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Huang TC, Liang KH, Chang TJ, Hung KF, Wang ML, Cheng YF, Liao YT, Yang DM. Structure-based approaches against COVID-19. J Chin Med Assoc 2024; 87:139-141. [PMID: 38305483 DOI: 10.1097/jcma.0000000000001043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has had a major impact on human life. This review highlights the versatile roles of both classical and modern structure-based approaches for COVID-19. X-ray crystallography, nuclear magnetic resonance spectroscopy, and cryogenic electron microscopy are the three cornerstones of classical structural biology. These technologies have helped provide fundamental and detailed knowledge regarding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the related human host proteins as well as enabled the identification of its target sites, facilitating the cessation of its transmission. Further progress into protein structure modeling was made using modern structure-based approaches derived from homology modeling and integrated with artificial intelligence (AI), facilitating advanced computational simulation tools to actively guide the design of new vaccines and the development of anti-SARS-CoV-2 drugs. This review presents the practical contributions and future directions of structure-based approaches for COVID-19.
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Affiliation(s)
- Ta-Chou Huang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Kung-Hao Liang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Institute of Biomedical Informatics, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Tai-Jay Chang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Laboratory of Genome Research, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Kai-Feng Hung
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Mong-Lien Wang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Yen-Fu Cheng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Yi-Ting Liao
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - De-Ming Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
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2
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Zmudzinski M, Rut W, Olech K, Granda J, Giurg M, Burda-Grabowska M, Kaleta R, Zgarbova M, Kasprzyk R, Zhang L, Sun X, Lv Z, Nayak D, Kesik-Brodacka M, Olsen SK, Weber J, Hilgenfeld R, Jemielity J, Drag M. Ebselen derivatives inhibit SARS-CoV-2 replication by inhibition of its essential proteins: PL pro and M pro proteases, and nsp14 guanine N7-methyltransferase. Sci Rep 2023; 13:9161. [PMID: 37280236 DOI: 10.1038/s41598-023-35907-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/25/2023] [Indexed: 06/08/2023] Open
Abstract
Proteases encoded by SARS-CoV-2 constitute a promising target for new therapies against COVID-19. SARS-CoV-2 main protease (Mpro, 3CLpro) and papain-like protease (PLpro) are responsible for viral polyprotein cleavage-a process crucial for viral survival and replication. Recently it was shown that 2-phenylbenzisoselenazol-3(2H)-one (ebselen), an organoselenium anti-inflammatory small-molecule drug, is a potent, covalent inhibitor of both the proteases and its potency was evaluated in enzymatic and antiviral assays. In this study, we screened a collection of 34 ebselen and ebselen diselenide derivatives for SARS-CoV-2 PLpro and Mpro inhibitors. Our studies revealed that ebselen derivatives are potent inhibitors of both the proteases. We identified three PLpro and four Mpro inhibitors superior to ebselen. Independently, ebselen was shown to inhibit the N7-methyltransferase activity of SARS-CoV-2 nsp14 protein involved in viral RNA cap modification. Hence, selected compounds were also evaluated as nsp14 inhibitors. In the second part of our work, we employed 11 ebselen analogues-bis(2-carbamoylaryl)phenyl diselenides-in biological assays to evaluate their anti-SARS-CoV-2 activity in Vero E6 cells. We present their antiviral and cytoprotective activity and also low cytotoxicity. Our work shows that ebselen, its derivatives, and diselenide analogues constitute a promising platform for development of new antivirals targeting the SARS-CoV-2 virus.
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Affiliation(s)
- Mikolaj Zmudzinski
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Kamila Olech
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Jarosław Granda
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Mirosław Giurg
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Małgorzata Burda-Grabowska
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Rafał Kaleta
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Michala Zgarbova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague, Czech Republic
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Linlin Zhang
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Zongyang Lv
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Digant Nayak
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | | | - Shaun K Olsen
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague, Czech Republic
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562, Lübeck, Germany
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
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3
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Iaconis D, Caccuri F, Manelfi C, Talarico C, Bugatti A, Filippini F, Zani A, Novelli R, Kuzikov M, Ellinger B, Gribbon P, Riecken K, Esposito F, Corona A, Tramontano E, Beccari AR, Caruso A, Allegretti M. DHFR Inhibitors Display a Pleiotropic Anti-Viral Activity against SARS-CoV-2: Insights into the Mechanisms of Action. Viruses 2023; 15:v15051128. [PMID: 37243214 DOI: 10.3390/v15051128] [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: 04/05/2023] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
During the COVID-19 pandemic, drug repurposing represented an effective strategy to obtain quick answers to medical emergencies. Based on previous data on methotrexate (MTX), we evaluated the anti-viral activity of several DHFR inhibitors in two cell lines. We observed that this class of compounds showed a significant influence on the virus-induced cytopathic effect (CPE) partly attributed to the intrinsic anti-metabolic activity of these drugs, but also to a specific anti-viral function. To elucidate the molecular mechanisms, we took advantage of our EXSCALATE platform for in-silico molecular modelling and further validated the influence of these inhibitors on nsp13 and viral entry. Interestingly, pralatrexate and trimetrexate showed superior effects in counteracting the viral infection compared to other DHFR inhibitors. Our results indicate that their higher activity is due to their polypharmacological and pleiotropic profile. These compounds can thus potentially give a clinical advantage in the management of SARS-CoV-2 infection in patients already treated with this class of drugs.
