korea
| | - Gwanyoung Kim
- Life Science Institute, Daewoong PharmaceuticalYonginSouth Korea
| | - Hwi‐yeol Yun
- College of PharmacyChungnam National UniversityDaejeonSouth Korea
- Department of Bio‐AI ConvergenceChungnam National UniversityDaejeonSouth Korea
| | - Jung‐woo Chae
- College of PharmacyChungnam National UniversityDaejeonSouth Korea
- Department of Bio‐AI ConvergenceChungnam National UniversityDaejeonSouth Korea
| |
Collapse
|
3
|
Siripongboonsitti T, Tawinprai K, Avirutnan P, Jitobaom K, Auewarakul P. A randomized trial to assess the acceleration of viral clearance by the combination Favipiravir/Ivermectin/Niclosamide in mild-to-moderate COVID-19 adult patients (FINCOV). J Infect Public Health 2024; 17:897-905. [PMID: 38569269 DOI: 10.1016/j.jiph.2024.03.030] [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] [Received: 11/20/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND The efficacy of the viral clearance and clinical outcomes of favipiravir (FPV) in outpatients being treated for coronavirus disease 2019 (COVID-19) is unclear. Ivermectin (IVM), niclosamide (NCL), and FPV demonstrated synergistic effects in vitro for exceed 78% inhibiting severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) replication. METHODS A phase 2, open-label, 1:1, randomized, controlled trial was conducted on Thai patients with mild-to-moderate COVID-19 who received either combination FPV/IVM/NCL therapy or FPV alone to assess the rate of viral clearance among individuals with mild-to-moderate COVID-19. RESULTS Sixty non-high-risk comorbid patients with mild-to-moderate COVID-19 were randomized; 30 received FPV/IVM/NCL, and 30 received FPV alone. Mixed-effects multiple linear regression analysis of the cycle threshold value from SARS-CoV-2 PCR demonstrated no statistically significant differences in viral clearance rates between the combined FPV/IVM/NCL therapy group and the FPV-alone group. World Health Organization Clinical Progression scores and symptomatic improvement did not differ between arms on days 3, 6, and 10, and no adverse events were reported. No patients required hospitalization, intensive care unit admission, or supplemental oxygen or died within 28 days. C-reactive protein on day 3 was lower in the FPV/IVM/NCL group. CONCLUSION Viral clearance rates did not differ significantly between the FPV/IVM/NCL combination therapy and FPV-alone groups of individuals with mild-to-moderate COVID-19, although the combined regimen demonstrated a synergistic effect in vitro. No discernible clinical benefit was observed. Further research is required to explore the potential benefits of FVP beyond its antiviral effects. TRIAL REGISTRATION TCTR20230403007, Registered 3 April 2023 - Retrospectively registered,https://trialsearch.who.int/Trial2.aspx?TrialID=TCTR20230403007.
Collapse
Affiliation(s)
- Taweegrit Siripongboonsitti
- Division of Infectious Diseases, Department of Medicine, Chulabhorn Hospital, Chulabhorn Royal Academy, Bangkok, Thailand; Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand.
| | - Kriangkrai Tawinprai
- Division of Infectious Diseases, Department of Medicine, Chulabhorn Hospital, Chulabhorn Royal Academy, Bangkok, Thailand; Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Panisadee Avirutnan
- Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kunlakanya Jitobaom
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Prasert Auewarakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| |
Collapse
|
4
|
Needham D. Niclosamide: A career builder. J Control Release 2024; 369:786-856. [PMID: 37544514 DOI: 10.1016/j.jconrel.2023.07.016] [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] [Received: 03/19/2023] [Revised: 06/24/2023] [Accepted: 07/08/2023] [Indexed: 08/08/2023]
Abstract
My contribution to honoring Professor Kinam Park celebrates and resonates with his scholarly career in drug delivery, his commitment to encouraging the next generation(s), and his efforts to keep us focused on clinically effective formulations. To do this I take as my example, niclosamide, a small molecule protonophore that, uniquely, can "target" all cell membranes, both plasma and organelle. As such, it acts upstream of many cell pathways and so has the potential to affect many of the essential events that a cell, and particularly a diseased cell or other entities like a virus, use to stay alive and prosper. Literature shows that it has so far been discovered to positively influence (at least): cancer, bacterial and viral infection, metabolic diseases such as Type II diabetes, NASH and NAFLD, artery constriction, endometriosis, neuropathic pain, rheumatoid arthritis, sclerodermatous graft-versus-host disease, systemic sclerosis, Parkinson's, and COPD. With such a fundamental action and broad-spectrum activity, I believe that studying niclosamide in all its manifestations, discovering if and to what extent it can contribute positively to disease control (and also where it can't), formulating it as effective therapeutics, and testing them in preclinical and clinical trials is a career builder for our next generation(s). The article is divided into two parts: Part I introduces niclosamide and other proton shunts mainly in cancer and viral infections and reviews an exponentially growing literature with some concepts and physicochemical properties that lead to its proton shunt mechanism. Part II focuses on repurposing by reformulation of niclosamide. I give two examples of "carrier-free formulations", - one for cancer (as a prodrug therapeutic of niclosamide stearate for i.v. and other administration routes, exemplified by our recent work on Osteosarcoma in mice and canine patients), and the other as a niclosamide solution formulation (that could provide the basis for a preventative nasal spray and early treatment option for COVID19 and other respiratory virus infections). My goal is to excite and enthuse, encourage, and motivate all involved in the drug development and testing process in academia, institutes, and industry, to learn more about this interesting molecule and others like it. To enable such endeavors, I give many proposed ideas throughout the document, that have been stimulated and inspired by gaps in the literature, urgent needs in disease, and new studies arising from our own work. The hope is that, by reading through this document and studying the suggested topics and references, the drug delivery and development community will continue our lineage and benefit from our legacy to achieve niclosamide's potential as an effective contributor to the treatment and control of many diseases and conditions.
Collapse
Affiliation(s)
- David Needham
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA; Translational Therapeutics, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK.
| |
Collapse
|
5
|
Freidel MR, Vakhariya PA, Sardarni SK, Armen RS. The Dual-Targeted Fusion Inhibitor Clofazimine Binds to the S2 Segment of the SARS-CoV-2 Spike Protein. Viruses 2024; 16:640. [PMID: 38675980 PMCID: PMC11054727 DOI: 10.3390/v16040640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/29/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Clofazimine and Arbidol have both been reported to be effective in vitro SARS-CoV-2 fusion inhibitors. Both are promising drugs that have been repurposed for the treatment of COVID-19 and have been used in several previous and ongoing clinical trials. Small-molecule bindings to expressed constructs of the trimeric S2 segment of Spike and the full-length SARS-CoV-2 Spike protein were measured using a Surface Plasmon Resonance (SPR) binding assay. We demonstrate that Clofazimine, Toremifene, Arbidol and its derivatives bind to the S2 segment of the Spike protein. Clofazimine provided the most reliable and highest-quality SPR data for binding with S2 over the conditions explored. A molecular docking approach was used to identify the most favorable binding sites on the S2 segment in the prefusion conformation, highlighting two possible small-molecule binding sites for fusion inhibitors. Results related to molecular docking and modeling of the structure-activity relationship (SAR) of a newly reported series of Clofazimine derivatives support the proposed Clofazimine binding site on the S2 segment. When the proposed Clofazimine binding site is superimposed with other experimentally determined coronavirus structures in structure-sequence alignments, the changes in sequence and structure may rationalize the broad-spectrum antiviral activity of Clofazimine in closely related coronaviruses such as SARS-CoV, MERS, hCoV-229E, and hCoV-OC43.
Collapse
Affiliation(s)
| | | | | | - Roger S. Armen
- Department of Pharmaceutical Sciences, College of Pharmacy, Thomas Jefferson University, 901 Walnut St. Suite 918, Philadelphia, PA 19170, USA (P.A.V.); (S.K.S.)
| |
Collapse
|
6
|
Chan JFW, Yuan S, Chu H, Sridhar S, Yuen KY. COVID-19 drug discovery and treatment options. Nat Rev Microbiol 2024:10.1038/s41579-024-01036-y. [PMID: 38622352 DOI: 10.1038/s41579-024-01036-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 04/17/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused substantial morbidity and mortality, and serious social and economic disruptions worldwide. Unvaccinated or incompletely vaccinated older individuals with underlying diseases are especially prone to severe disease. In patients with non-fatal disease, long COVID affecting multiple body systems may persist for months. Unlike SARS-CoV and Middle East respiratory syndrome coronavirus, which have either been mitigated or remained geographically restricted, SARS-CoV-2 has disseminated globally and is likely to continue circulating in humans with possible emergence of new variants that may render vaccines less effective. Thus, safe, effective and readily available COVID-19 therapeutics are urgently needed. In this Review, we summarize the major drug discovery approaches, preclinical antiviral evaluation models, representative virus-targeting and host-targeting therapeutic options, and key therapeutics currently in clinical use for COVID-19. Preparedness against future coronavirus pandemics relies not only on effective vaccines but also on broad-spectrum antivirals targeting conserved viral components or universal host targets, and new therapeutics that can precisely modulate the immune response during infection.
Collapse
Affiliation(s)
- Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, China
| | - Siddharth Sridhar
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
- Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China.
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, China.
| |
Collapse
|
7
|
Tang WF, Chang YH, Lin CC, Jheng JR, Hsieh CF, Chin YF, Chang TY, Lee JC, Liang PH, Lin CY, Lin GH, Cai JY, Chen YL, Chen YS, Tsai SK, Liu PC, Yang CM, Shadbahr T, Tang J, Hsu YL, Huang CH, Wang LY, Chen CC, Kau JH, Hung YJ, Lee HY, Wang WC, Tsai HP, Horng JT. BPR3P0128, a non-nucleoside RNA-dependent RNA polymerase inhibitor, inhibits SARS-CoV-2 variants of concern and exerts synergistic antiviral activity in combination with remdesivir. Antimicrob Agents Chemother 2024; 68:e0095623. [PMID: 38446062 PMCID: PMC10989008 DOI: 10.1128/aac.00956-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024] Open
Abstract
Viral RNA-dependent RNA polymerase (RdRp), a highly conserved molecule in RNA viruses, has recently emerged as a promising drug target for broad-acting inhibitors. Through a Vero E6-based anti-cytopathic effect assay, we found that BPR3P0128, which incorporates a quinoline core similar to hydroxychloroquine, outperformed the adenosine analog remdesivir in inhibiting RdRp activity (EC50 = 0.66 µM and 3 µM, respectively). BPR3P0128 demonstrated broad-spectrum activity against various severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern. When introduced after viral adsorption, BPR3P0128 significantly decreased SARS-CoV-2 replication; however, it did not affect the early entry stage, as evidenced by a time-of-drug-addition assay. This suggests that BPR3P0128's primary action takes place during viral replication. We also found that BPR3P0128 effectively reduced the expression of proinflammatory cytokines in human lung epithelial Calu-3 cells infected with SARS-CoV-2. Molecular docking analysis showed that BPR3P0128 targets the RdRp channel, inhibiting substrate entry, which implies it operates differently-but complementary-with remdesivir. Utilizing an optimized cell-based minigenome RdRp reporter assay, we confirmed that BPR3P0128 exhibited potent inhibitory activity. However, an enzyme-based RdRp assay employing purified recombinant nsp12/nsp7/nsp8 failed to corroborate this inhibitory activity. This suggests that BPR3P0128 may inhibit activity by targeting host-related RdRp-associated factors. Moreover, we discovered that a combination of BPR3P0128 and remdesivir had a synergistic effect-a result likely due to both drugs interacting with separate domains of the RdRp. This novel synergy between the two drugs reinforces the potential clinical value of the BPR3P0128-remdesivir combination in combating various SARS-CoV-2 variants of concern.
Collapse
Affiliation(s)
- Wen-Fang Tang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Yu-Hsiu Chang
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
- Department of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
| | - Cheng-Chin Lin
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Jia-Rong Jheng
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Chung-Fan Hsieh
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Department of Neurology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yuan-Fan Chin
- Department of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
| | - Tein-Yao Chang
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
- Department of Pathology and Graduate Institute of Pathology and Parasitology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Jin-Ching Lee
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chia-Yi Lin
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Guan-Hua Lin
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Jie-Yun Cai
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Yu-Li Chen
- Research Center for Industry of Human Ecology and Research Center for Chinese Herbal Medicine, Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Yuan-Siao Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Shan-Ko Tsai
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
| | - Ping-Cheng Liu
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
| | - Chuen-Mi Yang
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
| | - Tolou Shadbahr
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Yu-Lin Hsu
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
| | - Chih-Heng Huang
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
- Department of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Ling-Yu Wang
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Division of Medical Oncology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Cheng Cheung Chen
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Jyh-Hwa Kau
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
| | - Hsin-Yi Lee
- Institute of Biotechnology and Pharmaceutical Research, Value-Added MedChem Innovation Center, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Wen-Chieh Wang
- Institute of Biotechnology and Pharmaceutical Research, Value-Added MedChem Innovation Center, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Hui-Ping Tsai
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
| | - Jim-Tong Horng
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Research Center for Industry of Human Ecology and Research Center for Chinese Herbal Medicine, Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| |
Collapse
|
8
|
Shin WR, Kim DY, Kim SY, Ahn G, Park DY, Min J, Ahn JY, Kim YH. In vitro and in vivo validation of the antiviral effect of hCypA against SARS-CoV-2 via binding to the RBD of spike protein. Mol Ther 2024:S1525-0016(24)00170-9. [PMID: 38532628 DOI: 10.1016/j.ymthe.2024.03.029] [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: 09/22/2023] [Revised: 01/24/2024] [Accepted: 03/22/2024] [Indexed: 03/28/2024] Open
Abstract
The novel coronavirus disease 2019 has stimulated the rapid development of new biological therapeutics to inhibit SARS-CoV-2 infection; however, this remains a challenging task. In a previous study using structural analysis, we revealed that human cyclophilin A inhibits the entry of SARS-CoV-2 into host cells by interfering with the interaction of the receptor-binding domain of the spike protein with angiotensin-converting enzyme 2 on the host cell surface, highlighting its potential for antiviral therapy. For a comprehensive experimental validation, in this study, we verified the antiviral effects of human cyclophilin A against SARS-CoV-2, including its variants, using in vitro assays and experiments on an in vivo mouse model. Human cyclophilin A demonstrated a highly effective antiviral effect, with an 85% survival rate upon SARS-CoV-2 infection. It also reduced viral titers, inflammation in the lungs and brain, and cytokine release in the serum, suggesting a controlled immune response and potentially faster recovery. Overall, our study provides insights into the potential of human cyclophilin A as a therapeutic agent against SARS-CoV-2, which should guide future clinical trials that might provide an additional therapeutic option for patients.
