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COVID-19 therapeutics: Clinical application of repurposed drugs and futuristic strategies for target-based drug discovery. Genes Dis 2023; 10:1402-1428. [PMCID: PMC10079314 DOI: 10.1016/j.gendis.2022.12.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes the complicated disease COVID-19. Clinicians are continuously facing huge problems in the treatment of patients, as COVID-19-specific drugs are not available hence the principle of drug repurposing serves as a one-and-only hope. Globally, the repurposing of many drugs is underway; few of them are already approved by the regulatory bodies for their clinical use and most of them are in different phases of clinical trials. Here in this review, our main aim is to discuss in detail the up-to-date information on the target-based pharmacological classification of repurposed drugs, the potential mechanism of actions, and the current clinical trial status of various drugs which are under repurposing since early 2020. At last, we briefly proposed the probable pharmacological and therapeutic drug targets that may be preferred as a futuristic drug discovery approach in the development of effective medicines.
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2
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Dixit H, Kulharia M, Verma SK. Metalloproteome of human-infective RNA viruses: a study towards understanding the role of metal ions in virology. Pathog Dis 2023; 81:ftad020. [PMID: 37653445 DOI: 10.1093/femspd/ftad020] [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: 06/22/2023] [Revised: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023] Open
Abstract
Metalloproteins and metal-based inhibitors have been shown to effectively combat infectious diseases, particularly those caused by RNA viruses. In this study, a diverse set of bioinformatics methods was employed to identify metal-binding proteins of human RNA viruses. Seventy-three viral proteins with a high probability of being metal-binding proteins were identified. These proteins included 40 zinc-, 47 magnesium- and 14 manganese-binding proteins belonging to 29 viral species and eight significant viral families, including Coronaviridae, Flaviviridae and Retroviridae. Further functional characterization has revealed that these proteins play a critical role in several viral processes, including viral replication, fusion and host viral entry. They fall under the essential categories of viral proteins, including polymerase and protease enzymes. Magnesium ion is abundantly predicted to interact with these viral enzymes, followed by zinc. In addition, this study also examined the evolutionary aspects of predicted viral metalloproteins, offering essential insights into the metal utilization patterns among different viral species. The analysis indicates that the metal utilization patterns are conserved within the functional classes of the proteins. In conclusion, the findings of this study provide significant knowledge on viral metalloproteins that can serve as a valuable foundation for future research in this area.
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Affiliation(s)
- Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
| | - Mahesh Kulharia
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
- Department of Environmental Studies, University of Delhi 110007, Delhi, India
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3
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Benarous L, Benarous K, Muhammad G, Ali Z. Deep learning application detecting SARS-CoV-2 key enzymes inhibitors. CLUSTER COMPUTING 2023; 26:1169-1180. [PMID: 35874186 PMCID: PMC9295888 DOI: 10.1007/s10586-022-03656-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/28/2022] [Accepted: 06/17/2022] [Indexed: 05/14/2023]
Abstract
The fast spread of the COVID-19 over the world pressured scientists to find its cures. Especially, with the disastrous results, it engendered from human life losses to long-term impacts on infected people's health and the huge financial losses. In addition to the massive efforts made by researchers and medicals on finding safe, smart, fast, and efficient methods to accurately make an early diagnosis of the COVID-19. Some researchers focused on finding drugs to treat the disease and its symptoms, others worked on creating effective vaccines, while several concentrated on finding inhibitors for the key enzymes of the virus, to reduce its spreading and reproduction inside the human body. These enzymes' inhibitors are usually found in aliments, plants, fungi, or even in some drugs. Since these inhibitors slow and halt the replication of the virus in the human body, they can help fight it at an early stage saving the patient from death risk. Moreover, if the human body's immune system gets rid of the virus at the early stage it can be spared from the disastrous sequels it may leave inside the patient's body. Our research aims to find aliments and plants that are rich in these inhibitors. In this paper, we developed a deep learning application that is trained with various aliments, plants, and drugs to detect if a component contains SARS-CoV-2 key inhibitor(s) intending to help them find more sources containing these inhibitors. The application is trained to identify various sources rich in thirteen coronavirus-2 key inhibitors. The sources are currently just aliments, plants, and seeds and the identification is done by their names.
