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      Repurposing of FDA-approved antivirals, antibiotics, anthelmintics, antioxidants, and cell protectives against SARS-CoV-2 papain-like protease

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          Abstract

          SARS-CoV-2 or Coronavirus disease 19 (COVID-19) is a rapidly spreading, highly contagious, and sometimes fatal disease for which drug discovery and vaccine development are critical. SARS-CoV-2 papain-like protease (PL pro) was used to virtually screen 1697 clinical FDA-approved drugs. Among the top results expected to bind with SARS-CoV-2 PL pro strongly were three cell protectives and antioxidants (NAD+, quercitrin, and oxiglutatione), three antivirals (ritonavir, moroxydine, and zanamivir), two antimicrobials (doripenem and sulfaguanidine), two anticancer drugs, three benzimidazole anthelmintics, one antacid (famotidine), three anti-hypertensive ACE receptor blockers (candesartan, losartan, and valsartan) and other miscellaneous systemically or topically acting drugs. The binding patterns of these drugs were superior to the previously identified SARS CoV PL pro inhibitor, 6-mercaptopurine (6-MP), suggesting a potential for repurposing these drugs to treat COVID-19. The objective of drug repurposing is the rapid relocation of safe and approved drugs by bypassing the lengthy pharmacokinetic, toxicity, and preclinical phases. The ten drugs with the highest estimated docking scores with favorable pharmacokinetics were subjected to molecular dynamics (MD) simulations followed by molecular mechanics/generalized Born surface area (MM/GBSA) binding energy calculations. Phenformin, quercetin, and ritonavir all demonstrated prospective binding affinities for COVID-19 PL pro over 50 ns MD simulations, with binding energy values of −56.6, −40.9, and −37.6 kcal/mol, respectively. Energetic and structural analyses showed phenformin was more stable than quercetin and ritonavir. The list of the drugs provided herein constitutes a primer for clinical application in COVID-19 patients and guidance for further antiviral studies.

          Communicated by Ramaswamy H. Sarma

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          Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2

          Abstract From the beginning of 2002 and 2012, severe respiratory syndrome coronavirus (SARS‐CoV) and Middle East respiratory syndrome coronavirus (MERS‐CoV) crossed the species barriers to infect humans, causing thousands of infections and hundreds of deaths, respectively. Currently, a novel coronavirus (SARS‐CoV‐2), which has become the cause of the outbreak of Coronavirus Disease 2019 (COVID‐19), was discovered. Until 18 February 2020, there were 72 533 confirmed COVID‐19 cases (including 10 644 severe cases) and 1872 deaths in China. SARS‐CoV‐2 is spreading among the public and causing substantial burden due to its human‐to‐human transmission. However, the intermediate host of SARS‐CoV‐2 is still unclear. Finding the possible intermediate host of SARS‐CoV‐2 is imperative to prevent further spread of the epidemic. In this study, we used systematic comparison and analysis to predict the interaction between the receptor‐binding domain (RBD) of coronavirus spike protein and the host receptor, angiotensin‐converting enzyme 2 (ACE2). The interaction between the key amino acids of S protein RBD and ACE2 indicated that, other than pangolins and snakes, as previously suggested, turtles (Chrysemys picta bellii, Chelonia mydas, and Pelodiscus sinensis) may act as the potential intermediate hosts transmitting SARS‐CoV‐2 to humans.
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            Three Emerging Coronaviruses in Two Decades