Collapse
Affiliation(s)
- Woo-Ri Shin
- Department of Microbiology, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea; Department of Bioengineering, University of Pennsylvania, 210 S 33rd Street, Philadelphia, PA 19104, USA
| | - Do-Young Kim
- Department of Microbiology, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea
| | - Sang Yong Kim
- Department of Food Science and Biotechnology, Shin Ansan University, Danwon-Gu, Ansan 15435, Republic of Korea
| | - Gna Ahn
- Department of Microbiology, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea; Center for Ecology and Environmental Toxicology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Dae-Young Park
- Department of Microbiology, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea
| | - Jiho Min
- Graduate School of Semiconductor and Chemical Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-Gu Jeonju, Jeonbuk 54896, South Korea.
| | - Ji-Young Ahn
- Department of Microbiology, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea.
| | - Yang-Hoon Kim
- Department of Microbiology, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea.
| |
Collapse
|
9
|
Chen XF, Deng JM. The influence of novel coronavirus pneumonia on chronic disease management of asthma-a narrative review. J Thorac Dis 2024; 16:1590-1600. [PMID: 38505017 PMCID: PMC10944750 DOI: 10.21037/jtd-23-1139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 01/05/2024] [Indexed: 03/21/2024]
Abstract
Background and Objective The coronavirus disease 2019 (COVID-19) pandemic has taken a huge global toll on all fronts, creating new challenges for the diagnosis and treatment of respiratory diseases. For chronic management of asthma, on the one hand, the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may affect the asthma disease itself; on the other hand, in order to control the spread of the pandemic, forced isolation, mask-wearing and various disinfection measures also have an impact on the condition and medication of asthma patients. This article reviews the changes in chronic asthma management under the COVID-19 pandemic to provide reference for chronic disease management of asthma after the pandemic and for various public health emergencies in the future. Methods Online searching of literature was performed. The National Center for Biotechnology Information (NCBI), PubMed, Google Scholar, and EMBASE were searched. Key Content and Findings COVID-19 has had a huge impact on the world, and has also brought new challenges to the diagnosis and treatment of asthma and chronic disease management. On the one hand, the existence of the 2019 novel coronavirus directly affects the asthma disease itself, on the other hand, due to the particularity of the asthma disease itself, different levels of isolation and controls can cause patients with different degrees of medical difficulties; in addition, the application of various disinfectants in the environment also increases the risk of acute attacks of asthma patients, as well as mask-wearing, vaccination, anxiety about the disease, panic, etc., all of which have posed various degrees of impact on the condition and psychology of asthma patients. Conclusions The pandemic of COVID-19 has brought many difficulties to the chronic disease management of asthma, and has had a certain impact on the disease control of asthma patients. In the era with overflowing information, internet hospital is the current trend, and there is a long way to go for effectively penetrating medical resources virtually via the internet into chronic disease management of asthma.
Collapse
Affiliation(s)
- Xue-Fen Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Geriatrics Respiratory Medicine Department, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jing-Min Deng
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| |
Collapse
|
10
|
Kang MJ, Kim MJ, Kim A, Koo TS, Lee KR, Chae YJ. Pharmacokinetic interactions of niclosamide in rats: Involvement of organic anion transporters 1 and 3 and organic cation transporter 2. Chem Biol Interact 2024; 390:110886. [PMID: 38280639 DOI: 10.1016/j.cbi.2024.110886] [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] [Received: 10/16/2023] [Revised: 12/30/2023] [Accepted: 01/19/2024] [Indexed: 01/29/2024]
Abstract
Niclosamide is an anthelmintic drug with a long history of use and is generally safe and well tolerated in humans. As the conventional dose of niclosamide results in a low but certain level in systemic circulation, drug interactions with concomitant drugs should be considered. We aimed to investigate the interaction between niclosamide and drug transporters, as such information is currently limited. Niclosamide inhibited the transport activity of OATP1B1, OATP1B3, OAT1, OAT3, and OCT2 in vitro. Among them, the inhibitory effects on OAT1, OAT3, and OCT2 were strong, with IC50 values of less than 1 μM. When 3 mg/kg of niclosamide was co-administered to rats, systemic exposure to furosemide (a substrate of OAT1/3) and metformin (a substrate of OCT2) increased, and the renal clearance (CLr) of the drugs significantly decreased. These results suggest that niclosamide inhibits renal transporters, OAT1/3 and OCT2, not only in vitro but also in vivo, resulting in increased systemic exposure to the substrates of the transporters by strongly blocking the urinary elimination pathway in rats. The findings of this study will support a meticulous understanding of the transporter-mediated drug interactions of niclosamide and consequently aid in effective and safe use of niclosamide.
Collapse
Affiliation(s)
- Min-Ji Kang
- College of Pharmacy, Woosuk University, Wanju, 55338, Republic of Korea
| | - Min Ju Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
| | - Aeran Kim
- College of Pharmacy, Woosuk University, Wanju, 55338, Republic of Korea
| | - Tae-Sung Koo
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kyeong-Ryoon Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea; Department of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Yoon-Jee Chae
- College of Pharmacy, Woosuk University, Wanju, 55338, Republic of Korea; Research Institute of Pharmaceutical Sciences, Woosuk University, Wanju, 55338, Republic of Korea.
| |
Collapse
|
11
|
Alkafaas SS, Abdallah AM, Hassan MH, Hussien AM, Elkafas SS, Loutfy SA, Mikhail A, Murad OG, Elsalahaty MI, Hessien M, Elshazli RM, Alsaeed FA, Ahmed AE, Kamal HK, Hafez W, El-Saadony MT, El-Tarabily KA, Ghosh S. Molecular docking as a tool for the discovery of novel insight about the role of acid sphingomyelinase inhibitors in SARS- CoV-2 infectivity. BMC Public Health 2024; 24:395. [PMID: 38321448 PMCID: PMC10848368 DOI: 10.1186/s12889-024-17747-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024] Open
Abstract
Recently, COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants, caused > 6 million deaths. Symptoms included respiratory strain and complications, leading to severe pneumonia. SARS-CoV-2 attaches to the ACE-2 receptor of the host cell membrane to enter. Targeting the SARS-CoV-2 entry may effectively inhibit infection. Acid sphingomyelinase (ASMase) is a lysosomal protein that catalyzes the conversion of sphingolipid (sphingomyelin) to ceramide. Ceramide molecules aggregate/assemble on the plasma membrane to form "platforms" that facilitate the viral intake into the cell. Impairing the ASMase activity will eventually disrupt viral entry into the cell. In this review, we identified the metabolism of sphingolipids, sphingolipids' role in cell signal transduction cascades, and viral infection mechanisms. Also, we outlined ASMase structure and underlying mechanisms inhibiting viral entry 40 with the aid of inhibitors of acid sphingomyelinase (FIASMAs). In silico molecular docking analyses of FIASMAs with inhibitors revealed that dilazep (S = - 12.58 kcal/mol), emetine (S = - 11.65 kcal/mol), pimozide (S = - 11.29 kcal/mol), carvedilol (S = - 11.28 kcal/mol), mebeverine (S = - 11.14 kcal/mol), cepharanthine (S = - 11.06 kcal/mol), hydroxyzin (S = - 10.96 kcal/mol), astemizole (S = - 10.81 kcal/mol), sertindole (S = - 10.55 kcal/mol), and bepridil (S = - 10.47 kcal/mol) have higher inhibition activity than the candidate drug amiodarone (S = - 10.43 kcal/mol), making them better options for inhibition.
Collapse
Affiliation(s)
- Samar Sami Alkafaas
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Abanoub Mosaad Abdallah
- Narcotic Research Department, National Center for Social and Criminological Research (NCSCR), Giza, 11561, Egypt
| | - Mai H Hassan
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Aya Misbah Hussien
- Biotechnology department at Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Sara Samy Elkafas
- Production Engineering and Mechanical Design Department, Faculty of Engineering, Menofia University, Menofia, Egypt
- Faculty of Control System and Robotics, ITMO University, Saint-Petersburg, 197101, Russia
| | - Samah A Loutfy
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
- Nanotechnology Research Center, British University, Cairo, Egypt
| | - Abanoub Mikhail
- Department of Physics, Faculty of Science, Minia University, Minia, Egypt
- Faculty of Physics, ITMO University, Saint Petersburg, Russia
| | - Omnia G Murad
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Mohamed I Elsalahaty
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Mohamed Hessien
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Rami M Elshazli
- Biochemistry and Molecular Genetics Unit, Department of Basic Sciences, Faculty of Physical Therapy, Horus University - Egypt, New Damietta, 34517, Egypt
| | - Fatimah A Alsaeed
- Department of Biology, College of Science, King Khalid University, Muhayl, Saudi Arabia
| | - Ahmed Ezzat Ahmed
- Biology Department, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
| | - Hani K Kamal
- Anatomy and Histology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Wael Hafez
- NMC Royal Hospital, 16Th Street, 35233, Khalifa City, Abu Dhabi, United Arab Emirates
- Medical Research Division, Department of Internal Medicine, The National Research Centre, 12622, 33 El Buhouth St, Ad Doqi, Dokki, Cairo Governorate, Egypt
| | - Mohamed T El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
| | - Soumya Ghosh
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa
- Natural & Medical Science Research Center, University of Nizwa, Nizwa, Oman
| |
Collapse
|
12
|
Janin YL. On the origins of SARS-CoV-2 main protease inhibitors. RSC Med Chem 2024; 15:81-118. [PMID: 38283212 PMCID: PMC10809347 DOI: 10.1039/d3md00493g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024] Open
Abstract
In order to address the world-wide health challenge caused by the COVID-19 pandemic, the 3CL protease/SARS-CoV-2 main protease (SARS-CoV-2-Mpro) coded by its nsp5 gene became one of the biochemical targets for the design of antiviral drugs. In less than 3 years of research, 4 inhibitors of SARS-CoV-2-Mpro have actually been authorized for COVID-19 treatment (nirmatrelvir, ensitrelvir, leritrelvir and simnotrelvir) and more such as EDP-235, FB-2001 and STI-1558/Olgotrelvir or five undisclosed compounds (CDI-988, ASC11, ALG-097558, QLS1128 and H-10517) are undergoing clinical trials. This review is an attempt to picture this quite unprecedented medicinal chemistry feat and provide insights on how these cysteine protease inhibitors were discovered. Since many series of covalent SARS-CoV-2-Mpro inhibitors owe some of their origins to previous work on other proteases, we first provided a description of various inhibitors of cysteine-bearing human caspase-1 or cathepsin K, as well as inhibitors of serine proteases such as human dipeptidyl peptidase-4 or the hepatitis C protein complex NS3/4A. This is then followed by a description of the results of the approaches adopted (repurposing, structure-based and high throughput screening) to discover coronavirus main protease inhibitors.
Collapse
Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université 75005 Paris France
| |
Collapse
|
13
|
Martínez-Arribas B, Annang F, Díaz-González R, Pérez-Moreno G, Martín J, Mackenzie TA, Castillo F, Reyes F, Genilloud O, Ruiz-Pérez LM, Vicente F, Ramos MC, González-Pacanowska D. Establishment of a screening platform based on human coronavirus OC43 for the identification of microbial natural products with antiviral activity. Microbiol Spectr 2024; 12:e0167923. [PMID: 38009959 PMCID: PMC10783114 DOI: 10.1128/spectrum.01679-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 10/24/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE The COVID-19 pandemic has revealed the lack of effective treatments against betacoronaviruses and the urgent need for new broad-spectrum antivirals. Natural products are a valuable source of bioactive compounds with pharmaceutical potential that may lead to the discovery of new antiviral agents. Specifically, compared to conventional synthetic molecules, microbial natural extracts possess a unique and vast chemical diversity and are amenable to large-scale production. The implementation of a high-throughput screening platform using the betacoronavirus OC43 in a human cell line infection model has provided proof of concept of the approach and has allowed for the rapid and efficient evaluation of 1,280 microbial extracts. The identification of several active compounds validates the potential of the platform for the search for new compounds with antiviral capacity.
Collapse
Affiliation(s)
- Blanca Martínez-Arribas
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Frederick Annang
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Rosario Díaz-González
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Guiomar Pérez-Moreno
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Jesús Martín
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Thomas A. Mackenzie
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Francisco Castillo
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Fernando Reyes
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Luis Miguel Ruiz-Pérez
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Francisca Vicente
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - María C. Ramos
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| |
Collapse
|
14
|
Wu A, Shi K, Wang J, Zhang R, Wang Y. Targeting SARS-CoV-2 entry processes: The promising potential and future of host-targeted small-molecule inhibitors. Eur J Med Chem 2024; 263:115923. [PMID: 37981443 DOI: 10.1016/j.ejmech.2023.115923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/16/2023] [Accepted: 10/28/2023] [Indexed: 11/21/2023]
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has had a huge impact on global health. To respond to rapidly mutating viruses and to prepare for the next pandemic, there is an urgent need to develop small molecule therapies that target critical stages of the SARS-CoV-2 life cycle. Inhibiting the entry process of the virus can effectively control viral infection and play a role in prevention and treatment. Host factors involved in this process, such as ACE2, TMPRSS2, ADAM17, furin, PIKfyve, TPC2, CTSL, AAK1, V-ATPase, HSPG, and NRP1, have been found to be potentially good targets with stability. Through further exploration of the cell entry process of SARS-CoV-2, small-molecule drugs targeting these host factors have been developed. This review focuses on the structural functions of potential host cell targets during the entry of SARS-CoV-2 into host cells. The research progress, chemical structure, structure-activity relationship, and clinical value of small-molecule inhibitors against COVID-19 are reviewed to provide a reference for the development of small-molecule drugs against COVID-19.
Collapse
Affiliation(s)
- Aijia Wu
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Kunyu Shi
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Ruofei Zhang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yuxi Wang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China.
| |
Collapse
|
15
|
Qian B, Hu Y, Liu C, Zheng D, Han X, Gong M, Zou Y, Zeng D, Liao K, Miao Y, Wu X, Dai J, Wang Z, Xue F. Tetrandrine (TET) inhibits African swine fever virus entry into cells by blocking the PI3K/Akt pathway. Virus Res 2024; 339:199258. [PMID: 37923171 PMCID: PMC10661491 DOI: 10.1016/j.virusres.2023.199258] [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] [Received: 07/17/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
African Swine Fever Virus (ASFV) infection causes an acute and highly contagious disease in swine, resulting in significant economic losses and societal harm worldwide. Currently, there are no effective vaccines or antiviral drugs available for ASFV. Tetrandrine (TET) is extracted from the traditional Chinese herb Stephania tetrandrae, possesses diverse biological functions such as anti-inflammatory, anti-tumor, and antiviral activities. The study comprehensively evaluated the anti-ASFV effect of TET and validated it through biological assays. The dose-dependent inhibition of TET against ASFV was confirmed and a novel mechanism of TET's anti-ASFV activity was elucidated. TET effectively inhibits ASFV during internalization by blocking macropinocytosis through the inhibition of the PI3K/Akt pathway. The specific inhibitor LY294002, targeting the PI3K/Akt pathway, exhibits similar antiviral activity against ASFV as TET. Furthermore, the inhibitory effect of TET against other viruses such as Lumpy Skin Disease Virus (LSDV) and Porcine Epidemic Diarrhea Virus (PEDV) was also identified. Our findings suggest that TET effectively inhibits ASFV and reveal the potential for broad-spectrum antiviral drugs targeting the PI3K/Akt pathway.