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Affiliation(s)
- Daniela Iaconis
- EXSCALATE, Dompé Farmaceutici SpA, Via Tommaso De Amicis, 95, 80131 Napoli, Italy
| | - Francesca Caccuri
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Candida Manelfi
- EXSCALATE, Dompé Farmaceutici SpA, Via Tommaso De Amicis, 95, 80131 Napoli, Italy
| | - Carmine Talarico
- EXSCALATE, Dompé Farmaceutici SpA, Via Tommaso De Amicis, 95, 80131 Napoli, Italy
| | - Antonella Bugatti
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Federica Filippini
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Alberto Zani
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Rubina Novelli
- Dompè Famaceutici SpA, Via Campo di Pile snc, 67100 L'Aquila, Italy
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525 Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525 Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525 Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Kristoffer Riecken
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042 Monserrato (CA), Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042 Monserrato (CA), Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042 Monserrato (CA), Italy
| | | | - Arnaldo Caruso
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
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4
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Sayyed SK, Quraishi M, Jobby R, Rameshkumar N, Kayalvizhi N, Krishnan M, Sonawane T. A computational overview of integrase strand transfer inhibitors (INSTIs) against emerging and evolving drug-resistant HIV-1 integrase mutants. Arch Microbiol 2023; 205:142. [PMID: 36966200 PMCID: PMC10039815 DOI: 10.1007/s00203-023-03461-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/27/2023]
Abstract
AIDS (Acquired immunodeficiency syndrome) is one of the chronic and potentially life-threatening epidemics across the world. Hitherto, the non-existence of definitive drugs that could completely cure the Human immunodeficiency virus (HIV) implies an urgent necessity for the discovery of novel anti-HIV agents. Since integration is the most crucial stage in retroviral replication, hindering it can inhibit overall viral transmission. The 5 FDA-approved integrase inhibitors were computationally investigated, especially owing to the rising multiple mutations against their susceptibility. This comparative study will open new possibilities to guide the rational design of novel lead compounds for antiretroviral therapies (ARTs), more specifically the structure-based design of novel Integrase strand transfer inhibitors (INSTIs) that may possess a better resistance profile than present drugs. Further, we have discussed potent anti-HIV natural compounds and their interactions as an alternative approach, recommending the urgent need to tap into the rich vein of indigenous knowledge for reverse pharmacology. Moreover, herein, we discuss existing evidence that might change in the near future.
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Affiliation(s)
- Sharif Karim Sayyed
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India
| | - Marzuqa Quraishi
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India
| | - Renitta Jobby
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India
| | | | - Nagarajan Kayalvizhi
- Regenerative Medicine Laboratory, Department of Zoology, School of Life Sciences, Periyar University, Salem, Tamil Nadu, 636011, India
| | | | - Tareeka Sonawane
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India.
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5
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Fijałkowski Ł, Skubiszewska M, Grześk G, Koech FK, Nowaczyk A. Acetylsalicylic Acid-Primus Inter Pares in Pharmacology. Molecules 2022; 27:8412. [PMID: 36500502 PMCID: PMC9738180 DOI: 10.3390/molecules27238412] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 11/24/2022] [Accepted: 11/27/2022] [Indexed: 12/05/2022] Open
Abstract
Acetylsalicylic acid (ASA) is one of the first drugs to be obtained by synthesis while being the most used. It has experienced the longest lasting commercial success and is considered the most popular drug of the modern era. ASA, originally used as an anti-inflammatory medication, nowadays is predominantly used as an antiplatelet agent for prophylaxis in cardiac patients. Many studies show that the benefits of using ASA far outweigh the potential risk of side effects. With particular emphasis on the possibility of ASA repositioning for new therapies, extending the indications for use beyond the diseases from the spectrum of atherosclerotic diseases, such as cancer, requires shifting the benefit-risk ratio, although very good, even more towards safety. Interesting activities consisting not only of changing the formulation but also modifying the drug molecule seem to be an important goal of the 21st century. ASA has become a milestone in two important fields: pharmacy and medicine. For a pharmacist, ASA is a long-used drug for which individual indications are practically maintained. For a doctor, acetylsalicylic acid is primarily an antiplatelet drug that saves millions of lives of patients with coronary heart disease or after a stroke. These facts do not exempt us from improving therapeutic methods based on ASA, the main goal of which is to reduce the risk of side effects, as well as to extend effectiveness. Modified acetylsalicylic acid molecules already seem to be a promising therapeutic option.
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Affiliation(s)
- Łukasz Fijałkowski
- Department of Pharmacometrics and Molecular Modeling, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 2 dr. A. Jurasza St., 85-094 Bydgoszcz, Poland
| | - Magdalena Skubiszewska
- Department of Pharmacometrics and Molecular Modeling, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 2 dr. A. Jurasza St., 85-094 Bydgoszcz, Poland
| | - Grzegorz Grześk
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 75 Ujejskiego St., 85-168 Bydgoszcz, Poland
| | | | - Alicja Nowaczyk
- Department of Pharmacometrics and Molecular Modeling, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 2 dr. A. Jurasza St., 85-094 Bydgoszcz, Poland
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6
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Repositioning Drugs for Rare Diseases Based on Biological Features and Computational Approaches. Healthcare (Basel) 2022; 10:healthcare10091784. [PMID: 36141396 PMCID: PMC9498751 DOI: 10.3390/healthcare10091784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Rare diseases are a group of uncommon diseases in the world population. To date, about 7000 rare diseases have been documented. However, most of them do not have a known treatment. As a result of the relatively low demand for their treatments caused by their scarce prevalence, the pharmaceutical industry has not sufficiently encouraged the research to develop drugs to treat them. This work aims to analyse potential drug-repositioning strategies for this kind of disease. Drug repositioning seeks to find new uses for existing drugs. In this context, it seeks to discover if rare diseases could be treated with medicines previously indicated to heal other diseases. Our approaches tackle the problem by employing computational methods that calculate similarities between rare and non-rare diseases, considering biological features such as genes, proteins, and symptoms. Drug candidates for repositioning will be checked against clinical trials found in the scientific literature. In this study, 13 different rare diseases have been selected for which potential drugs could be repositioned. By verifying these drugs in the scientific literature, successful cases were found for 75% of the rare diseases studied. The genetic associations and phenotypical features of the rare diseases were examined. In addition, the verified drugs were classified according to the anatomical therapeutic chemical (ATC) code to highlight the types with a higher predisposition to be repositioned. These promising results open the door for further research in this field of study.