            In the past two decades, the world has seen three coronaviruses emerge and cause outbreaks that have caused considerable global health consternation. Coronaviruses are enveloped, nonsegmented, single-stranded, positive-sense RNA viruses that have a characteristic appearance on electron microscopy negative staining Image 1 . As a matter of fact, the characteristic electron microscopy appearance was the clue to amplify and sequence nucleic acids from Dr Urbani’s (one of the health care providers who died of severe acute respiratory syndrome [SARS] in 2003) respiratory specimen using a consensus coronavirus primer. 1 The sequence of the virus was significantly different from other coronaviruses known to cause human disease at the time. The virus was ultimately named SARS-CoV, as febrile patients had severe acute respiratory syndrome and could present with pneumonia and lower respiratory symptoms such as cough and dyspnea. 2 The SARS-CoV outbreak started in Guangdong, China, and spread to many countries in Southeast Asia, North America, Europe, and South Africa. Transmission was primarily person to person through droplets that occurred during coughing or sneezing, through personal contact (shaking hands), or by touching contaminated surfaces. Of note, health professionals were particularly at risk of acquiring the disease, as transmission also occurred if isolation precautions were not followed and during certain procedures. The last case of SARS-CoV occurred in September 2003, after having infected over 8,000 persons and causing 774 deaths with a case fatality rate calculated at 9.5%. Image 1 Electron microscopy photograph of negative stain of a coronavirus (image from the Public Health Image Library). Nine years later, a new coronavirus that causes respiratory disease appeared in the Middle East, thus the name of MERS-CoV. Symptoms of MERS-CoV are nonspecific, but many patients end up with severe acute respiratory distress. In these patients, travel history is imperative, as all cases have been linked to persons in or near the Arabian Peninsula. Similar to SARS-CoV, health professionals are at higher risk of acquiring the disease, as demonstrated in the outbreak in South Korea. 3 However, in comparison with SARS-CoV, MERS-CoV is still circulating, and the case fatality rate is much higher (around 35%). What has allowed control of MERS-CoV is a low R0 (approximately 1), meaning each person with the disease transmits it to only one other person (the SARS-CoV R0 was of approximately 4). In December 30, 2019, a cluster of patients with pneumonia of unknown etiology was observed in Wuhan, China, and reported to the World Health Organization (WHO) China bureau in Beijing. A week later, January 7, 2020, a new coronavirus (SARS-CoV-2) was isolated from these patients. This virus was initially referred to as novel coronavirus 2019 (2019-nCoV) but was given the official name of COVID-19 by the WHO on February 11, 2020. This new virus has infected more people than either of its two predecessors. Several factors have allowed the rapid spread of this virus: Wuhan is the capital of China’s Hubei province, with over 11,000,000 inhabitants, and it is a major transportation hub, which increases person-to-person contact and adds to the possibility of exporting cases to other locations. At this point, the R0 is calculated between 2 and 3.5, indicating that one patient can transmit the disease to two to three other people. Patients with the COVID-19 infection proven by polymerase chain reaction have been an average age of 55 years (cases in children seem to be rare). 4 They present with fever, dry cough, and shortness of breath and, in the most severe cases, have pneumonia. The case fatality rate is around 2% to 3%. SARS-CoV-2 will cause many more deaths than its predecessors, even though the mortality rate is lower than MERS-CoV infections, because there have been so many more cases. Chinese authorities have taken the global threat very seriously, and the containment measures have been unprecedented (closing airports, train stations, and roads to Wuhan; building hospitals in record time). However, cases with SARS-CoV-2 are already being reported in many countries, including the United States. The question of how to approach these patients for diagnosis and treatment is pressing. For patients in the United States, the Centers for Disease Control and Prevention (CDC) is continuously updating information and has instructions on who to test and the workflow to follow regarding specimen handling. 5 In brief, testing for SARS-CoV-2 needs to be sent to the state laboratory after consultation with it regarding patient clinical characteristics, the specimens it will receive, and packaging of the sample using shipping regulations for category B agents. Other tests, such as CBC count, chemistries, and microbiology (including molecular testing for other respiratory viruses), can be handled using universal precautions (face protection, gloves, and disposable gowns) in hospital laboratories, so as not to delay other necessary treatment. It should be noted that although some multiplex molecular panels include primers for SARS-CoV, MERS-CoV, and other coronaviruses responsible for upper respiratory infections (HcoV 229E, NL63, OC43, and HKU1), they do not detect COVID-19. The CDC is advising not to perform viral cultures in patients under investigation for either MERS-CoV or SARS-CoV-2. The WHO also has a webpage with guidance regarding multiple aspects, including surveillance, patient management, and laboratory testing specific for SARS-CoV-2. 6 Once a patient has been defined as infected with SARS-CoV-2, he or she should be treated, taking into consideration airborne and contact precautions. Most of the measures are symptomatic, although some antiviral medications have been used. Last, at this point, reports of autopsies or lung tissue samples of patients with SARS-CoV-2 have not been published. However, based on imaging studies and what we know of SARS-CoV and MERS-CoV, patients with the most severe disease will likely show diffuse alveolar damage with hyaline membrane formation, inflammation in the alveolar walls, desquamation of pneumocytes, and, if the case is complicated by a secondary bacterial pneumonia, intra-alveolar inflammatory infiltrate by neutrophils. Any other specific features, such as multinucleated cells or potential viral inclusions, remain to be discovered through pathologic studies of patients with this new virus. In summary, the story of SARS-CoV-2 continues to evolve. Because SARS-CoV and MERS-CoV have had different behaviors, SARS-CoV-2 will likely have unique features of its own that we will learn as the outbreak progresses.
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              Virtual screening and repurposing of FDA approved drugs against COVID-19 main protease