Collapse
Affiliation(s)
- Bingxu Qian
- National Key Laboratory of Meat Quality Control and New Resource Creation, Nanjing Agricultural University, Nanjing, China; China Animal Health and Epidemiology Center, Qingdao, China
| | - Yongxin Hu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Cong Liu
- National Key Laboratory of Meat Quality Control and New Resource Creation, Nanjing Agricultural University, Nanjing, China
| | - Dongxia Zheng
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Xiuju Han
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Mingxia Gong
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Yanli Zou
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Dexin Zeng
- Technical Center of Hefei Customs, Hefei, China; Technology Center of Hefei Customs, and Anhui Province Key Laboratory of Analysis and Detection for Food Safety, Hefei, China
| | - Kai Liao
- National Key Laboratory of Meat Quality Control and New Resource Creation, Nanjing Agricultural University, Nanjing, China
| | - Yurun Miao
- National Key Laboratory of Meat Quality Control and New Resource Creation, Nanjing Agricultural University, Nanjing, China
| | - Xiaodong Wu
- China Animal Health and Epidemiology Center, Qingdao, China.
| | - Jianjun Dai
- National Key Laboratory of Meat Quality Control and New Resource Creation, Nanjing Agricultural University, Nanjing, China
| | - Zhiliang Wang
- China Animal Health and Epidemiology Center, Qingdao, China.
| | - Feng Xue
- National Key Laboratory of Meat Quality Control and New Resource Creation, Nanjing Agricultural University, Nanjing, China; Sanya Institute of Nanjing Agricultural University, Sanya, China.
| |
Collapse
|
16
|
Arreola J, Pérez-Cornejo P, Segura-Covarrubias G, Corral-Fernández N, León-Aparicio D, Guzmán-Hernández ML. Function and Regulation of the Calcium-Activated Chloride Channel Anoctamin 1 (TMEM16A). Handb Exp Pharmacol 2024; 283:101-151. [PMID: 35768554 DOI: 10.1007/164_2022_592] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Various human tissues express the calcium-activated chloride channel Anoctamin 1 (ANO1), also known as TMEM16A. ANO1 allows the passive chloride flux that controls different physiological functions ranging from muscle contraction, fluid and hormone secretion, gastrointestinal motility, and electrical excitability. Overexpression of ANO1 is associated with pathological conditions such as hypertension and cancer. The molecular cloning of ANO1 has led to a surge in structural, functional, and physiological studies of the channel in several tissues. ANO1 is a homodimer channel harboring two pores - one in each monomer - that work independently. Each pore is activated by voltage-dependent binding of two intracellular calcium ions to a high-affinity-binding site. In addition, the binding of phosphatidylinositol 4,5-bisphosphate to sites scattered throughout the cytosolic side of the protein aids the calcium activation process. Furthermore, many pharmacological studies have established ANO1 as a target of promising compounds that could treat several illnesses. This chapter describes our current understanding of the physiological roles of ANO1 and its regulation under physiological conditions as well as new pharmacological compounds with potential therapeutic applications.
Collapse
Affiliation(s)
- Jorge Arreola
- Physics Institute, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico.
| | - Patricia Pérez-Cornejo
- Department of Physiology and Biophysics, School of Medicine of Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Guadalupe Segura-Covarrubias
- Physics Institute, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Nancy Corral-Fernández
- Department of Physiology and Biophysics, School of Medicine of Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Daniel León-Aparicio
- Physics Institute, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | | |
Collapse
|
17
|
Khazir J, Ahmed S, Thakur RK, Hussain M, Gandhi SG, Babbar S, Mir SA, Shafi N, Tonfack LB, Rajpal VR, Maqbool T, Mir BA, Peer LA. Repurposing of Plant-based Antiviral Molecules for the Treatment of COVID-19. Curr Top Med Chem 2024; 24:614-633. [PMID: 38477206 DOI: 10.2174/0115680266276749240206101847] [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] [Received: 09/28/2023] [Revised: 12/30/2023] [Accepted: 01/10/2024] [Indexed: 03/14/2024]
Abstract
COVID-19, stemming from SARS-CoV-2, poses a formidable threat to global healthcare, with a staggering 77 million confirmed cases and 690,067 deaths recorded till December 24, 2023. Given the absence of specific drugs for this viral infection, the exploration of novel antiviral compounds becomes imperative. High-throughput technologies are actively engaged in drug discovery, and there is a parallel effort to repurpose plant-based molecules with established antiviral properties. In this context, the review meticulously delves into the potential of plant-based folk remedies and existing molecules. These substances have showcased substantial viral inhibition in diverse in vivo, in silico, and in vitro studies, particularly against critical viral protein targets, including SARS-CoV-2. The findings position these plant-based molecules as promising antiviral drug candidates for the swift advancement of treatments for COVID-19. It is noteworthy that the inherent attributes of these plant-based molecules, such as their natural origin, potency, safety, and cost-effectiveness, contribute to their appeal as lead candidates. The review advocates for further exploration through comprehensive in vivo studies conducted on animal models, emphasizing the potential of plant-based compounds to help in the ongoing quest to develop effective antivirals against COVID-19.
Collapse
Affiliation(s)
- Jabeena Khazir
- Department of Chemistry, HKM Govt. Degree College Eidgah, Cluster University Srinagar, J&K, 190001, India
| | - Sajad Ahmed
- Indian Institute of Integrative Medicine, Canal Road Jammu, 180001, J&K, India
| | - Rakesh Kr Thakur
- Amity Institute of Biotechnology, Amity University, Noida, 201313, India
| | - Manzoor Hussain
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
- Department of Botany, North Campus, University of Kashmir, Delina, Baramulla, J&K, 193103, India
| | - Sumit G Gandhi
- Indian Institute of Integrative Medicine, Canal Road Jammu, 180001, J&K, India
| | - Sadhana Babbar
- Department of Botany, Swami Shradhanand College, University of Delhi, Delhi, 110036, India
| | - Shabir Ahmad Mir
- Department of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah, 11952, Saudi Arabia
| | - Nusrat Shafi
- Department of Chemistry, HKM Govt. Degree College Eidgah, Cluster University Srinagar, J&K, 190001, India
| | - Libert Brice Tonfack
- Laboratory of Biotechnology and Environment, Department of Plant Biology, Faculty of Science, University of Yaounde I, PO Box 812, Yaounde, Cameroon
| | - Vijay Rani Rajpal
- Department of Botany, Hans Raj College, University of Delhi, Delhi, 110007, India
| | - Tariq Maqbool
- Laboratory of Nanotherapeutics and Regenerative Medicine, University of Kashmir, Srinagar, 190006, India
| | - Bilal Ahmad Mir
- Department of Botany, North Campus, University of Kashmir, Delina, Baramulla, J&K, 193103, India
| | - Latif Ahmad Peer
- Department of Botany, University of Kashmir, Srinagar, J&K, 190006, India
| |
Collapse
|
18
|
Ahmad I, Fatemi SN, Ghaheri M, Rezvani A, Khezri DA, Natami M, Yasamineh S, Gholizadeh O, Bahmanyar Z. An overview of the role of Niemann-pick C1 (NPC1) in viral infections and inhibition of viral infections through NPC1 inhibitor. Cell Commun Signal 2023; 21:352. [PMID: 38098077 PMCID: PMC10722723 DOI: 10.1186/s12964-023-01376-x] [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] [Received: 08/15/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses communicate with their hosts through interactions with proteins, lipids, and carbohydrate moieties on the plasma membrane (PM), often resulting in viral absorption via receptor-mediated endocytosis. Many viruses cannot multiply unless the host's cholesterol level remains steady. The large endo/lysosomal membrane protein (MP) Niemann-Pick C1 (NPC1), which is involved in cellular cholesterol transport, is a crucial intracellular receptor for viral infection. NPC1 is a ubiquitous housekeeping protein essential for the controlled cholesterol efflux from lysosomes. Its human absence results in Niemann-Pick type C disease, a deadly lysosomal storage disorder. NPC1 is a crucial viral receptor and an essential host component for filovirus entrance, infection, and pathogenesis. For filovirus entrance, NPC1's cellular function is unnecessary. Furthermore, blocking NPC1 limits the entry and replication of the African swine fever virus by disrupting cholesterol homeostasis. Cell entrance of quasi-enveloped variants of hepatitis A virus and hepatitis E virus has also been linked to NPC1. By controlling cholesterol levels, NPC1 is also necessary for the effective release of reovirus cores into the cytoplasm. Drugs that limit NPC1's activity are effective against several viruses, including SARS-CoV and Type I Feline Coronavirus (F-CoV). These findings reveal NPC1 as a potential therapeutic target for treating viral illnesses and demonstrate its significance for several viral infections. This article provides a synopsis of NPC1's function in viral infections and a review of NPC1 inhibitors that may be used to counteract viral infections. Video Abstract.
Collapse
Affiliation(s)
- Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | | | - Mohammad Ghaheri
- Student Research Committee, Alborz University of Medical Sciences, Karaj, Iran
| | - Ali Rezvani
- Anesthesiology Department, Case Western Reserve University, Cleveland, USA
| | - Dorsa Azizi Khezri
- Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Natami
- Department of Urology, Shahid Mohammadi Hospital, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | | | | | - Zahra Bahmanyar
- School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
19
|
Jash R, Prasanth DSNBK, Jash M, Suneetha A. Small molecules in the race of COVID-19 drug development. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2023; 25:1133-1154. [PMID: 37066495 DOI: 10.1080/10286020.2023.2197595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
COVID-19, caused by SARS-CoV-2, is spreading worldwide, regardless of different continents, increasing the death toll to almost five million, with more than 300 million reported cases. Researchers have been fighting the greatest threats to human civilization. This report provides a glimpse of ongoing small-molecule research on COVID-19 drugs to save millions of lives, which may provide researchers with a better understanding of rigorously investigated therapeutic agents. This report emphasizes the chemical structures and mechanisms of activity along with drug target information for several small molecules, including marketable drugs and agents under investigation.
Collapse
Affiliation(s)
- Rajiv Jash
- Department of Pharmacy, Sanaka Educational Trust Group of Institutions, Durgapur, West Bengal 713 212, India
| | - D S N B K Prasanth
- Department of Pharmacognosy, KVSR Siddhartha College of Pharmaceutical Sciences, Vijayawada, Andhra Pradesh 520 010, India
| | - Moumita Jash
- Department of Pharmacy, Sanaka Educational Trust Group of Institutions, Durgapur, West Bengal 713 212, India
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan 342037, India
| | - Achanti Suneetha
- Department of Pharmaceutical Analysis, KVSR Siddhartha College of Pharmaceutical Sciences, Vijayawada, Andhra Pradesh 520 010, India
| |
Collapse
|
20
|
Lawrence MJ, Grayson P, Jeffrey JD, Docker MF, Garroway CJ, Wilson JM, Manzon RG, Wilkie MP, Jeffries KM. Differences in the transcriptome response in the gills of sea lamprey acutely exposed to 3-trifluoromethyl-4-nitrophenol (TFM), niclosamide or a TFM:niclosamide mixture. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101122. [PMID: 37659214 DOI: 10.1016/j.cbd.2023.101122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 09/04/2023]
Abstract
Sea lamprey (Petromyzon marinus) control in the Laurentian Great Lakes of North America makes use of two pesticides: 3-trifluoromethyl-4-nitrophenol (TFM) and niclosamide, which are often co-applied. Sea lamprey appear to be vulnerable to these agents resulting from a lack of detoxification responses with evidence suggesting that lampricide mixtures produce a synergistic effect. However, there is a lack of information pertaining to the physiological responses of sea lamprey to niclosamide and TFM:niclosamide mixtures. Here, we characterized the transcriptomic responses of the sea lamprey to TFM, niclosamide, and a TFM:niclosamide (1.5 %) mixture in the gill. Along with a control, larval sea lamprey were exposed to each treatment for 6 h, after which gill tissues were extracted for measuring whole-transcriptome responses using RNA sequencing. Differential gene expression patterns were summarized, which included identifying the broad roles of genes and common expression patterns among the treatments. While niclosamide treatment resulted in no differentially expressed genes, TFM- and mixture-treated fish had several differentially expressed genes that were associated with the cell cycle, DNA damage, metabolism, immune function, and detoxification. However, there was no common differential expression among treatments. For the first time, we characterized the transcriptomic response of sea lamprey to niclosamide and a TFM:niclosamide mixture and identified that these agents impact mRNA transcript abundance of genes associated with the cell cycle and cellular death, and immune function, which are likely mediated through mitochondrial dysregulation. These results may help to inform the production of more targeted and effective lampricides in sea lamprey control efforts.
Collapse
Affiliation(s)
- M J Lawrence
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
| | - P Grayson
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - J D Jeffrey
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - M F Docker
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - C J Garroway
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - J M Wilson
- Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
| | - R G Manzon
- Department of Biology, University of Regina, Regina, SK S4S 0A2, Canada
| | - M P Wilkie
- Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
| | - K M Jeffries
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| |
Collapse
|
21
|
Yu SY, Choi M, Ryoo S, Cheong C, Huh K, Yoon YK, Jeong SJ. Clinical efficacy of inhaled corticosteroids in patients with coronavirus disease 2019: A living review and meta-analysis. PLoS One 2023; 18:e0294872. [PMID: 38015868 PMCID: PMC10684004 DOI: 10.1371/journal.pone.0294872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/09/2023] [Indexed: 11/30/2023] Open
Abstract
Inhaled corticosteroids are known to be relatively safe for long-term use in inflammatory respiratory diseases and it has been repurposed as one of the potential therapies for outpatients with coronavirus disease 2019 (COVID-19). However, inhaled corticosteroids have not been accepted for COVID-19 as a standard therapy because of its lack of proven benefits. Therefore, this study aimed to evaluate the effectiveness of inhaled corticosteroids in patients with COVID-19. Randomized controlled trials comparing the efficacy of inhaled corticosteroid treatment in patients with COVID-19 were identified through literature electronic database searches up to March 10, 2023. Meta-analyses were conducted for predefined outcomes, and the certainty of evidence was graded using the grading of recommendations, assessment, development, and evaluation approach. Overall, seven trials (eight articles) were included in this systematic review. Compared with usual care, inhaled corticosteroids was associated with significantly improved clinical recovery at 7 and 14 days in patients with COVID-19. In subgroup analysis, only budesonide showed significant efficacy in clinical recovery, whereas no significant benefit was observed for ciclesonide. Moreover, inhaled corticosteroids use was not significantly associated with all-cause hospitalization, all-cause mortality, admission to intensive care unit, or the use of mechanical ventilation. Our systematic review used evidence with very low to moderate certainty. Although based on limited evidence, our results suggest that inhaled corticosteroids treatment, especially budesonide, improves the clinical recovery of patients with COVID-19. More trials and meta-analyses are needed to assess the efficacy of inhaled corticosteroids for COVID-19 treatment.