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Shi C, Zhu J, Shen Y, Luo S, Zhu H, Song R. Off-Policy Confidence Interval Estimation with Confounded Markov Decision Process. J Am Stat Assoc 2022. [DOI: 10.1080/01621459.2022.2110876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
| | | | - Ye Shen
- North Carolina State University
| | | | - Hongtu Zhu
- University of North Carolina at Chapel Hill
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8
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Ghafouri M, Saadati H, Taghavi MR, Azimian A, Alesheikh P, Mohajerzadeh MS, Behnamfar M, Pakzad M, Rameshrad M. Survival of the hospitalized patients with COVID-19 receiving Atorvastatin: a randomized clinical trial. J Med Virol 2022; 94:3160-3168. [PMID: 35274326 PMCID: PMC9088596 DOI: 10.1002/jmv.27710] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 01/08/2023]
Abstract
As statins decrease the progression of sepsis and its related mortality, this study aimed to evaluate the effect of atorvastatin on survival and symptom improvement in hospitalized patients with COVID‐19. This randomized controlled trial was performed on 156 hospitalized patients with COVID‐19 in Bojnourd city in 2021. Patients were randomly divided into comparison (standard therapy: hydroxychloroquine + Kaletra®) and intervention groups (atorvastatin 20 mg, SD, plus standard therapy). The main outcomes were the rate of symptom improvement, duration of hospitalization, need for intubation, and mortality rate. In this study, seven patients died, two patients (2.6%) in the comparison group and five (6.6%) in the intervention group. The mean hospitalization days (p = 0.001), the pulse rate (p = 0.004), and the frequency of hospitalization in the ICU ward (18.4% vs. 1.3%) were longer and greater in the intervention group. The remission probability in the comparison group was greater (p = 0.0001). The median hospitalization days in the intervention group was longer (p < 0.001) and remission in the comparison group occurred 1.71 times sooner (hazard ratio = 1.70, 95% confidence interval = 1.22–2.38, p = 0.002). Totally, adding atorvastatin to the standard regime in this study increased hospitalization days and imposed negative effects on symptom improvement in hospitalized patients with COVID‐19.
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Affiliation(s)
- Majid Ghafouri
- Department of Internal Medicine, School of Medicine, Vector-borne Diseases Research Center, Imam Hassan Hospital, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Hassan Saadati
- Department of Epidemiology and Biostatistics, School of Health, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mohammad Reza Taghavi
- Department of Internal Medicine, School of Medicine, Vector-borne Diseases Research Center, Imam Hassan Hospital, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Amir Azimian
- Department of Pathology and Laboratory Sciences, School of Medicine, Vector-borne Diseases Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Peiman Alesheikh
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mina Sadat Mohajerzadeh
- Department of Radiology and Medical Physics, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Morteza Behnamfar
- Student research committee, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Marzih Pakzad
- Imam Hassan Hospital, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Maryam Rameshrad
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
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9
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Bradykinin-target therapies in SARS-CoV-2 infection: current evidence and perspectives. Naunyn Schmiedebergs Arch Pharmacol 2022; 395:275-283. [PMID: 35089406 PMCID: PMC8795307 DOI: 10.1007/s00210-022-02206-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 01/17/2022] [Indexed: 12/26/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a potentially fatal disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that preferentially infects the respiratory tract. Bradykinin (BK) is a hypotensive substance that recently emerged as one of the mechanisms to explain COVID-19-related complications. Concerning this, in this review, we try to address the complex link between BK and pathophysiology of COVID-19, investigating the role of this peptide as a potential target for pharmacological modulation in the management of SARS-CoV-2. The pathology of COVID-19 may be more a result of the BK storm than the cytokine storm, and which BK imbalance is a relevant factor in the respiratory disorders caused by SARS-CoV-2 infection. Regarding this, an interesting point of intervention for this disease is to modulate BK signaling. Some drugs, such as icatibant, ecallantide, and noscapine, and even a human monoclonal antibody, lanadelumab, have been studied for their potential utility in COVID-19 by modulating BK signaling. The interaction of the BK pathway and the involvement of cytokines such as IL-6 and IL1 may be key to the use of blockers, even if only as adjuvants. In fact, reduction of BK, mainly DABK, is considered a relevant strategy to improve clinical conditions of COVID-19 patients. In this context, despite the current unproven clinical efficacy, drugs repurposing that block B1 or B2 receptor activation have gained prominence for the treatment of COVID-19 in the world.
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10
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Cryo-EM structures of human bradykinin receptor-G q proteins complexes. Nat Commun 2022; 13:714. [PMID: 35132089 PMCID: PMC8821558 DOI: 10.1038/s41467-022-28399-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/18/2022] [Indexed: 12/23/2022] Open
Abstract
The type 2 bradykinin receptor (B2R) is a G protein-coupled receptor (GPCR) in the cardiovascular system, and the dysfunction of B2R leads to inflammation, hereditary angioedema, and pain. Bradykinin and kallidin are both endogenous peptide agonists of B2R, acting as vasodilators to protect the cardiovascular system. Here we determine two cryo-electron microscopy (cryo-EM) structures of human B2R-Gq in complex with bradykinin and kallidin at 3.0 Å and 2.9 Å resolution, respectively. The ligand-binding pocket accommodates S-shaped peptides, with aspartic acids and glutamates as an anion trap. The phenylalanines at the tail of the peptides induce significant conformational changes in the toggle switch W2836.48, the conserved PIF, DRY, and NPxxY motifs, for the B2R activation. This further induces the extensive interactions of the intracellular loops ICL2/3 and helix 8 with Gq proteins. Our structures elucidate the molecular mechanisms for the ligand binding, receptor activation, and Gq proteins coupling of B2R.