              Aims In December 2019, the Coronavirus disease-2019 (COVID-19) virus has emerged in Wuhan, China. In this research, the first resolved COVID-19 crystal structure (main protease) was targeted in a virtual screening study by of FDA approved drugs dataset. In addition, a knowledge gap in relations of COVID-19 with the previously known fatal Coronaviruses (CoVs) epidemics, SARS and MERS CoVs, was covered by investigation of sequence statistics and phylogenetics. Materials and methods Molecular modeling, virtual screening, docking, sequence comparison statistics and phylogenetics of the COVID-19 main protease were investigated. Key findings COVID-19 Mpro formed a phylogenetic group with SARS CoV that was distant from MERS CoV. The identity% was 96.061 and 51.61 for COVID-19/SARS and COVID-19/MERS CoV sequence comparisons, respectively. The top 20 drugs in the virtual screening studies comprised a broad-spectrum antiviral (ribavirin), anti-hepatitis B virus (telbivudine), two vitamins (vitamin B12 and nicotinamide) and other miscellaneous systemically acting drugs. Of special interest, ribavirin had been used in treating cases of SARS CoV. Significance The present study provided a comprehensive targeting of the first resolved COVID+19 structure of Mpro and found a suitable save drugs for repurposing against the viral Mpro. Ribavirin, telbivudine, vitamin B12 and nicotinamide can be combined and used for COVID treatment. This initiative relocates already marketed and approved safe drugs for potential use in COVID-treatment.
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                Author and article information

                Journal
                J Biomol Struct Dyn
                J. Biomol. Struct. Dyn
                TBSD
                tbsd20
                Journal of Biomolecular Structure & Dynamics
                Taylor & Francis
                0739-1102
                1538-0254
                2020
                29 June 2020
                : 1-8
                Affiliations
                [a ]Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University , Al-ahsa, Saudi Arabia;
                [b ]Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University , Kafrelshikh, Egypt;
                [c ]Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University , Minia, Egypt;
                [d ]Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University , Gifu, Japan;
                [e ]Department of Pathology, College of Veterinary Medicine, King Faisal University , Al-ahsa, Saudi Arabia;
                [f ]Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University , Al-Ahsa, Saudi Arabia
                Author notes

                Supplemental data for this article can be accessed online at https://doi.org/10.1080/07391102.2020.1784291.

                CONTACT Mahmoud Kandeel mkandeel@ 123456kfu.edu.sa Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University , Al-hofuf, Al-ahsa, 31982, Saudi Arabia

                *Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa.

                #Department of Pharmacology, Faculty of Medicine, Minia University, 61511 El-Minia, Egypt

                Author information
                http://orcid.org/0000-0003-4819-2040
                Article
                1784291
                10.1080/07391102.2020.1784291
                7332862
                32597315
                06ba9ff9-8b3a-4d31-8a10-85a7a39fb362
                © 2020 Informa UK Limited, trading as Taylor & Francis Group
                History
                : 07 June 2020
                : 13 June 2020
                Page count
                Figures: 4, Tables: 4, Pages: 8, Words: 5210
                Categories
                Research Article

                covid-19,molecular dynamics,sars-cov-2,plpro,protease
                covid-19, molecular dynamics, sars-cov-2, plpro, protease

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