Collapse
Affiliation(s)
- Su-Yeon Yu
- Department of Medical Information, College of Nursing and Health, Kongju National University, Gongju, Republic of Korea
| | - Miyoung Choi
- Division for Healthcare Technology Assessment Research, National Evidence-based Healthcare Collaborating Agency, Seoul, Republic of Korea
| | - Seungeun Ryoo
- Division for Healthcare Technology Assessment Research, National Evidence-based Healthcare Collaborating Agency, Seoul, Republic of Korea
- Department of Public Health, Korea University Graduate School, Seoul, Korea
| | - Chelim Cheong
- Health-Care Insight Research, Seoul, Republic of Korea
| | - Kyungmin Huh
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Young Kyung Yoon
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Su Jin Jeong
- Division of Infectious Disease, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| |
Collapse
|
22
|
Stagnoli S, Macari G, Corsi P, Capone B, Vidaurrazaga A, Ereño-Orbea J, Ardá A, Polticelli F, Jiménez-Barbero J, Abrescia NGA, Coluzza I. Targeting the Spike: Repurposing Mithramycin and Dihydroergotamine to Block SARS-CoV-2 Infection. ACS OMEGA 2023; 8:43490-43499. [PMID: 38027314 PMCID: PMC10666140 DOI: 10.1021/acsomega.3c02921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/15/2023] [Indexed: 12/01/2023]
Abstract
The urgency to find complementary therapies to current SARS-CoV-2 vaccines, whose effectiveness is preserved over time and not compromised by the emergence of new and emerging variants, has become a critical health challenge. We investigate the possibility of jamming the opening of the Receptor Binding Domain (RBD) of the spike protein of SARS-CoV-2 with small compounds. Through in silico screening, we identified two potential candidates that would lock the Receptor Binding Domain (RBD) in a closed configuration, preventing the virus from infecting the host cells. We show that two drugs already approved by the FDA, mithramycin and dihydroergotamine, can block infection using concentrations in the μM range in cell-based assays. Further STD-NMR experiments support dihydroergotamine's direct interaction with the spike protein. Overall, our results indicate that repurposing of these compounds might lead to potential clinical drug candidates for the treatment of SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Soledad Stagnoli
- Structure
and Cell Biology of Viruses Lab, Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research
and Technology Alliance (BRTA), 48160 Derio, Spain
| | - Gabriele Macari
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
| | - Pietro Corsi
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
| | - Barbara Capone
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
| | - Ander Vidaurrazaga
- Structure
and Cell Biology of Viruses Lab, Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research
and Technology Alliance (BRTA), 48160 Derio, Spain
| | - June Ereño-Orbea
- Chemical
Glycobiology Laboratory, CIC bioGUNE, BRTA, 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
| | - Ana Ardá
- Chemical
Glycobiology Laboratory, CIC bioGUNE, BRTA, 48160 Derio, Spain
| | - Fabio Polticelli
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
- National
Institute of Nuclear Physics, Roma Tre Section, 00154 Rome, Italy
| | - Jesús Jiménez-Barbero
- Chemical
Glycobiology Laboratory, CIC bioGUNE, BRTA, 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
- Centro
de
Investigación Biomédica En Red de Enfermedades Respiratorias.
(CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department
of Organic & Inorganic Chemistry, Faculty
of Science and Technology University of the Basque Country, EHU-UPV, 48940 Leioa, Spain
| | - Nicola GA Abrescia
- Structure
and Cell Biology of Viruses Lab, Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research
and Technology Alliance (BRTA), 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), Instituto de Salud
Carlos III, 28029 Madrid, Spain
| | - Ivan Coluzza
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
- Computational
Soft Matter and Biophysics Lab, Basque Center
for Materials, Applications and Nanostructures (BCMaterials), Buil. Martina Casiano, Pl. 3 Parque
Científico UPV/EHU Barrio Sarriena, 48940 Leioa, Spain
| |
Collapse
|
23
|
Suzuki M, Matsunaga A, Miyoshi-Akiyama T, Terada-Hirashima J, Sadamasu K, Nagashima M, Takasaki J, Izumi S, Hojo M, Ishizaka Y, Sugiyama H. Inhaled ciclesonide does not affect production of antibodies or elimination of virus in patients with COVID-19: Subanalysis of a multicenter, open-label randomized trial. Drug Discov Ther 2023; 17:304-311. [PMID: 37899206 DOI: 10.5582/ddt.2023.01078] [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: 10/31/2023]
Abstract
During an earlier multicenter, open-label, randomized controlled trial designed to evaluate the effectiveness of high-dose inhaled ciclesonide in patients with asymptomatic or mild coronavirus disease 2019 (COVID-19), we observed that worsening of shadows on CT without worsening of clinical symptoms was more common with ciclesonide. The present study sought to determine if an association exists between worsening CT shadows and impaired antibody production in patients treated with inhaled ciclesonide. Eighty-nine of the 90 patients in the original study were prospectively enrolled. After exclusions, there were 36 patients each in the ciclesonide and control groups. We analyzed antibody titers against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein at various time points. Changes in viral load during treatment were compared. There was no significant difference in age, sex, body mass index, background clinical characteristics, or symptoms between the two groups. Although evaluation on day 8 suggested a greater tendency for worsening shadows on CT in the ciclesonide group (p = 0.072), there was no significant difference between them in the ability to produce antibodies (p = 0.379) or the maximum antibody titer during the clinical course. In both groups, worsening CT shadows and higher viral loads were observed on days 1-8, suggesting ciclesonide does not affect clearance of the virus (p = 0.134). High-dose inhaled ciclesonide did not impair production of antibodies against SARS-CoV-2 or affect elimination of the virus, suggesting that this treatment can be used safely in patients with COVID-19 patients who use inhaled steroids for asthma and other diseases.
Collapse
Affiliation(s)
- Manabu Suzuki
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Akihiro Matsunaga
- Department of Intractable Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Tohru Miyoshi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Junko Terada-Hirashima
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Jin Takasaki
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinyu Izumi
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masayuki Hojo
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yukihito Ishizaka
- Department of Intractable Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Haruhito Sugiyama
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| |
Collapse
|
24
|
de Oliveira DF. In silico identification of five binding sites on the SARS-CoV-2 spike protein and selection of seven ligands for such sites. J Biomol Struct Dyn 2023:1-19. [PMID: 37921757 DOI: 10.1080/07391102.2023.2278077] [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: 01/27/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023]
Abstract
To contribute to the development of products capable of complexing with the SARS-CoV-2 spike protein, and thus preventing the virus from entering the host cell, this work aimed at discovering binding sites in the whole protein structure, as well as selecting substances capable of binding efficiently to such sites. Initially, the three-dimensional structure of the protein, with all receptor binding domains in the closed state, underwent blind docking with 38 substances potentially capable of binding to this protein according to the literature. This allowed the identification of five binding sites. Then, those substances with more affinities for these sites underwent pharmacophoric search in the ZINC15 database. The 14,329 substances selected from ZINC15 were subjected to docking to the five selected sites of the spike protein. The ligands with more affinities for the protein sites, as well as the selected sites themselves, were used in the de novo design of new ligands that were also docked to the binding sites of the protein. The best ligands, regardless of their origins, were used to form complexes with the spike protein, which were subsequently used in molecular dynamics simulations and calculations of ligands affinities to the protein through the molecular mechanics/Poisson-Boltzmann surface area method (MMPBSA). Seven substances with good affinities to the spike protein (-12.9 to -20.6 kcal/mol), satisfactory druggability (Bioavailability score: 0.17 to 0.55), and low acute toxicity to mice (LD50: 751 to 1421 mg/kg) were selected as potentially useful for the future development of new products to manage COVID-19 infections.Communicated by Ramaswamy H. Sarma.
Collapse
|
25
|
Moschovou K, Antoniou M, Chontzopoulou E, Papavasileiou KD, Melagraki G, Afantitis A, Mavromoustakos T. Exploring the Binding Effects of Natural Products and Antihypertensive Drugs on SARS-CoV-2: An In Silico Investigation of Main Protease and Spike Protein. Int J Mol Sci 2023; 24:15894. [PMID: 37958877 PMCID: PMC10649947 DOI: 10.3390/ijms242115894] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
In this in silico study, we conducted an in-depth exploration of the potential of natural products and antihypertensive molecules that could serve as inhibitors targeting the key proteins of the SARS-CoV-2 virus: the main protease (Mpro) and the spike (S) protein. By utilizing Induced Fit Docking (IFD), we assessed the binding affinities of the molecules under study to these crucial viral components. To further comprehend the stability and molecular interactions of the "protein-ligand" complexes that derived from docking studies, we performed molecular dynamics (MD) simulations, shedding light on the molecular basis of potential drug candidates for COVID-19 treatment. Moreover, we employed Molecular Mechanics Generalized Born Surface Area (MM-GBSA) calculations on all "protein-ligand" complexes, underscoring the robust binding capabilities of rosmarinic acid, curcumin, and quercetin against Mpro, and salvianolic acid b, rosmarinic acid, and quercetin toward the S protein. Furthermore, in order to expand our search for potent inhibitors, we conducted a structure similarity analysis, using the Enalos Suite, based on the molecules that indicated the most favored results in the in silico studies. The Enalos Suite generated 115 structurally similar compounds to salvianolic acid, rosmarinic acid, and quercetin. These compounds underwent IFD calculations, leading to the identification of two salvianolic acid analogues that exhibited strong binding to all the examined binding sites in both proteins, showcasing their potential as multi-target inhibitors. These findings introduce exciting possibilities for the development of novel therapeutic agents aiming to effectively disrupt the SARS-CoV-2 virus lifecycle.
Collapse
Affiliation(s)
- Kalliopi Moschovou
- Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Maria Antoniou
- Department of ChemoInformatics, NovaMechanics Ltd., 1046 Nicosia, Cyprus
- Department of Chemoinformatics, NovaMechanics MIKE, 18536 Piraeus, Greece
| | - Eleni Chontzopoulou
- Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Konstantinos D. Papavasileiou
- Department of ChemoInformatics, NovaMechanics Ltd., 1046 Nicosia, Cyprus
- Department of Chemoinformatics, NovaMechanics MIKE, 18536 Piraeus, Greece
| | - Georgia Melagraki
- Division of Physical Sciences & Applications, Hellenic Military Academy, 16672 Vari, Greece
| | - Antreas Afantitis
- Department of ChemoInformatics, NovaMechanics Ltd., 1046 Nicosia, Cyprus
- Department of Chemoinformatics, NovaMechanics MIKE, 18536 Piraeus, Greece
| | - Thomas Mavromoustakos
- Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
| |
Collapse
|
26
|
Chen J, Farraj RA, Limonta D, Tabatabaei Dakhili SA, Kerek EM, Bhattacharya A, Reformat FM, Mabrouk OM, Brigant B, Pfeifer TA, McDermott MT, Ussher JR, Hobman TC, Glover JNM, Hubbard BP. Reversible and irreversible inhibitors of coronavirus Nsp15 endoribonuclease. J Biol Chem 2023; 299:105341. [PMID: 37832873 PMCID: PMC10656235 DOI: 10.1016/j.jbc.2023.105341] [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] [Received: 05/31/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2, the causative agent of coronavirus disease 2019, has resulted in the largest pandemic in recent history. Current therapeutic strategies to mitigate this disease have focused on the development of vaccines and on drugs that inhibit the viral 3CL protease or RNA-dependent RNA polymerase enzymes. A less-explored and potentially complementary drug target is Nsp15, a uracil-specific RNA endonuclease that shields coronaviruses and other nidoviruses from mammalian innate immune defenses. Here, we perform a high-throughput screen of over 100,000 small molecules to identify Nsp15 inhibitors. We characterize the potency, mechanism, selectivity, and predicted binding mode of five lead compounds. We show that one of these, IPA-3, is an irreversible inhibitor that might act via covalent modification of Cys residues within Nsp15. Moreover, we demonstrate that three of these inhibitors (hexachlorophene, IPA-3, and CID5675221) block severe acute respiratory syndrome coronavirus 2 replication in cells at subtoxic doses. This study provides a pipeline for the identification of Nsp15 inhibitors and pinpoints lead compounds for further development against coronavirus disease 2019 and related coronavirus infections.
Collapse
Affiliation(s)
- Jerry Chen
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Rabih Abou Farraj
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel Limonta
- Department of Cell Biology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA; Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, California, USA
| | | | - Evan M Kerek
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Ashim Bhattacharya
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Filip M Reformat
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Ola M Mabrouk
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Benjamin Brigant
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tom A Pfeifer
- High Throughput Biology Facility, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark T McDermott
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - John R Ussher
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Tom C Hobman
- Department of Cell Biology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Basil P Hubbard
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
27
|
Jones T, Monakhova N, Guivel-Benhassine F, Lepioshkin A, Bruel T, Lane TR, Schwartz O, Puhl AC, Makarov V, Ekins S. Synthesis and Evaluation of 9-Aminoacridines with SARS-CoV-2 Antiviral Activity. ACS OMEGA 2023; 8:40817-40822. [PMID: 37929131 PMCID: PMC10620940 DOI: 10.1021/acsomega.3c05900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/04/2023] [Indexed: 11/07/2023]
Abstract
There have been relatively few small molecules developed with direct activity against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Two existing antimalarial drugs, pyronaridine and quinacrine, display whole cell activity against SARS-CoV-2 in A549 + ACE2 cells (pretreatment, IC50 = 0.23 and 0.19 μM, respectively) with moderate cytotoxicity (CC50 = 11.53 and 9.24 μM, respectively). Moreover, pyronaridine displays in vitro activity against SARS-CoV-2 PLpro (IC50 = 1.8 μM). Given their existing antiviral activity, these compounds are strong candidates for repurposing against COVID-19 and prompt us to study the structure-activity relationship of the 9-aminoacridine scaffold against SARS-CoV-2 using traditional medicinal chemistry to identify promising new analogs. Our studies identified several novel analogs possessing potent in vitro activity in U2-OS ACE2 GFP 1-10 and 1-11 (IC50 < 1.0 μM) as well as moderate cytotoxicity (CC50 > 4.0 μM). Compounds such as 7g, 9c, and 7e were more active, demonstrating selectivity indices SI > 10, and 9c displayed the strongest activity (IC50 ≤ 0.42 μM, CC50 ≥ 4.41 μM, SI > 10) among them, indicating that it has potential as a new lead molecule in this series against COVID-19.