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11
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Serra A, Fratello M, Federico A, Ojha R, Provenzani R, Tasnadi E, Cattelani L, Del Giudice G, Kinaret PAS, Saarimäki LA, Pavel A, Kuivanen S, Cerullo V, Vapalahti O, Horvath P, Lieto AD, Yli-Kauhaluoma J, Balistreri G, Greco D. Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation. Brief Bioinform 2021; 23:6484515. [PMID: 34962256 PMCID: PMC8769897 DOI: 10.1093/bib/bbab507] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/12/2022] Open
Abstract
The pharmacological arsenal against the COVID-19 pandemic is largely based on generic anti-inflammatory strategies or poorly scalable solutions. Moreover, as the ongoing vaccination campaign is rolling slower than wished, affordable and effective therapeutics are needed. To this end, there is increasing attention toward computational methods for drug repositioning and de novo drug design. Here, multiple data-driven computational approaches are systematically integrated to perform a virtual screening and prioritize candidate drugs for the treatment of COVID-19. From the list of prioritized drugs, a subset of representative candidates to test in human cells is selected. Two compounds, 7-hydroxystaurosporine and bafetinib, show synergistic antiviral effects in vitro and strongly inhibit viral-induced syncytia formation. Moreover, since existing drug repositioning methods provide limited usable information for de novo drug design, the relevant chemical substructures of the identified drugs are extracted to provide a chemical vocabulary that may help to design new effective drugs.
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Affiliation(s)
- Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Michele Fratello
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Ravi Ojha
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Riccardo Provenzani
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Ervin Tasnadi
- Synthetic and Systems Biology Unit, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
| | - Luca Cattelani
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Giusy Del Giudice
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Pia A S Kinaret
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Laura A Saarimäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Alisa Pavel
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Suvi Kuivanen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vincenzo Cerullo
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Peter Horvath
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.,Synthetic and Systems Biology Unit, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
| | - Antonio Di Lieto
- Department of Forensic Psychiatry, Aarhus University, Aarhus, Denmark
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Giuseppe Balistreri
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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12
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Emrani J, Ahmed M, Jeffers-Francis L, Teleha JC, Mowa N, Newman RH, Thomas MD. SARS-COV-2, infection, transmission, transcription, translation, proteins, and treatment: A review. Int J Biol Macromol 2021; 193:1249-1273. [PMID: 34756970 PMCID: PMC8552795 DOI: 10.1016/j.ijbiomac.2021.10.172] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/21/2021] [Indexed: 01/18/2023]
Abstract
In this review, we describe the key molecular entities involved in the process of infection by SARS-CoV-2, while also detailing how those key entities influence the spread of the disease. We further introduce the molecular mechanisms of preventive and treatment strategies including drugs, antibodies, and vaccines.
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Affiliation(s)
- Jahangir Emrani
- Department of Chemistry, North Carolina A&T State University, Greensboro, NC 27411, United States of America.
| | - Maryam Ahmed
- Department of Biology, Appalachian State University, Boone, NC 28608, United States of America
| | - Liesl Jeffers-Francis
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, United States of America
| | - John C Teleha
- Department of Reference and Instruction, North Carolina A&T State University, Greensboro, NC 27411, United States of America
| | - Nathan Mowa
- Department of Biology, Appalachian State University, Boone, NC 28608, United States of America
| | - Robert H Newman
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, United States of America
| | - Misty D Thomas
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, United States of America
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13
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Wang J, Zhu K, Xue Y, Wen G, Tao L. Research Progress in the Treatment of Complications and Sequelae of COVID-19. Front Med (Lausanne) 2021; 8:757605. [PMID: 34926504 PMCID: PMC8674502 DOI: 10.3389/fmed.2021.757605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/10/2021] [Indexed: 12/22/2022] Open
Abstract
With the improvement in the understanding of COVID-19 and the widespread vaccination of COVID-19 vaccines in various countries, the epidemic will be brought under control soon. However, multiple viruses could result in the post-viral syndrome, which is also common among patients with COVID-19. Therefore, the long-term consequences and the corresponding treatment of COVID-19 should be the focus in the post-epidemic era. In this review, we summarize the therapeutic strategies for the complications and sequelae of eight major systems caused by COVID-19, including respiratory system, cardiovascular system, neurological system, digestive system, urinary system, endocrine system, reproductive system and skeletal complication. In addition, we also sorted out the side effects reported in the vaccine trials. The purpose of this article is to remind people of possible complications and sequelae of COVID-19 and provide robust guidance on the treatment. It is extremely important to conduct long-term observational prognosis research on a larger scale, so as to have a comprehensive understanding of the impact of the SARS-CoV-2 on the human body and reduce complications to the greatest extent.
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Affiliation(s)
- Jinpeng Wang
- Department of Orthopedics, First Hospital of China Medical University, Shenyang, China
| | - Kuoyun Zhu
- Department of Orthopedics, First Hospital of China Medical University, Shenyang, China
| | - Yuchuan Xue
- The First Department of Clinical Medicine, China Medical University, Shenyang, China
| | - Guangfu Wen
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Lin Tao
- Department of Orthopedics, First Hospital of China Medical University, Shenyang, China
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14
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Kumar S, Saurabh MK, Narasimha VL, Maharshi V. Efficacy of Interferon-β in Moderate-to-Severe Hospitalised Cases of COVID-19: A Systematic Review and Meta-analysis. Clin Drug Investig 2021; 41:1037-1046. [PMID: 34687413 PMCID: PMC8540871 DOI: 10.1007/s40261-021-01092-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2021] [Indexed: 11/30/2022]
Abstract
Background and Objective Interferon-β, as with several other anti-viral agents, has been investigated as a treatment option for COVID-19 as a repurposed drug. The present study is a systematic review and meta-analysis of interferon-β to determine its efficacy among moderate-to-severe COVID-19 patients. Methods A systematic literature search was done using relevant terms for ‘COVID-19’ and ‘interferon-β’. Randomised controlled trials (RCT) evaluating the efficacy of interferon-β in COVID-19 were included. Data were extracted for outcome measures, namely mortality, time to clinical improvement and length of hospital stay. Random effects meta-analysis was performed using RevMan V.5.4.1 to calculate overall effect estimate as odds ratio/hazard ratio for categorical variables and mean difference for continuous variable. Result Eight RCTs were eligible for qualitative synthesis and seven for meta-analysis. The overall effect estimate (odds ratio [OR] 0.59; 95 % CI 0.91, 1.12) and (mean difference [MD] − 1.41; 95 % CI − 2.84, 0.02) indicated no statistically significant difference between effect of IFN-β and that of control on mortality and length of hospital stay, respectively. However, the overall effect estimate (hazard ratio [HR] 1.95; 95 % CI 1.36, 2.79) denoted a favourable effect of INF-β on reducing the time to clinical improvement in moderate-to-severe COVID-19 patients. Conclusion Addition of interferon-β to standard of care resulted in significant reduction in time to clinical improvement but no significant benefit in terms of reduction in mortality and length of hospital stay in moderate-to-severe cases of COVID-19.
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Affiliation(s)
- Subodh Kumar
- All India Institute of Medical Sciences, Deoghar, India
| | | | | | - Vikas Maharshi
- All India Institute of Medical Sciences, Deoghar, India.
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15
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Prieto Santamaría L, Ugarte Carro E, Díaz Uzquiano M, Menasalvas Ruiz E, Pérez Gallardo Y, Rodríguez-González A. A data-driven methodology towards evaluating the potential of drug repurposing hypotheses. Comput Struct Biotechnol J 2021; 19:4559-4573. [PMID: 34471499 PMCID: PMC8387760 DOI: 10.1016/j.csbj.2021.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/08/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022] Open
Abstract
Drug repurposing has become a widely used strategy to accelerate the process of finding treatments. While classical de novo drug development involves high costs, risks, and time-consuming paths, drug repurposing allows to reuse already-existing and approved drugs for new indications. Numerous research has been carried out in this field, both in vitro and in silico. Computational drug repurposing methods make use of modern heterogeneous biomedical data to identify and prioritize new indications for old drugs. In the current paper, we present a new complete methodology to evaluate new potentially repurposable drugs based on disease-gene and disease-phenotype associations, identifying significant differences between repurposing and non-repurposing data. We have collected a set of known successful drug repurposing case studies from the literature and we have analysed their dissimilarities with other biomedical data not necessarily participating in repurposing processes. The information used has been obtained from the DISNET platform. We have performed three analyses (at the genetical, phenotypical, and categorization levels), to conclude that there is a statistically significant difference between actual repurposing-related information and non-repurposing data. The insights obtained could be relevant when suggesting new potential drug repurposing hypotheses.
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Key Words
- ACE, Angiotensin I Converting Enzyme
- AHR, Aryl Hydrocarbon Receptor
- ALK, Anaplastic Lymphoma Kinase
- API, Application Programming Interface
- CMap, Connectivity Map
- COX-2, Cyclooxygenase 2
- CUI, Concept Unique Identifier
- DISNET knowledge base
- DR, Drug Repurposing or Drug Repositioning
- DRD3, Dopamine Receptor D3
- Data integration
- Disease understanding
- Drug repositioning
- Drug repurposing
- Drug-disease validation
- ESR1, Estrogen Receptor 1
- ESR2, Estrogen Receptor 2
- FCGR2A, Fc Fragment Of IgG Receptor IIa
- FCGR3A, Fc Fragment Of IgG Receptor IIIa
- FCGR3B, Fc Fragment Of IgG Receptor IIIb
- GDA, Gene Disease Association
- ICD-10-CM, International Classification of Diseases, 10th revision, Clinical Modification
- ID, Identifier
- KDR, Kinase insert Domain Receptor
- LTα, Lymphotoxin alpha
- MeSH-PA, Medical Subject Headings – Pharmacological Action
- ND, New Disease
- NLM, National Library of Medicine
- OD, Original Disease
- PTGS2, Prostaglandin-endoperoxidase synthase 2
- SM, Supplementary Material
- SRD5A1, Steroid 5 Alpha-Reductase 1
- SRD5A2, Steroid 5 Alpha-Reductase 2
- TNFα, Tumour Necrosis Factor alpha
- UMLS, Unified Medical Language System
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Affiliation(s)
- Lucía Prieto Santamaría
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain.,ETS Ingenieros Informáticos, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain.,Ezeris Networks Global Services S.L., 28028 Madrid, Spain
| | - Esther Ugarte Carro
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain
| | - Marina Díaz Uzquiano
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain
| | - Ernestina Menasalvas Ruiz
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain.,ETS Ingenieros Informáticos, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain
| | | | - Alejandro Rodríguez-González
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain.,ETS Ingenieros Informáticos, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain
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16
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Mashayekhi-Sardoo H, Hosseinjani H. A new application of mTOR inhibitor drugs as potential therapeutic agents for COVID-19. J Basic Clin Physiol Pharmacol 2021; 33:17-25. [PMID: 34218545 DOI: 10.1515/jbcpp-2020-0495] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 06/01/2021] [Indexed: 01/08/2023]
Abstract
Since December 2019, the COVID-19 emerging pandemic caused by SARS-CoV-2 has resulted in one of the most important global health threats. Concerning the absence of an approved effective vaccine or drug for the treatment and outcome improvement of COVID-19 patients, and the role of SARS-CoV-2 in activation of mammalian target of rapamycin (mTOR) pathway, we decided to review the previous data regarding the therapeutic effect of mTOR inhibitor drugs in COVID-19 patients. We searched the scientific databases such as Web of Science, Embase, Medline (PubMed), Scopus, and Google Scholar using appropriate keywords to find suitable studies or suggestions until October 2020. The findings of the current study confirmed that mTOR inhibitor drugs through suggested mechanisms such as T cell adjustment, induction of autophagy without apoptosis, reduction of viral replication, restoration of the T-cell function, decrease cytokine storm, and moderation of the mTOR-PI3K-AKT pathway activation bring about a therapeutic impact in COVID-19 patients. Taken together, it is necessary to find a suitable therapy for the COVID-19 pandemic emerging. In this regard, we clarify that it is valuable to consider the therapeutic effect of mTOR inhibitor drugs and metformin by its mTOR inhibition property in the treatment of COVID-19 patients.