Collapse
Affiliation(s)
- Thane Jones
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Natalia Monakhova
- Federal
Research Centre “Fundamentals of Biotechnology” of the
Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, Moscow 119071, Russia
| | | | - Alexander Lepioshkin
- Federal
Research Centre “Fundamentals of Biotechnology” of the
Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, Moscow 119071, Russia
| | - Timothée Bruel
- Institut
Pasteur, 28 rue du Dr Roux, Paris Cedex 15 75724, France
| | - Thomas R. Lane
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Olivier Schwartz
- Institut
Pasteur, 28 rue du Dr Roux, Paris Cedex 15 75724, France
| | - Ana C. Puhl
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Vadim Makarov
- Federal
Research Centre “Fundamentals of Biotechnology” of the
Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, Moscow 119071, Russia
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| |
Collapse
|
28
|
Gallardo-Toledo E, Neary M, Sharp J, Herriott J, Kijak E, Bramwell C, Curley P, Arshad U, Pertinez H, Rajoli RKR, Valentijn A, Cox H, Tatham L, Kipar A, Stewart JP, Owen A. Chemoprophylactic Assessment of Combined Intranasal SARS-CoV-2 Polymerase and Exonuclease Inhibition in Syrian Golden Hamsters. Viruses 2023; 15:2161. [PMID: 38005839 PMCID: PMC10675045 DOI: 10.3390/v15112161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Pibrentasvir (PIB) has been demonstrated to block exonuclease activity of the SARS-CoV-2 polymerase, protecting favipiravir (FVP) and remdesivir (RDV) from post-incorporation excision and eliciting antiviral synergy in vitro. The present study investigated the chemoprophylactic efficacy of PIB, FVP, RDV, FVP with PIB, or RDV with PIB dosed intranasally twice a day, using a Syrian golden hamster contact transmission model. Compared to the saline control, viral RNA levels were significantly lower in throat swabs in FVP (day 7), RDV (day 3, 5, 7), and RDV+PIB (day 3, 5) treatment groups. Similarly, findings were evident for nasal turbinate after PIB and RDV treatment, and lungs after PIB, FVP, and FVP+PIB treatment at day 7. Lung viral RNA levels after RDV and RDV+PIB treatment were only detectable in two animals per group, but the overall difference was not statistically significant. In situ examination of the lungs confirmed SARS-CoV-2 infection in all animals, except for one in each of the RDV and RDV+PIB treatment groups, which tested negative in all virus detection approaches. Overall, prevention of transmission was observed in most animals treated with RDV, while other agents reduced the viral load following contact transmission. No benefit of combining FVP or RDV with PIB was observed.
Collapse
Affiliation(s)
- Eduardo Gallardo-Toledo
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Megan Neary
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Joanne Sharp
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Joanne Herriott
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Edyta Kijak
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Chloe Bramwell
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Paul Curley
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Usman Arshad
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Henry Pertinez
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Rajith K. R. Rajoli
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Anthony Valentijn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Helen Cox
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Lee Tatham
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Anja Kipar
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - James P. Stewart
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Andrew Owen
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| |
Collapse
|
29
|
Tai Y, Tian M, Chen Y, You P, Song X, Xu B, Duan C, Jin D. Preparation of PLGA microspheres loaded with niclosamide via microfluidic technology and their inhibition of Caco-2 cell activity in vitro. Front Chem 2023; 11:1249293. [PMID: 37780982 PMCID: PMC10537947 DOI: 10.3389/fchem.2023.1249293] [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: 06/28/2023] [Accepted: 09/04/2023] [Indexed: 10/03/2023] Open
Abstract
Niclosamide (NIC) is a multifunctional drug that regulates various signaling pathways and biological processes. It is widely used for the treatment of cancer, viral infections, and metabolic disorders. However, its low water solubility limits its efficacy. In this study, poly(lactic-co-glycolic acid) (PLGA) and hyaluronic acid (HA), which exhibit good biocompatibility, biodegradability, and non-immunogenicity, were conjugated with niclosamide to prepare PLGA-HA-niclosamide polymeric nanoparticles (NIC@PLGA-HA) using microfluidic technology. The obtained microspheres had a uniform size distribution, with an average mean size of 442.0 ± 18.8 nm and zeta potential of -25.4 ± 0.41 mV, indicating their stable dispersion in water. The drug-loading efficiency was 8.70%. The drug-loaded microspheres showed sustained release behavior at pH 7.4 and 5.0, but not at pH 2.0, and the drug release kinetics were described by a quasi-first-order kinetic equation. The effect of the drug-loaded microspheres on the proliferation of Caco-2 cells was detected using the MTT assay. Hydrophilic HA-modified NIC@PLGA-HA microspheres prepared via microfluidic technology increased the cellular uptake by Caco-2 cells. Compared to the same concentration of NIC, the NIC@PLGA-HA microspheres demonstrated a stronger inhibitory effect on Caco-2 cells owing to the combined effect of PLGA, HA, and NIC. Therefore, the pH-responsive NIC@PLGA-HA microspheres synthesized using microfluid technology increased the solubility of NIC and improved its biological activity, thus contributing to the demand for intestinal drug carriers.
Collapse
Affiliation(s)
- Yulei Tai
- School Laboratory of Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Menglun Tian
- School Laboratory of Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yu Chen
- School Laboratory of Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Peijun You
- School Laboratory of Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Xiaojun Song
- School Laboratory of Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Bangting Xu
- School Laboratory of Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Cidong Duan
- School Laboratory of Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Dazhi Jin
- School Laboratory of Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, Zhejiang, China
| |
Collapse
|
30
|
Ahmed IS, Tapponi SL, Widatallah ME, Alakkad YM, Haider M. Unmasking the enigma: An in-depth analysis of COVID-19 impact on the pediatric population. J Infect Public Health 2023; 16:1346-1360. [PMID: 37433256 PMCID: PMC10299956 DOI: 10.1016/j.jiph.2023.06.017] [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] [Received: 05/26/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/13/2023] Open
Abstract
OBJECTIVES COVID-19, caused by the novel coronavirus, has had a profound and wide-reaching impact on individuals of all age groups across the globe, including children. This review article aims to provide a comprehensive analysis of COVID-19 in children, covering essential topics such as epidemiology, transmission, pathogenesis, clinical features, risk factors, diagnosis, treatment, vaccination, and others. By delving into the current understanding of the disease and addressing the challenges that lie ahead, this article seeks to shed light on the unique considerations surrounding COVID-19 in children and contribute to a deeper comprehension of this global health crisis affecting our youngest population. METHODS A comprehensive literature search was conducted to gather the most recent and relevant information regarding COVID-19 in children. Multiple renowned databases, including MEDLINE, PubMed, Scopus, as well as authoritative sources such as the World Health Organization (WHO), the U.S. Food and Drug Administration (FDA), the European Medicines Agency (EMA), and the National Institutes of Health (NIH) websites and others were thoroughly searched. The search included articles, guidelines, reports, clinical trials results and expert opinions published within the past three years, ensuring the inclusion of the latest research findings on COVID-19 in children. Several relevant keywords, including "COVID-19," "SARS-CoV-2," "children," "pediatrics," and related terms were used to maximize the scope of the search and retrieve a comprehensive set of articles. RESULTS AND CONCLUSION Three years since the onset of the COVID-19 pandemic, our understanding of its impact on children has evolved, but many questions remain unanswered. While SAR-CoV-2 generally leads to mild illness in children, the occurrence of severe cases and the potential for long-term effects cannot be overlooked. Efforts to comprehensively study COVID-19 in children must continue to improve preventive strategies, identify high-risk populations, and ensure optimal management. By unraveling the enigma surrounding COVID-19 in children, we can strive towards safeguarding their health and well-being in the face of future global health challenges.
Collapse
Affiliation(s)
- Iman Saad Ahmed
- Department of Pharmaceutics & Pharmaceutical Technology, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates.
| | - Sara Luay Tapponi
- Department of Pharmaceutics & Pharmaceutical Technology, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Marwa Eltahir Widatallah
- Department of Pharmaceutics & Pharmaceutical Technology, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Yumna Mohamed Alakkad
- Department of Pharmaceutics & Pharmaceutical Technology, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohamed Haider
- Department of Pharmaceutics & Pharmaceutical Technology, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| |
Collapse
|
31
|
Zhurinov MZ, Miftakhova AF, Keyer V, Shulgau ZT, Solodova EV, Kalykberdiyev MK, Abilmagzhanov AZ, Talgatov ET, Ait S, Shustov AV. Glycyrrhiza glabra L. Extracts and Other Therapeutics against SARS-CoV-2 in Central Eurasia: Available but Overlooked. Molecules 2023; 28:6142. [PMID: 37630394 PMCID: PMC10458004 DOI: 10.3390/molecules28166142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/07/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
In Central Eurasia, the availability of drugs that are inhibitors of the SARS-CoV-2 virus and have proven clinical efficacy is still limited. The aim of this study was to evaluate the activity of drugs that were available in Kazakhstan during the acute phase of the epidemic against SARS-CoV-2. Antiviral activity is reported for Favipiravir, Tilorone, and Cridanimod, which are registered drugs used for the treatment of respiratory viral infections in Kazakhstan. A licorice (Glycyrrhiza glabra) extract was also incorporated into this study because it offered an opportunity to develop plant-derived antivirals. The Favipiravir drug, which had been advertised in local markets as an anti-COVID cure, showed no activity against SARS-CoV-2 in cell cultures. On the contrary, Cridanimod showed impressive high activity (median inhibitory concentration 66 μg/mL) against SARS-CoV-2, justifying further studies of Cridanimod in clinical trials. Tilorone, despite being in the same pharmacological group as Cridanimod, stimulated SARS-CoV-2 replication in cultures. The licorice extract inhibited SARS-CoV-2 replication in cultures, with a high median effective concentration of 16.86 mg/mL. Conclusions: The synthetic, low-molecular-weight compound Cridanimod suppresses SARS-CoV-2 replication at notably low concentrations, and this drug is not toxic to cells at therapeutic concentrations. In contrast to its role as an inducer of interferons, Cridanimod is active in cells that have a genetic defect in interferon production, suggesting a different mechanism of action. Cridanimod is an attractive drug for inclusion in clinical trials against SARS-CoV-2 and, presumably, other coronaviruses. The extract from licorice shows low activity against SARS-CoV-2. At the same time, high doses of 2 g/kg of this plant extract show little or no acute toxicity in animal studies; for this reason, licorice products can still be considered for further development as a safe, orally administered adjunctive therapy.
Collapse
Affiliation(s)
- Murat Zh. Zhurinov
- “D.V. Sokolskiy Institute of Fuel, Catalysis and Electrochemistry” JSC, Almaty 050010, Kazakhstan
| | - Alfira F. Miftakhova
- “D.V. Sokolskiy Institute of Fuel, Catalysis and Electrochemistry” JSC, Almaty 050010, Kazakhstan
- Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Viktoriya Keyer
- Laboratory for Genetic Engineering, RSE “National Center for Biotechnology”, Astana 010000, Kazakhstan
| | - Zarina T. Shulgau
- Laboratory for Genetic Engineering, RSE “National Center for Biotechnology”, Astana 010000, Kazakhstan
| | - Elena V. Solodova
- “D.V. Sokolskiy Institute of Fuel, Catalysis and Electrochemistry” JSC, Almaty 050010, Kazakhstan
- Department of Biochemical Engineering, International Engineering Technological University, Almaty 050040, Kazakhstan
| | - Maxat K. Kalykberdiyev
- “D.V. Sokolskiy Institute of Fuel, Catalysis and Electrochemistry” JSC, Almaty 050010, Kazakhstan
| | - Arlan Z. Abilmagzhanov
- “D.V. Sokolskiy Institute of Fuel, Catalysis and Electrochemistry” JSC, Almaty 050010, Kazakhstan
| | - Eldar T. Talgatov
- “D.V. Sokolskiy Institute of Fuel, Catalysis and Electrochemistry” JSC, Almaty 050010, Kazakhstan
| | - Sauyk Ait
- “D.V. Sokolskiy Institute of Fuel, Catalysis and Electrochemistry” JSC, Almaty 050010, Kazakhstan
| | - Alexandr V. Shustov
- Laboratory for Genetic Engineering, RSE “National Center for Biotechnology”, Astana 010000, Kazakhstan
| |
Collapse
|
32
|
Cicka D, Niu Q, Qui M, Qian K, Miller E, Fan D, Mo X, Ivanov AA, Sarafianos SG, Du Y, Fu H. TMPRSS2 and SARS-CoV-2 SPIKE interaction assay for uHTS. J Mol Cell Biol 2023; 15:mjad017. [PMID: 36921991 PMCID: PMC10399917 DOI: 10.1093/jmcb/mjad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 11/21/2022] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
SARS-CoV-2, the coronavirus that causes the disease COVID-19, has claimed millions of lives over the past 2 years. This demands rapid development of effective therapeutic agents that target various phases of the viral replication cycle. The interaction between host transmembrane serine protease 2 (TMPRSS2) and viral SPIKE protein is an important initial step in SARS-CoV-2 infection, offering an opportunity for therapeutic development of viral entry inhibitors. Here, we report the development of a time-resolved fluorescence/Förster resonance energy transfer (TR-FRET) assay for monitoring the TMPRSS2-SPIKE interaction in lysate from cells co-expressing these proteins. The assay was configured in a 384-well-plate format for high-throughput screening with robust assay performance. To enable large-scale compound screening, we further miniaturized the assay into 1536-well ultrahigh-throughput screening (uHTS) format. A pilot screen demonstrated the utilization of the assay for uHTS. Our optimized TR-FRET uHTS assay provides an enabling platform for expanded screening campaigns to discover new classes of small-molecule inhibitors that target the SPIKE and TMPRSS2 protein-protein interaction.