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Affiliation(s)
- Habibeh Mashayekhi-Sardoo
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hesamoddin Hosseinjani
- Department of Clinical Pharmacy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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17
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Porto WF. Virtual screening of peptides with high affinity for SARS-CoV-2 main protease. Comput Biol Med 2021; 133:104363. [PMID: 33862305 PMCID: PMC8018786 DOI: 10.1016/j.compbiomed.2021.104363] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/26/2022]
Abstract
The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 2,000,000 deaths worldwide. Currently, vaccine development and drug repurposing have been the main strategies to find a COVID-19 treatment. However, the development of new drugs could be the solution if the main strategies fail. Here, a virtual screening of pentapeptides was applied in order to identify peptides with high affinity to SARS-CoV-2 main protease (Mpro). Over 70,000 peptides were screened employing a genetic algorithm that uses a docking score as the fitness function. The algorithm was coupled with a RESTful API to persist data and avoid redundancy. The docking exhaustiveness was adapted to the number of peptides in each virtual screening step, where the higher the number of peptides, the lower the docking exhaustiveness. Two potential peptides were selected (HHYWH and HYWWT), which have higher affinity to Mpro than to human proteases. Albeit preliminary, the data presented here provide some basis for the rational design of peptide-based drugs to treat COVID-19.
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18
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Wang M, Withers JB, Ricchiuto P, Voitalov I, McAnally M, Sanchez HN, Saleh A, Akmaev VR, Ghiassian SD. A systems-based method to repurpose marketed therapeutics for antiviral use: a SARS-CoV-2 case study. Life Sci Alliance 2021; 4:e202000904. [PMID: 33593923 PMCID: PMC7893815 DOI: 10.26508/lsa.202000904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/02/2023] Open
Abstract
This study describes two complementary methods that use network-based and sequence similarity tools to identify drug repurposing opportunities predicted to modulate viral proteins. This approach could be rapidly adapted to new and emerging viruses. The first method built and studied a virus-host-physical interaction network; a three-layer multimodal network of drug target proteins, human protein-protein interactions, and viral-host protein-protein interactions. The second method evaluated sequence similarity between viral proteins and other proteins, visualized by constructing a virus-host-similarity interaction network. Methods were validated on the human immunodeficiency virus, hepatitis B, hepatitis C, and human papillomavirus, then deployed on SARS-CoV-2. Comparison of virus-host-physical interaction predictions to known antiviral drugs had AUCs of 0.69, 0.59, 0.78, and 0.67, respectively, reflecting that the scores are predictive of effective drugs. For SARS-CoV-2, 569 candidate drugs were predicted, of which 37 had been included in clinical trials for SARS-CoV-2 (AUC = 0.75, P-value 3.21 × 10-3). As further validation, top-ranked candidate antiviral drugs were analyzed for binding to protein targets in silico; binding scores generated by BindScope indicated a 70% success rate.
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Affiliation(s)
| | | | | | | | | | | | - Alif Saleh
- Scipher Medicine Corporation, Waltham, MA, USA
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19
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Nain Z, Rana HK, Liò P, Islam SMS, Summers MA, Moni MA. Pathogenetic profiling of COVID-19 and SARS-like viruses. Brief Bioinform 2021; 22:1175-1196. [PMID: 32778874 PMCID: PMC7454314 DOI: 10.1093/bib/bbaa173] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/23/2020] [Accepted: 07/08/2020] [Indexed: 12/15/2022] Open
Abstract
The novel coronavirus (2019-nCoV) has recently emerged, causing COVID-19 outbreaks and significant societal/global disruption. Importantly, COVID-19 infection resembles SARS-like complications. However, the lack of knowledge about the underlying genetic mechanisms of COVID-19 warrants the development of prospective control measures. In this study, we employed whole-genome alignment and digital DNA-DNA hybridization analyses to assess genomic linkage between 2019-nCoV and other coronaviruses. To understand the pathogenetic behavior of 2019-nCoV, we compared gene expression datasets of viral infections closest to 2019-nCoV with four COVID-19 clinical presentations followed by functional enrichment of shared dysregulated genes. Potential chemical antagonists were also identified using protein-chemical interaction analysis. Based on phylogram analysis, the 2019-nCoV was found genetically closest to SARS-CoVs. In addition, we identified 562 upregulated and 738 downregulated genes (adj. P ≤ 0.05) with SARS-CoV infection. Among the dysregulated genes, SARS-CoV shared ≤19 upregulated and ≤22 downregulated genes with each of different COVID-19 complications. Notably, upregulation of BCL6 and PFKFB3 genes was common to SARS-CoV, pneumonia and severe acute respiratory syndrome, while they shared CRIP2, NSG1 and TNFRSF21 genes in downregulation. Besides, 14 genes were common to different SARS-CoV comorbidities that might influence COVID-19 disease. We also observed similarities in pathways that can lead to COVID-19 and SARS-CoV diseases. Finally, protein-chemical interactions suggest cyclosporine, resveratrol and quercetin as promising drug candidates against COVID-19 as well as other SARS-like viral infections. The pathogenetic analyses, along with identified biomarkers, signaling pathways and chemical antagonists, could prove useful for novel drug development in the fight against the current global 2019-nCoV pandemic.