Collapse
Affiliation(s)
- Danielle Cicka
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Graduate Program in Molecular and Systems Pharmacology, Laney Graduate School of Emory University, Atlanta, GA 30322, USA
| | - Qiankun Niu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Min Qui
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kun Qian
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric Miller
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Dacheng Fan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xiulei Mo
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Andrey A Ivanov
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
33
|
Wang Z, Yang L. The Therapeutic Potential of Natural Dietary Flavonoids against SARS-CoV-2 Infection. Nutrients 2023; 15:3443. [PMID: 37571380 PMCID: PMC10421531 DOI: 10.3390/nu15153443] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
The exploration of non-toxic and cost-effective dietary components, such as epigallocatechin 3-gallate and myricetin, for health improvement and disease treatment has recently attracted substantial research attention. The recent COVID-19 pandemic has provided a unique opportunity for the investigation and identification of dietary components capable of treating viral infections, as well as gathering the evidence needed to address the major challenges presented by public health emergencies. Dietary components hold great potential as a starting point for further drug development for the treatment and prevention of SARS-CoV-2 infection owing to their good safety, broad-spectrum antiviral activities, and multi-organ protective capacity. Here, we review current knowledge of the characteristics-chemical composition, bioactive properties, and putative mechanisms of action-of natural bioactive dietary flavonoids with the potential for targeting SARS-CoV-2 and its variants. Notably, we present promising strategies (combination therapy, lead optimization, and drug delivery) to overcome the inherent deficiencies of natural dietary flavonoids, such as limited bioavailability and poor stability.
Collapse
Affiliation(s)
- Zhonglei Wang
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, China
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus, Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Liyan Yang
- School of Physics and Physical Engineering, Qufu Normal University, Qufu 273165, China
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| |
Collapse
|
34
|
Mir IH, Thirunavukkarasu C. The relevance of acid sphingomyelinase as a potential target for therapeutic intervention in hepatic disorders: current scenario and anticipated trends. Arch Toxicol 2023; 97:2069-2087. [PMID: 37248308 PMCID: PMC10226719 DOI: 10.1007/s00204-023-03529-w] [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] [Received: 03/23/2023] [Accepted: 05/22/2023] [Indexed: 05/31/2023]
Abstract
Acid sphingomyelinase (ASMase) serves as one of the most remarkable enzymes in sphingolipid biology. ASMase facilitates the hydrolysis of sphingomyelin, yielding ceramide and phosphorylcholine via the phospholipase C signal transduction pathway. Owing to its prominent intervention in apoptosis, ASMase, and its product ceramide is now at the bleeding edge of lipid research due to the coalesced efforts of several research institutions over the past 40 years. ASMase-catalyzed ceramide synthesis profoundly alters the physiological properties of membrane structure in response to a broad range of stimulations, orchestrating signaling cascades for endoplasmic reticulum stress, autophagy, and lysosomal membrane permeabilization, which influences the development of hepatic disorders, such as steatohepatitis, hepatic fibrosis, drug-induced liver injury, and hepatocellular carcinoma. As a result, the potential to modulate the ASMase action with appropriate pharmaceutical antagonists has sparked a lot of curiosity. This article emphasizes the fundamental mechanisms of the systems that govern ASMase aberrations in various hepatic pathologies. Furthermore, we present an insight into the potential therapeutic agents used to mitigate ASMase irregularities and the paramountcy of such inhibitors in drug repurposing.
Collapse
Affiliation(s)
- Ishfaq Hassan Mir
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry, 605 014, India
| | | |
Collapse
|
35
|
Al-Karmalawy AA, Alnajjar R, Elmaaty AA, Binjubair FA, Al-Rashood ST, Mansour BS, Elkamhawy A, Eldehna WM, Mansour KA. Investigating the promising SARS-CoV-2 main protease inhibitory activity of secoiridoids isolated from Jasminum humile; in silico and in Vitro assessments with structure-activity relationship. J Biomol Struct Dyn 2023:1-13. [PMID: 37505066 DOI: 10.1080/07391102.2023.2240419] [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: 04/06/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023]
Abstract
The proteolytic enzyme 3 C-like protease (3Clpro or Mpro) is considered the most important target for SARS-CoV-2 which could be attributed to its crucial role in viral maturation and/or replication. Besides, natural phytoconstituents from plant origin are always promising lead compounds in the drug discovery area. Herein, the previously isolated and identified seven compounds from Jasminum humile (J. humile) were examined in vitro and in silico against the SARS-CoV-2 Mpro. First, the Vero E6 cells were utilized to pursue the potential of the investigated compounds (both in fractions and individual isolates) using the MTT assay. The total extract (T1) displayed the most significant activity against SARS-CoV-2 with IC50 = 29.36 µg/mL. Besides, the fractions (Fr1 and Fr3) showed good activity against the SARS-CoV-2 with IC50 values of 70.42, and 73.09 µg/mL, respectively. Then, the SARS-CoV-2 Mpro inhibitory assay was utilized to emphasize the inhibitory potential of the investigated isolates. MJN, JMD, and IJM candidates displayed prominent Mpro inhibitory potentials with IC50 = 30.44, 30.24, and 56.25 µM, respectively. Moreover, molecular docking of the identified seven compounds against the Mpro of SARS-CoV-2 showed that the five secoiridoids achieved superior results. MJN, JSM, IJM, and JMD showed higher affinities towards the Mpro target compared to the co-crystallized antagonist. Furthermore, the most active complexes (MJN, JSM, IJM, and JMD-Mpro) were subjected to MD simulations run for 150 ns and MM-GBSA calculations, compared to the co-crystallized inhibitor (O6K-Mpro). Finally, the SAR study clarified that JMD achieved the best anti-SARS-CoV-2 Mpro activity followed by MJN.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ahmed A Al-Karmalawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
| | - Radwan Alnajjar
- Department of Chemistry, Faculty of Science, University of Benghazi, Benghazi, Libya
- PharmD, Faculty of Pharmacy, Libyan International Medical University, Benghazi, Libya
| | - Ayman Abo Elmaaty
- Department of Medicinal Chemistry, Faculty of Pharmacy, Port Said University, Port Said, Egypt
| | - Faizah A Binjubair
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Sara T Al-Rashood
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Basma S Mansour
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Elkamhawy
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Republic of Korea
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
- School of Biotechnology, Badr University in Cairo, Badr City, Egypt
| | - Khaled Ahmed Mansour
- Department of Pharmacognosy, Faculty of Pharmacy, Horus University in Egypt, New Damietta, Egypt
| |
Collapse
|
36
|
Yang Z, Zhang Q, Wu X, Hao S, Hao X, Jones E, Zhang Y, Qiu J, Xu L. Repurposing Niclosamide as a Novel Anti-SARS-CoV-2 Drug by Restricting Entry Protein CD147. Biomedicines 2023; 11:2019. [PMID: 37509657 PMCID: PMC10377517 DOI: 10.3390/biomedicines11072019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the global coronavirus disease 2019 (COVID-19) pandemic, and the search for effective treatments has been limited. Furthermore, the rapid mutations of SARS-CoV-2 have posed challenges to existing vaccines and neutralizing antibodies, as they struggle to keep up with the increased viral transmissibility and immune evasion. However, there is hope in targeting the CD147-spike protein, which serves as an alternative point for the entry of SARS-CoV-2 into host cells. This protein has emerged as a promising therapeutic target for the development of drugs against COVID-19. Here, we demonstrate that the RNA-binding protein Human-antigen R (HuR) plays a crucial role in the post-transcriptional regulation of CD147 by directly binding to its 3'-untranslated region (UTR). We observed a decrease in CD147 levels across multiple cell lines upon HuR depletion. Furthermore, we identified that niclosamide can reduce CD147 by lowering the cytoplasmic translocation of HuR and reducing CD147 glycosylation. Moreover, our investigation revealed that SARS-CoV-2 infection induces an upregulation of CD147 in ACE2-expressing A549 cells, which can be effectively neutralized by niclosamide in a dose-dependent manner. Overall, our study unveils a novel regulatory mechanism of regulating CD147 through HuR and suggests niclosamide as a promising therapeutic option against COVID-19.
Collapse
Affiliation(s)
- Zhe Yang
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
| | - Qi Zhang
- Higuchi Biosciences Center, The University of Kansas, Lawrence, KS 66045, USA
| | - Xiaoqing Wu
- Higuchi Biosciences Center, The University of Kansas, Lawrence, KS 66045, USA
- The University of Kansas Cancer Center, The University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Siyuan Hao
- Department of Microbiology, Molecular Genetics and Immunology, The University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Xinbao Hao
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
| | - Elizabeth Jones
- Department of Pharmacology, Toxicology & Therapeutics, The University of Kansas Medical Center, Kansas City, KS 66160, USA; (E.J.)
| | - Yuxia Zhang
- Department of Pharmacology, Toxicology & Therapeutics, The University of Kansas Medical Center, Kansas City, KS 66160, USA; (E.J.)
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, The University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Liang Xu
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
- The University of Kansas Cancer Center, The University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Radiation Oncology, The University of Kansas Medical Center, Kansas City, KS 66160, USA
| |
Collapse
|
37
|
Gurukkalot K, Rajendran V. Repurposing Polyether Ionophores as a New-Class of Anti-SARS-Cov-2 Agents as Adjunct Therapy. Curr Microbiol 2023; 80:273. [PMID: 37414909 DOI: 10.1007/s00284-023-03366-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023]
Abstract
The emergence of SARS-CoV-2 and its variants have posed a significant threat to humankind in tackling the viral spread. Furthermore, currently repurposed drugs and frontline antiviral agents have failed to cure severe ongoing infections effectively. This insufficiency has fuelled research for potent and safe therapeutic agents to treat COVID-19. Nonetheless, various vaccine candidates have displayed a differential efficacy and need for repetitive dosing. The FDA-approved polyether ionophore veterinary antibiotic for treating coccidiosis has been repurposed for treating SARS-CoV-2 infection (as shown by both in vitro and in vivo studies) and other deadly human viruses. Based on selectivity index values, ionophores display therapeutic effects at sub-nanomolar concentrations and exhibit selective killing ability. They act on different viral targets (structural and non-structural proteins), host-cell components leading to SARS-CoV-2 inhibition, and their activity is further enhanced by Zn2+ supplementation. This review summarizes the anti-SARS-CoV-2 potential and molecular viral targets of selective ionophores like monensin, salinomycin, maduramicin, CP-80,219, nanchangmycin, narasin, X-206 and valinomycin. Ionophore combinations with Zn2+ are a new therapeutic strategy that warrants further investigation for possible human benefits.
Collapse
Affiliation(s)
- Keerthana Gurukkalot
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Vinoth Rajendran
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
| |
Collapse
|
38
|
Xu J, Xue Y, Bolinger AA, Li J, Zhou M, Chen H, Li H, Zhou J. Therapeutic potential of salicylamide derivatives for combating viral infections. Med Res Rev 2023; 43:897-931. [PMID: 36905090 PMCID: PMC10247541 DOI: 10.1002/med.21940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 11/09/2022] [Accepted: 02/26/2023] [Indexed: 03/12/2023]
Abstract
Since time immemorial human beings have constantly been fighting against viral infections. The ongoing and devastating coronavirus disease 2019 pandemic represents one of the most severe and most significant public health emergencies in human history, highlighting an urgent need to develop broad-spectrum antiviral agents. Salicylamide (2-hydroxybenzamide) derivatives, represented by niclosamide and nitazoxanide, inhibit the replication of a broad range of RNA and DNA viruses such as flavivirus, influenza A virus, and coronavirus. Moreover, nitazoxanide was effective in clinical trials against different viral infections including diarrhea caused by rotavirus and norovirus, uncomplicated influenza A and B, hepatitis B, and hepatitis C. In this review, we summarize the broad antiviral activities of salicylamide derivatives, the clinical progress, and the potential targets or mechanisms against different viral infections and highlight their therapeutic potential in combating the circulating and emerging viral infections in the future.
Collapse
Affiliation(s)
- Jimin Xu
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Yu Xue
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Andrew A. Bolinger
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jun Li
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Mingxiang Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Hongmin Li
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| |
Collapse
|
39
|
Razzaq M, Han JH, Ravichandran S, Kim J, Bae JY, Park MS, Kannappan S, Chung WC, Ahn JH, Song MJ, Kim KK. Stabilization of RNA G-quadruplexes in the SARS-CoV-2 genome inhibits viral infection via translational suppression. Arch Pharm Res 2023; 46:598-615. [PMID: 37563335 DOI: 10.1007/s12272-023-01458-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023]
Abstract
The G-quadruplex (G4) formed in single-stranded DNAs or RNAs plays a key role in diverse biological processes and is considered as a potential antiviral target. In the genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 25 putative G4-forming sequences are predicted; however, the effects of G4-binding ligands on SARS-CoV-2 replication have not been studied in the context of viral infection. In this study, we investigated whether G4-ligands suppressed SARS-CoV-2 replication and whether their antiviral activity involved stabilization of viral RNA G4s and suppression of viral gene expression. We found that pyridostatin (PDS) suppressed viral gene expression and genome replication as effectively as the RNA polymerase inhibitor remdesivir. Biophysical analyses revealed that the 25 predicted G4s in the SARS-CoV-2 genome formed a parallel G4 structure. In particular, G4-644 and G4-3467 located in the 5' region of ORF1a, formed a G4 structure that could be effectively stabilized by PDS. We also showed that PDS significantly suppressed translation of the reporter genes containing these G4s. Taken together, our results demonstrate that stabilization of RNA G4s by PDS in the SARS-CoV-2 genome inhibits viral infection via translational suppression, highlighting the therapeutic potential of G4-ligands in SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Maria Razzaq
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Ji Ho Han
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Subramaniyam Ravichandran
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
- Department of Biology, Stanford University, Stanford, United States of America
| | - Jaehyun Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Joon-Yong Bae
- Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Shrute Kannappan
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Woo-Chang Chung
- Department of Microbiology, Graduate School of Basic Medical Science (GSBMS), Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Jin-Hyun Ahn
- Department of Microbiology, Graduate School of Basic Medical Science (GSBMS), Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea.
| | - Moon Jung Song
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea.
| |
Collapse
|
40
|
Tomezsko PJ, Phillipson CW, Walsh ME. Lessons Learned From Limited Overlap of 15 In Vitro COVID-19 Drug Repurposing Screens. Health Secur 2023; 21:249-257. [PMID: 37196212 PMCID: PMC10357111 DOI: 10.1089/hs.2022.0132] [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] [Received: 10/03/2022] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 05/19/2023] Open
Abstract
Drug repurposing can quickly and cost-effectively identify medical countermeasures against pathogens with pandemic potential and could be used as a down-selection method for selecting US Food and Drug Administration-approved drugs to test in clinical trials. We compared results from 15 high-throughput in vitro screening efforts that tested approved and clinically evaluated drugs for activity against SARS-CoV-2 replication. From the 15 studies, 304 drugs were identified as displaying the highest level of confidence from the individual screens. Of those 304 drugs, 30 were identified in 2 or more screens, while only 3 drugs (apilimod, tetrandrine, and salinomycin) were identified in 4 screens. The lack of concordance in high-confidence hits and variations in protocols makes it challenging to use the collective data as down-selection criteria for identifying repurposing candidates to move into a clinical trial.
Collapse
Affiliation(s)
- Phillip J. Tomezsko
- Phillip J. Tomezsko, PhD, is Technical Staff, Counter WMD Systems Group, MIT Lincoln Laboratory, Lexington, MA
| | | | - Matthew E. Walsh
- Matthew E. Walsh was Associate Technical Staff, Biological and Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA
- Matthew E. Walsh is currently a PhD Student, Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| |
Collapse
|
41
|
Ma X, Liu L, Sun J, Zhang Y, Liu Y, Liu M, Wang B, Chang Y, Han Y, Gai Z. Expression of circulating angiotensin-converting enzyme 2 in children with asthma and the effects of inhaled corticosteroids. Immun Inflamm Dis 2023; 11:e922. [PMID: 37506151 PMCID: PMC10373566 DOI: 10.1002/iid3.922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/03/2023] [Accepted: 06/07/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND The global spread of coronavirus disease 2019 (COVID-19) has resulted in a significant disease burden, yet asthma patients do not have the expected high morbidity and mortality rates in the pandemics of COVID-19. OBJECTIVE To find the difference of angiotensin-converting enzyme 2 (ACE2) in asthma and nonasthma children and evaluate the effect of inhaled corticosteroids (ICS) on its expression. METHODS The ACE2, immunoglobulin E (IgE), and eosinophils were tested in different children. RESULTS A total of 157 children aged 3-16 years were enrolled. The expression of ACE2 in asthma children were lower than nonasthma children (T = -2.512, p = .013). Allergic nonasthma children had a significant higher ACE2 expression than children with allergic asthma (p = .013) and nonallergic asthma (p = .029). The expression of ACE2 had no significant difference between first-diagnosed asthma children and that had been treated with ICS for ≥6 months (F = 0.028, p = .598). The allergic asthma children showed a significantly higher eosinophils cells (EC) count than the allergic nonasthma (W = 200, p < .001) and nonallergic nonasthma children (W = 1089, p < .001). Nonallergic asthma children also had a significant higher EC count than the allergic non-asthma (W = 182.5, p < .001) and nonallergic non-asthma (W = 200.5, p < .001) children. There was no significant difference in IgE levels between asthmatic children and non-asthmatic children (W = 2792.5, p = .18). CONCLUSION Circulating ACE2 levels in asthmatic children were lower than those in non-asthmatic children and ICS treatment for ≥6 months did not affect the expression of ACE2 in peripheral blood in the asthma children.
Collapse
Affiliation(s)
- Xiang Ma
- Department of Respiratory Diseases, Children's Hospital affiliated to Shandong University, Jinan, China
- Jinan Key Lab of Respiratory Diseases for Children, Jinan Children's Hospital, Jinan, China
| | - Lesen Liu
- Department of Infectious Diseases, Huaiyin People's Hospital, Jinan, China
| | - Jing Sun
- Department of Respiratory Diseases, Children's Hospital affiliated to Shandong University, Jinan, China
- Jinan Key Lab of Respiratory Diseases for Children, Jinan Children's Hospital, Jinan, China
| | - Yun Zhang
- Department of Respiratory Diseases, Children's Hospital affiliated to Shandong University, Jinan, China
- Jinan Key Lab of Respiratory Diseases for Children, Jinan Children's Hospital, Jinan, China
| | - Yanqin Liu
- Department of Respiratory Diseases, Children's Hospital affiliated to Shandong University, Jinan, China
- Jinan Key Lab of Respiratory Diseases for Children, Jinan Children's Hospital, Jinan, China
| | - Miao Liu
- Department of Respiratory Diseases, Children's Hospital affiliated to Shandong University, Jinan, China
- Jinan Key Lab of Respiratory Diseases for Children, Jinan Children's Hospital, Jinan, China
| | - Bing Wang
- Department of Respiratory Diseases, Children's Hospital affiliated to Shandong University, Jinan, China
- Jinan Key Lab of Respiratory Diseases for Children, Jinan Children's Hospital, Jinan, China
| | - Yuna Chang
- Department of Respiratory Diseases, Children's Hospital affiliated to Shandong University, Jinan, China
- Jinan Key Lab of Respiratory Diseases for Children, Jinan Children's Hospital, Jinan, China
| | - Yuling Han
- Department of Respiratory Diseases, Children's Hospital affiliated to Shandong University, Jinan, China
| | - Zhongtao Gai
- Jinan Key Lab of Respiratory Diseases for Children, Jinan Children's Hospital, Jinan, China
| |
Collapse
|
42
|
Huang Z, Zhang P, Deng L. DeepCoVDR: deep transfer learning with graph transformer and cross-attention for predicting COVID-19 drug response. Bioinformatics 2023; 39:i475-i483. [PMID: 37387168 DOI: 10.1093/bioinformatics/btad244] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION The coronavirus disease 2019 (COVID-19) remains a global public health emergency. Although people, especially those with underlying health conditions, could benefit from several approved COVID-19 therapeutics, the development of effective antiviral COVID-19 drugs is still a very urgent problem. Accurate and robust drug response prediction to a new chemical compound is critical for discovering safe and effective COVID-19 therapeutics. RESULTS In this study, we propose DeepCoVDR, a novel COVID-19 drug response prediction method based on deep transfer learning with graph transformer and cross-attention. First, we adopt a graph transformer and feed-forward neural network to mine the drug and cell line information. Then, we use a cross-attention module that calculates the interaction between the drug and cell line. After that, DeepCoVDR combines drug and cell line representation and their interaction features to predict drug response. To solve the problem of SARS-CoV-2 data scarcity, we apply transfer learning and use the SARS-CoV-2 dataset to fine-tune the model pretrained on the cancer dataset. The experiments of regression and classification show that DeepCoVDR outperforms baseline methods. We also evaluate DeepCoVDR on the cancer dataset, and the results indicate that our approach has high performance compared with other state-of-the-art methods. Moreover, we use DeepCoVDR to predict COVID-19 drugs from FDA-approved drugs and demonstrate the effectiveness of DeepCoVDR in identifying novel COVID-19 drugs. AVAILABILITY AND IMPLEMENTATION https://github.com/Hhhzj-7/DeepCoVDR.
Collapse
Affiliation(s)
- Zhijian Huang
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Pan Zhang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410083, China
| | - Lei Deng
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
| |
Collapse
|
43
|
Ruatta SM, Prada Gori DN, Fló Díaz M, Lorenzelli F, Perelmuter K, Alberca LN, Bellera CL, Medeiros A, López GV, Ingold M, Porcal W, Dibello E, Ihnatenko I, Kunick C, Incerti M, Luzardo M, Colobbio M, Ramos JC, Manta E, Minini L, Lavaggi ML, Hernández P, Šarlauskas J, Huerta García CS, Castillo R, Hernández-Campos A, Ribaudo G, Zagotto G, Carlucci R, Medrán NS, Labadie GR, Martinez-Amezaga M, Delpiccolo CML, Mata EG, Scarone L, Posada L, Serra G, Calogeropoulou T, Prousis K, Detsi A, Cabrera M, Alvarez G, Aicardo A, Araújo V, Chavarría C, Mašič LP, Gantner ME, Llanos MA, Rodríguez S, Gavernet L, Park S, Heo J, Lee H, Paul Park KH, Bollati-Fogolín M, Pritsch O, Shum D, Talevi A, Comini MA. Garbage in, garbage out: how reliable training data improved a virtual screening approach against SARS-CoV-2 MPro. Front Pharmacol 2023; 14:1193282. [PMID: 37426813 PMCID: PMC10323144 DOI: 10.3389/fphar.2023.1193282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction: The identification of chemical compounds that interfere with SARS-CoV-2 replication continues to be a priority in several academic and pharmaceutical laboratories. Computational tools and approaches have the power to integrate, process and analyze multiple data in a short time. However, these initiatives may yield unrealistic results if the applied models are not inferred from reliable data and the resulting predictions are not confirmed by experimental evidence. Methods: We undertook a drug discovery campaign against the essential major protease (MPro) from SARS-CoV-2, which relied on an in silico search strategy -performed in a large and diverse chemolibrary- complemented by experimental validation. The computational method comprises a recently reported ligand-based approach developed upon refinement/learning cycles, and structure-based approximations. Search models were applied to both retrospective (in silico) and prospective (experimentally confirmed) screening. Results: The first generation of ligand-based models were fed by data, which to a great extent, had not been published in peer-reviewed articles. The first screening campaign performed with 188 compounds (46 in silico hits and 100 analogues, and 40 unrelated compounds: flavonols and pyrazoles) yielded three hits against MPro (IC50 ≤ 25 μM): two analogues of in silico hits (one glycoside and one benzo-thiazol) and one flavonol. A second generation of ligand-based models was developed based on this negative information and newly published peer-reviewed data for MPro inhibitors. This led to 43 new hit candidates belonging to different chemical families. From 45 compounds (28 in silico hits and 17 related analogues) tested in the second screening campaign, eight inhibited MPro with IC50 = 0.12-20 μM and five of them also impaired the proliferation of SARS-CoV-2 in Vero cells (EC50 7-45 μM). Discussion: Our study provides an example of a virtuous loop between computational and experimental approaches applied to target-focused drug discovery against a major and global pathogen, reaffirming the well-known "garbage in, garbage out" machine learning principle.
Collapse
Affiliation(s)
- Santiago M. Ruatta
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Denis N. Prada Gori
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
| | - Martín Fló Díaz
- Laboratory of Immunovirology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Franca Lorenzelli
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Karen Perelmuter
- Cell Biology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Lucas N. Alberca
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Carolina L. Bellera
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Andrea Medeiros
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Gloria V. López
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Vascular Biology and Drug Discovery Lab, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Mariana Ingold
- Vascular Biology and Drug Discovery Lab, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Williams Porcal
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Vascular Biology and Drug Discovery Lab, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Estefanía Dibello
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Irina Ihnatenko
- PVZ—Center of Pharmaceutical Engineering, Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Conrad Kunick
- PVZ—Center of Pharmaceutical Engineering, Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Marcelo Incerti
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Martín Luzardo
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Maximiliano Colobbio
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Química Fina, Facultad de Química, Instituto Polo Tecnológico de Pando, Universidad de la República, Montevideo, Uruguay
| | - Juan Carlos Ramos
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Química Fina, Facultad de Química, Instituto Polo Tecnológico de Pando, Universidad de la República, Montevideo, Uruguay
| | - Eduardo Manta
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Química Fina, Facultad de Química, Instituto Polo Tecnológico de Pando, Universidad de la República, Montevideo, Uruguay
| | - Lucía Minini
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - María Laura Lavaggi
- Laboratorio de Química Biológica Ambiental, Sede Rivera, Centro Universitario Regional Noreste, Universidad de la República, Montevideo, Uruguay
| | - Paola Hernández
- Departamento de Genética, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Jonas Šarlauskas
- Life Sciences Centre, Department of Xenobiotic Biochemistry, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | | | - Rafael Castillo
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Mexico, Mexico
| | - Alicia Hernández-Campos
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Mexico, Mexico
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Renzo Carlucci
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Noelia S. Medrán
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo R. Labadie
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Maitena Martinez-Amezaga
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carina M. L. Delpiccolo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Ernesto G. Mata
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Laura Scarone
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Laura Posada
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Gloria Serra
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | | | - Kyriakos Prousis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Anastasia Detsi
- Laboratory of Organic Chemistry, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Mauricio Cabrera
- Laboratorio de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú, Uruguay
| | - Guzmán Alvarez
- Laboratorio de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú, Uruguay
| | - Adrián Aicardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Departamento de Nutrición Clínica, Escuela de Nutrición, Universidad de la República, Montevideo, Uruguay
| | - Verena Araújo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Departamento de Alimentos, Escuela de Nutrición, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Chavarría
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | | | - Melisa E. Gantner
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Manuel A. Llanos
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Santiago Rodríguez
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
| | - Luciana Gavernet
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Soonju Park
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Jinyeong Heo
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Honggun Lee
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Kyu-Ho Paul Park
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | | | - Otto Pritsch
- Laboratory of Immunovirology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - David Shum
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Alan Talevi
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marcelo A. Comini
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| |
Collapse
|
44
|
Xue Y, Mei H, Chen Y, Griffin JD, Liu Q, Weisberg E, Yang J. Repurposing clinically available drugs and therapies for pathogenic targets to combat SARS-CoV-2. MedComm (Beijing) 2023; 4:e254. [PMID: 37193304 PMCID: PMC10183156 DOI: 10.1002/mco2.254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/11/2023] [Accepted: 03/07/2023] [Indexed: 05/18/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has affected a large portion of the global population, both physically and mentally. Current evidence suggests that the rapidly evolving coronavirus subvariants risk rendering vaccines and antibodies ineffective due to their potential to evade existing immunity, with enhanced transmission activity and higher reinfection rates that could lead to new outbreaks across the globe. The goal of viral management is to disrupt the viral life cycle as well as to relieve severe symptoms such as lung damage, cytokine storm, and organ failure. In the fight against viruses, the combination of viral genome sequencing, elucidation of the structure of viral proteins, and identifying proteins that are highly conserved across multiple coronaviruses has revealed many potential molecular targets. In addition, the time- and cost-effective repurposing of preexisting antiviral drugs or approved/clinical drugs for these targets offers considerable clinical advantages for COVID-19 patients. This review provides a comprehensive overview of various identified pathogenic targets and pathways as well as corresponding repurposed approved/clinical drugs and their potential against COVID-19. These findings provide new insight into the discovery of novel therapeutic strategies that could be applied to the control of disease symptoms emanating from evolving SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Yiying Xue
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Husheng Mei
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
- University of Science and Technology of ChinaHefeiAnhuiChina
| | - Yisa Chen
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - James D. Griffin
- Department of Medical Oncology, Dana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medicine, Harvard Medical SchoolBostonMassachusettsUSA
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
- University of Science and Technology of ChinaHefeiAnhuiChina
- Hefei Cancer HospitalChinese Academy of SciencesHefeiChina
| | - Ellen Weisberg
- Department of Medical Oncology, Dana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medicine, Harvard Medical SchoolBostonMassachusettsUSA
| | - Jing Yang
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
| |
Collapse
|
45
|
Rahaman M, Gupta P, Hossain M, Periyasami G, Das P. Effect of carbons' structure and type on AC electrical properties of polymer composites: predicting the percolation threshold of permittivity through different models. Colloid Polym Sci 2023; 301:1-19. [PMID: 37360022 PMCID: PMC10203672 DOI: 10.1007/s00396-023-05120-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 06/28/2023]
Abstract
The AC electrical properties of EVA- and NBR-based composites filled with different conductive fillers were investigated. Result shows several magnitudes of increment in AC electrical conductivity and dielectric permittivity after the addition of these conductive fillers, indicating that these materials can be used as supercapacitors. The magnitude of increment was varied according to polymer and filler types. Herein, we also have tested the applicability of different sigmoidal models to find out the percolation threshold value of permittivity for these binary polymer composite systems. It is observed that except sigmoidal-Boltzmann and sigmoidal-dose-response models, other sigmoidal models exhibit different values of percolation threshold when considered for any particular polymer composite system. The paper discusses the variation in results of percolation threshold with an emphasis on the advantages, disadvantages and limitations of these models. We also have applied the classical percolation theory to predict the percolation threshold of permittivity and compared with all the reported sigmoidal models. To judge the unanimous acceptability of these models, they tested vis-à-vis the permittivity results of various polymer composites reported in published literature. To comprehend, all the models except the sigmoidal-logistic-1 model were successfully applicable for predicting the percolation threshold of permittivity for polymer composites. Supplementary Information The online version contains supplementary material available at 10.1007/s00396-023-05120-2.