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Affiliation(s)
- Zulkar Nain
- Department of Genetic Engineering and Biotechnology, East West University, Bangladesh
| | - Humayan Kabir Rana
- Department of Computer Science and Engineering, Green University of Bangladesh
| | - Pietro Liò
- Artificial Intelligence Group at the University of Cambridge
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20
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Gatti M, De Ponti F. Drug Repurposing in the COVID-19 Era: Insights from Case Studies Showing Pharmaceutical Peculiarities. Pharmaceutics 2021; 13:pharmaceutics13030302. [PMID: 33668969 PMCID: PMC7996547 DOI: 10.3390/pharmaceutics13030302] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/18/2021] [Accepted: 02/21/2021] [Indexed: 12/12/2022] Open
Abstract
COVID-19 may lead to severe respiratory distress syndrome and high risk of death in some patients. So far (January 2021), only the antiviral remdesivir has been approved, although no significant benefits in terms of mortality and clinical improvement were recently reported. In a setting where effective and safe treatments for COVID-19 are urgently needed, drug repurposing may take advantage of the fact that the safety profile of an agent is already well known and allows rapid investigation of the efficacy of potential treatments, at lower costs and with reduced risk of failure. Furthermore, novel pharmaceutical formulations of older agents (e.g., aerosolized administration of chloroquine/hydroxychloroquine, remdesivir, heparin, pirfenidone) have been tested in order to increase pulmonary delivery and/or antiviral effects of potentially active drugs, thus overcoming pharmacokinetic issues. In our review, we will highlight the importance of the drug repurposing strategy in the context of COVID-19, including regulatory and ethical aspects, with a specific focus on novel pharmaceutical formulations and routes of administration.
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21
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Interferon-beta offers promising avenues to COVID-19 treatment: a systematic review and meta-analysis of clinical trial studies. Naunyn Schmiedebergs Arch Pharmacol 2021; 394:829-838. [PMID: 33587164 PMCID: PMC7883756 DOI: 10.1007/s00210-021-02061-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/04/2021] [Indexed: 11/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 principally weakens the hosts’ innate immune system by impairing the interferon function and production. Type I interferons (IFNs) especially IFN-β are best known for their antiviral activities. IFNs accompanied by the standard care protocols have opened up unique opportunities for treating the coronavirus disease 2019 (COVID-19). The databases including PubMed, SCOPUS, EMBASE, and Google Scholar were searched up to October 30, 2020. The primary and secondary outcomes were considered discharge and mortality, respectively. The abovementioned outcomes of standard care protocol were compared with the standard care plus IFN-β in the confirmed COVID-19 patients. Out of 356 records identified, 12 randomized clinical trial studies were selected for full-text screening. Finally, 5 papers were included in the systematic review and 3 papers in the meta-analysis. The average mortality rate was reported as 6.195% and 18.02% in intervention and control groups, respectively. Likewise, the median days of hospitalization were lower in the intervention group (9 days) than the control group (12.25 days). According to meta-analysis, IFN-β was found to increase the overall discharge rate (RR = 3.05; 95% CI: 1.09–5.01). Our findings revealed that early administration of IFN-β in combination with antiviral drugs is a promising therapeutic strategy against COVID-19.
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22
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Patel S, Saxena B, Mehta P. Recent updates in the clinical trials of therapeutic monoclonal antibodies targeting cytokine storm for the management of COVID-19. Heliyon 2021; 7:e06158. [PMID: 33553708 PMCID: PMC7846241 DOI: 10.1016/j.heliyon.2021.e06158] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/23/2020] [Accepted: 01/27/2021] [Indexed: 02/07/2023] Open
Abstract
Clinical studies have identified a cytokine storm in the third stage of disease progression in critical ill patients with coronavirus disease 2019 (COVID-19). Hence, effectively suppressing the uncontrolled immune response of the host towards the invaded viruses in a cytokine storm is a critical step to prevent the deterioration of patient conditions and decrease the rate of mortality. Therapeutic monoclonal antibodies (mAbs) are found to be effective for the management of acute respiratory distress syndrome in patients with COVID-19. In this review, we compiled all therapeutic mAbs targeting cytokine storm, which are in clinical trials for its repurposing in the management of COVID-19. Compilation of clinical trial data indicated that therapeutic monoclonal antibodies targeting interleukins (IL-6, IL-1ra, IL-8, IL-1β, IL-17A, IL-33), interferon-gamma, tumor necrosis factor-alpha, P-selectin, connective tissue growth factor, plasma kallikrein, tumor necrosis factor superfamily 14, granulocyte macrophage colony stimulating factor, colony stimulating factor 1 receptor, C-C chemokine receptor type 5, cluster of differentiation 14 and 147, vascular endothelial growth factor, programmed cell death protein-1, Angiopoietin - 2, human factor XIIa, complementary protein 5, natural killer cell receptor G2A, human epidermal growth factor receptor 2, immunoglobulin-like transcript 7 receptor, complement component fragment 5a receptor and viral attachment to the human cell were under investigation for management of severely ill patients with COVID-19. Among these, about 65 clinical trials are targeting IL-6 inhibition as the most promising one and Tocilizumab, an IL-6 inhibitor is considered to be the potential candidate to treat cytokine storm associated with the COVID-19.