Collapse
Affiliation(s)
- Mostafizur Rahaman
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451 Saudi Arabia
| | - Prashant Gupta
- MIT-Centre for Advanced Materials Research and Technology (M-CAMRT), Department of Plastic and Polymer Engineering, Maharashtra Institute of Technology, Aurangabad, 431010 Maharashtra India
| | - Mokarram Hossain
- College of Engineering, Zienkiewicz Centre for Computational Engineering, Swansea University, Swansea, SA1 8EN UK
| | - Govindasami Periyasami
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451 Saudi Arabia
| | - Paramita Das
- Department of Chemical Engineering, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066 Madhya Pradesh India
| |
Collapse
|
46
|
Zhang Y, Duan Z, Guan Y, Xu T, Fu Y, Li G. Identification of 3 key genes as novel diagnostic and therapeutic targets for OA and COVID-19. Front Immunol 2023; 14:1167639. [PMID: 37283761 PMCID: PMC10239847 DOI: 10.3389/fimmu.2023.1167639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
Background Corona Virus Disease 2019 (COVID-19) and Osteoarthritis (OA) are diseases that seriously affect the physical and mental health and life quality of patients, particularly elderly patients. However, the association between COVID-19 and osteoarthritis at the genetic level has not been investigated. This study is intended to analyze the pathogenesis shared by OA and COVID-19 and to identify drugs that could be used to treat SARS-CoV-2-infected OA patients. Methods The four datasets of OA and COVID-19 (GSE114007, GSE55235, GSE147507, and GSE17111) used for the analysis in this paper were obtained from the GEO database. Common genes of OA and COVID-19 were identified through Weighted Gene Co-Expression Network Analysis (WGCNA) and differential gene expression analysis. The least absolute shrinkage and selection operator (LASSO) algorithm was used to screen key genes, which were analyzed for expression patterns by single-cell analysis. Finally, drug prediction and molecular docking were carried out using the Drug Signatures Database (DSigDB) and AutoDockTools. Results Firstly, WGCNA identified a total of 26 genes common between OA and COVID-19, and functional analysis of the common genes revealed the common pathological processes and molecular changes between OA and COVID-19 are mainly related to immune dysfunction. In addition, we screened 3 key genes, DDIT3, MAFF, and PNRC1, and uncovered that key genes are possibly involved in the pathogenesis of OA and COVID-19 through high expression in neutrophils. Finally, we established a regulatory network of common genes between OA and COVID-19, and the free energy of binding estimation was used to identify suitable medicines for the treatment of OA patients infected with SARS-CoV-2. Conclusion In the present study, we succeeded in identifying 3 key genes, DDIT3, MAFF, and PNRC1, which are possibly involved in the development of both OA and COVID-19 and have high diagnostic value for OA and COVID-19. In addition, niclosamide, ciclopirox, and ticlopidine were found to be potentially useful for the treatment of OA patients infected with SARS-CoV-2.
Collapse
|
47
|
Khadilkar A, Bunch ZL, Wagoner J, Ravindran V, Oda JM, Vidar WS, Clark TN, Manwill PK, Todd DA, Barr SA, Olinger LK, Fink SL, Strangman WK, Linington RG, MacMillan JB, Cech NB, Polyak SJ. Modulation of in Vitro SARS-CoV-2 Infection by Stephania tetrandra and Its Alkaloid Constituents. JOURNAL OF NATURAL PRODUCTS 2023; 86:1061-1073. [PMID: 37043739 PMCID: PMC10108733 DOI: 10.1021/acs.jnatprod.3c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Indexed: 05/05/2023]
Abstract
Botanical natural products have been widely consumed for their purported usefulness against COVID-19. Here, six botanical species from multiple sources and 173 isolated natural product compounds were screened for blockade of wild-type (WT) SARS-CoV-2 infection in human 293T epithelial cells overexpressing ACE-2 and TMPRSS2 protease (293TAT). Antiviral activity was demonstrated by an extract from Stephania tetrandra. Extract fractionation, liquid chromatography-mass spectrometry (LC-MS), antiviral assays, and computational analyses revealed that the alkaloid fraction and purified alkaloids tetrandrine, fangchinoline, and cepharanthine inhibited WT SARS-CoV-2 infection. The alkaloids and alkaloid fraction also inhibited the delta variant of concern but not WT SARS-CoV-2 in VeroAT cells. Membrane permeability assays demonstrate that the alkaloids are biologically available, although fangchinoline showed lower permeability than tetrandrine. At high concentrations, the extract, alkaloid fractions, and pure alkaloids induced phospholipidosis in 293TAT cells and less so in VeroAT cells. Gene expression profiling during virus infection suggested that alkaloid fraction and tetrandrine displayed similar effects on cellular gene expression and pathways, while fangchinoline showed distinct effects on cells. Our study demonstrates a multifaceted approach to systematically investigate the diverse activities conferred by complex botanical mixtures, their cell-context specificity, and their pleiotropic effects on biological systems.
Collapse
Affiliation(s)
- Aswad Khadilkar
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95964, United States
| | - Zoie L. Bunch
- Department
of Chemistry and Biochemistry, University
of North Carolina, Greensboro, North Carolina 27412, United States
| | - Jessica Wagoner
- Department
of Laboratory Medicine and Pathology, University
of Washington, Seattle, Washington 98195,United States
| | - Vandana Ravindran
- Oslo
Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, Oslo 0313, Norway
| | - Jessica M. Oda
- Department
of Laboratory Medicine and Pathology, University
of Washington, Seattle, Washington 98195,United States
| | - Warren S. Vidar
- Department
of Chemistry and Biochemistry, University
of North Carolina, Greensboro, North Carolina 27412, United States
| | - Trevor N. Clark
- Department
of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Preston K. Manwill
- Department
of Chemistry and Biochemistry, University
of North Carolina, Greensboro, North Carolina 27412, United States
| | - Daniel A. Todd
- Department
of Chemistry and Biochemistry, University
of North Carolina, Greensboro, North Carolina 27412, United States
| | - Sarah A. Barr
- Department
of Chemistry and Biochemistry, University
of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Lauren K. Olinger
- Department
of Biology and Marine Biology, University
of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Susan L. Fink
- Department
of Laboratory Medicine and Pathology, University
of Washington, Seattle, Washington 98195,United States
| | - Wendy K. Strangman
- Department
of Chemistry and Biochemistry, University
of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Roger G. Linington
- Department
of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - John B. MacMillan
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95964, United States
| | - Nadja B. Cech
- Department
of Chemistry and Biochemistry, University
of North Carolina, Greensboro, North Carolina 27412, United States
| | - Stephen J. Polyak
- Department
of Laboratory Medicine and Pathology, University
of Washington, Seattle, Washington 98195,United States
| |
Collapse
|
48
|
Yang Z, Zhang Q, Wu X, Hao S, Hao X, Jones E, Zhang Y, Qiu J, Xu L. Repurposing niclosamide as a novel anti-SARS-Cov-2 drug by restricting entry protein CD147. RESEARCH SQUARE 2023:rs.3.rs-2763207. [PMID: 37090542 PMCID: PMC10120763 DOI: 10.21203/rs.3.rs-2763207/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Background The burst of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing the global COVID-19 pandemic. But until today only limited numbers of drugs are discovered to treat COVID-19 patients. Even worse, the rapid mutations of SARS-CoV-2 compromise the effectiveness of existing vaccines and neutralizing antibodies due to the increased viral transmissibility and immune escape. CD147-spike protein, one of the entries of SRAR-CoV-2 into host cells, has been reported as a promising therapeutic target for developing drugs against COVID-19. Methods CRISPR-Cas9 induced gene knockout, western blotting, tet-off protein overexpression, ribonucleoprotein IP and RNA-IP were used to confirm the regulation of HuR on mRNA of CD147. Regulation of niclosamide on HuR nucleo-translocation was assessed by immunofluorescence staining of cell lines, IHC staining of tissue of mouse model and western blotting. Finally, the suppression of niclosamide on SARS-CoV-2 infection induced CD147 was evaluated by ACE2-expressing A549 cells and western blotting. Results We first discovered a novel regulation mechanism of CD147 via the RNA-binding protein HuR. We found that HuR regulates CD147 post-transcription by directly bound to its 3'-UTR. The loss of HuR reduced CD147 in multiple cell lines. Niclosamide inhibited CD147 function by blocking HuR cytoplasmic translocation and diminishing CD147 glycosylation. SARS-CoV-2 infection induced CD147 in ACE2-expressing A549 cells, which could be neutralized by niclosamide in a dose-dependent manner. Conclusion Together, our study reveals a novel regulation mechanism of CD147 and niclosamide can be repurposed as an effective COVID-19 drug by targeting the virus entry, CD147-spike protein.
Collapse
|
49
|
Chatterjee A, Walters R, Shafi Z, Ahmed OS, Sebek M, Gysi D, Yu R, Eliassi-Rad T, Barabási AL, Menichetti G. Improving the generalizability of protein-ligand binding predictions with AI-Bind. Nat Commun 2023; 14:1989. [PMID: 37031187 PMCID: PMC10082765 DOI: 10.1038/s41467-023-37572-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 03/23/2023] [Indexed: 04/10/2023] Open
Abstract
Identifying novel drug-target interactions is a critical and rate-limiting step in drug discovery. While deep learning models have been proposed to accelerate the identification process, here we show that state-of-the-art models fail to generalize to novel (i.e., never-before-seen) structures. We unveil the mechanisms responsible for this shortcoming, demonstrating how models rely on shortcuts that leverage the topology of the protein-ligand bipartite network, rather than learning the node features. Here we introduce AI-Bind, a pipeline that combines network-based sampling strategies with unsupervised pre-training to improve binding predictions for novel proteins and ligands. We validate AI-Bind predictions via docking simulations and comparison with recent experimental evidence, and step up the process of interpreting machine learning prediction of protein-ligand binding by identifying potential active binding sites on the amino acid sequence. AI-Bind is a high-throughput approach to identify drug-target combinations with the potential of becoming a powerful tool in drug discovery.
Collapse
Affiliation(s)
- Ayan Chatterjee
- Network Science Institute, Northeastern University, Boston, MA, USA
| | - Robin Walters
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Zohair Shafi
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Omair Shafi Ahmed
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Michael Sebek
- Network Science Institute, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Deisy Gysi
- Network Science Institute, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rose Yu
- Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Tina Eliassi-Rad
- Network Science Institute, Northeastern University, Boston, MA, USA
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
- Santa Fe Institute, Santa Fe, NM, USA
- The Institute for Experiential AI, Northeastern University, Boston, MA, USA
| | - Albert-László Barabási
- Network Science Institute, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
- Department of Network and Data Science, Central European University, Budapest, Hungary
| | - Giulia Menichetti
- Network Science Institute, Northeastern University, Boston, MA, USA.
- Department of Physics, Northeastern University, Boston, MA, USA.
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
50
|
Vignaux P, Lane TR, Puhl AC, Hau RK, Wright SH, Cherrington NJ, Ekins S. Transporter Inhibition Profile for the Antivirals Tilorone, Quinacrine and Pyronaridine. ACS OMEGA 2023; 8:12532-12537. [PMID: 37033868 PMCID: PMC10077433 DOI: 10.1021/acsomega.3c00724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/16/2023] [Indexed: 05/28/2023]
Abstract
Pyronaridine, tilorone and quinacrine are cationic molecules that have in vitro activity against Ebola, SARS-CoV-2 and other viruses. All three molecules have also demonstrated in vivo activity against Ebola in mice, while pyronaridine showed in vivo efficacy against SARS-CoV-2 in mice. We have recently tested these molecules and other antivirals against human organic cation transporters (OCTs) and apical multidrug and toxin extruders (MATEs). Quinacrine was found to be an inhibitor of OCT2, while tilorone and pyronaridine were less potent, and these displayed variability depending on the substrate used. To assess whether any of these three molecules have other potential interactions with additional transporters, we have now screened them at 10 μM against various human efflux and uptake transporters including P-gp, OATP1B3, OAT1, OAT3, MRP1, MRP2, MRP3, BCRP, as well as confirmational testing against OCT1, OCT2, MATE1 and MATE2K. Interestingly, in this study tilorone appears to be a more potent inhibitor of OCT1 and OCT2 than pyronaridine or quinacrine. However, both pyronaridine and quinacrine appear to be more potent inhibitors of MATE1 and MATE2K. None of the three compounds inhibited MRP1, MRP2, MRP3, OAT1, OAT3, P-gp or OATP1B3. Similarly, we previously showed that tilorone and pyronaridine do not inhibit OATP1B1 and have confirmed that quinacrine behaves similarly. In total, these observations suggest that the three compounds only appear to interact with OCTs and MATEs to differing extents, suggesting they may be involved in fewer clinically relevant drug-transporter interactions involving pharmaceutical substrates of the other major transporters tested.
Collapse
Affiliation(s)
- Patricia
A. Vignaux
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Thomas R. Lane
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Ana C. Puhl
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Raymond K. Hau
- Department
of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Stephen H. Wright
- Department
of Physiology, College of Medicine, University
of Arizona, Tucson, Arizona 85721, United
States
| | - Nathan J. Cherrington
- Department
of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| |
Collapse
|