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Affiliation(s)
- Shikha Patel
- Department of Pharmaceutical Analysis, Institute of Pharmacy, Nirma University, S.G. Highway, Ahmedabad, 382481, India
| | - Bhagawati Saxena
- Department of Pharmacology, Institute of Pharmacy, Nirma University, S.G. Highway, Ahmedabad, 382481, India
| | - Priti Mehta
- Department of Pharmaceutical Analysis, Institute of Pharmacy, Nirma University, S.G. Highway, Ahmedabad, 382481, India
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23
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Brendler T, Al‐Harrasi A, Bauer R, Gafner S, Hardy ML, Heinrich M, Hosseinzadeh H, Izzo AA, Michaelis M, Nassiri‐Asl M, Panossian A, Wasser SP, Williamson EM. Botanical drugs and supplements affecting the immune response in the time of
COVID
‐19: Implications for research and clinical practice. Phytother Res 2020; 35:3013-3031. [DOI: 10.1002/ptr.7008] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/16/2020] [Accepted: 12/16/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Thomas Brendler
- Department of Botany and Plant Biotechnology University of Johannesburg Johannesburg South Africa
- Plantaphile Collingswood New Jersey USA
| | - Ahmed Al‐Harrasi
- Natural and Medical Sciences Research Centre University of Nizwa Nizwa Oman
| | - Rudolf Bauer
- Institute of Pharmaceutical Sciences, Department of Pharmacognosy University of Graz Graz Austria
| | | | - Mary L. Hardy
- Association of Integrative and Holistic Medicine San Diego California USA
| | - Michael Heinrich
- Research Group ‘Pharmacognosy and Phytotherapy’, UCL School of Pharmacy University of London London UK
- Graduate Institute of Integrated Medicine, College of Chinese Medicine China Medical University Taichung Taiwan
| | - Hossein Hosseinzadeh
- Pharmaceutical Research Center, Pharmaceutical Technology Institute Mashhad University of Medical Sciences Mashhad Iran
- Department of Pharmacodynamics and Toxicology, School of Pharmacy Mashhad University of Medical Sciences Mashhad Iran
| | - Angelo A. Izzo
- Department of Pharmacy, School of Medicine University of Naples Federico II Naples Italy
| | - Martin Michaelis
- Industrial Biotechnology Centre and School of Biosciences University of Kent Canterbury UK
| | - Marjan Nassiri‐Asl
- Department of Pharmacology, School of Medicine Shahid Beheshti University of Medical Sciences Tehran Iran
- Neurobiology Research Center Shahid Beheshti University of Medical Sciences Tehran Iran
| | | | - Solomon P. Wasser
- Institute of Evolution and Department of Evolutionary and Environmental Biology University of Haifa Haifa Israel
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24
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Babaei F, Mirzababaei M, Nassiri-Asl M, Hosseinzadeh H. Review of registered clinical trials for the treatment of COVID-19. Drug Dev Res 2020; 82:474-493. [PMID: 33251593 PMCID: PMC7753306 DOI: 10.1002/ddr.21762] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/05/2020] [Accepted: 11/13/2020] [Indexed: 01/08/2023]
Abstract
Coronavirus disease 2019 (COVID‐19) is a viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). The disease was first reported in December 2019 in Wuhan, China, but now more than 200 countries have been affected and the coronavirus pandemic is still ongoing. The severity of COVID‐19 symptoms can range from mild to severe. FDA approved remdesivir as a treatment of COVID‐19 so far. Various clinical trials are underway to find an effective method to treat patients with COVID‐19. This review aimed at summarizing 219 registered clinical trials in the ClinicalTrials.gov database with possible mechanisms, and novel findings of them, and other recent publications related to COVID‐19. According to our analyses, various treatment approaches and drugs are being investigated to find an effective drug to cure COVID‐19 and among all strategies, three important mechanisms are suggested to be important against COVID‐19 including antiviral, anti‐inflammatory, and immunomodulatory properties. Our review can help future studies get on the way to finding an effective drug for COVID‐19 treatment by providing ideas for similar researches.
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Affiliation(s)
- Fatemeh Babaei
- Department of Clinical Biochemistry, School of Medicine, Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Mirzababaei
- Department of Clinical Biochemistry, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Marjan Nassiri-Asl
- Department of Pharmacology and Neurobiology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Hosseinzadeh
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.,Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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25
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Rasaeifar B, Gomez-Gutierrez P, Perez JJ. Molecular Features of Non-Selective Small Molecule Antagonists of the Bradykinin Receptors. Pharmaceuticals (Basel) 2020; 13:E259. [PMID: 32967280 PMCID: PMC7558388 DOI: 10.3390/ph13090259] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/18/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023] Open
Abstract
Angiotensin converting enzyme 2 (ACE2) downregulation is a key negative factor for the severity of lung edema and acute lung failure observed in patients infected with SARS-CoV-2. ACE2 downregulation affects the levels of diverse peptide mediators of the renin-agiotensin-aldestosterone and kallikrein-kinin systems, compromising vascular hemostasis. Increasing evidence suggests that the inflammatory response observed in covid-19 patients is initiated by the action of kinins on the bradykinin receptors. Accordingly, the use of bradykinin antagonists should be considered as a strategy for therapeutic intervention against covid-19 illness progression. Presently, icatibant is the only bradykinin antagonist drug approved. In the present report, we investigated the molecular features characterizing non-selective antagonists targeting the bradykinin receptors and carried out a in silico screening of approved drugs, aimed at the identification of compounds with a non-selective bradykinin antagonist profile that can be evaluated for drug repurposing. The study permitted to identify eight compounds as prospective non-selective antagonists of the bradykinin receptors, including raloxifene; sildenafil; cefepime; cefpirome; imatinib; ponatinib; abemaciclib and entrectinib.
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Affiliation(s)
| | | | - Juan J. Perez
- Department of Chemical Engineering, Universitat Politecnica de Catalunya. ETSEIB. Av. Diagonal, 647, 08028 Barcelona, Spain; (B.R.); (P.G.-G.)
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