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Affiliation(s)
- Leila Benarous
- LIM Laboratory (Laboratoire d’informatique Et de Mathématique), Department of Computer Science, Faculty of Science, University of Amar Telidji, Laghouat, Algeria
- LISSI-Tinc-NET Laboratory, University of Paris-Est Creteil, 94400 Vitry-sur-Seine, France
| | - Khedidja Benarous
- Science Fundamental Laboratory, Department of Biology, Faculty of Sciences, University of Amar Telidji, Laghouat, Algeria
| | - Ghulam Muhammad
- Department of Computer Engineering, College of Computer and Information Sciences, King Saud University, Riyadh, 11543 Saudi Arabia
| | - Zulfiqar Ali
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, CO4 3SQ UK
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4
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Devi PB, Asthana Y, Sumitha A, Sagayaraj IR. Molecular Docking and the Pharmacokinetic Properties of the Anti-Viral Compounds Towards SARS-CoV- An In-silico Approach. INTERNATIONAL JOURNAL OF PHARMACEUTICAL RESEARCH AND ALLIED SCIENCES 2023. [DOI: 10.51847/z2mkwovoqc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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5
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Coffin AB, Dale E, Doppenberg E, Fearington F, Hayward T, Hill J, Molano O. Putative COVID-19 therapies imatinib, lopinavir, ritonavir, and ivermectin cause hair cell damage: A targeted screen in the zebrafish lateral line. Front Cell Neurosci 2022; 16:941031. [PMID: 36090793 PMCID: PMC9448854 DOI: 10.3389/fncel.2022.941031] [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: 05/11/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
The biomedical community is rapidly developing COVID-19 drugs to bring much-need therapies to market, with over 900 drugs and drug combinations currently in clinical trials. While this pace of drug development is necessary, the risk of producing therapies with significant side-effects is also increased. One likely side-effect of some COVID-19 drugs is hearing loss, yet hearing is not assessed during preclinical development or clinical trials. We used the zebrafish lateral line, an established model for drug-induced sensory hair cell damage, to assess the ototoxic potential of seven drugs in clinical trials for treatment of COVID-19. We found that ivermectin, lopinavir, imatinib, and ritonavir were significantly toxic to lateral line hair cells. By contrast, the approved COVID-19 therapies dexamethasone and remdesivir did not cause damage. We also did not observe damage from the antibiotic azithromycin. Neither lopinavir nor ritonavir altered the number of pre-synaptic ribbons per surviving hair cell, while there was an increase in ribbons following imatinib or ivermectin exposure. Damage from lopinavir, imatinib, and ivermectin was specific to hair cells, with no overall cytotoxicity noted following TUNEL labeling. Ritonavir may be generally cytotoxic, as determined by an increase in the number of TUNEL-positive non-hair cells following ritonavir exposure. Pharmacological inhibition of the mechanotransduction (MET) channel attenuated damage caused by lopinavir and ritonavir but did not alter imatinib or ivermectin toxicity. These results suggest that lopinavir and ritonavir may enter hair cells through the MET channel, similar to known ototoxins such as aminoglycoside antibiotics. Finally, we asked if ivermectin was ototoxic to rats in vivo. While ivermectin is not recommended by the FDA for treating COVID-19, many people have chosen to take ivermectin without a doctor’s guidance, often with serious side-effects. Rats received daily subcutaneous injections for 10 days with a clinically relevant ivermectin dose (0.2 mg/kg). In contrast to our zebrafish assays, ivermectin did not cause ototoxicity in rats. Our research suggests that some drugs in clinical trials for COVID-19 may be ototoxic. This work can help identify drugs with the fewest side-effects and determine which therapies warrant audiometric monitoring.
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Affiliation(s)
- Allison B. Coffin
- Department of Integrative Physiology and Neuroscience, Washington State University, Vancouver, WA, United States
- College of Arts and Sciences, Washington State University, Vancouver, WA, United States
- *Correspondence: Allison B. Coffin,
| | - Emily Dale
- College of Arts and Sciences, Washington State University, Vancouver, WA, United States
| | - Emilee Doppenberg
- College of Arts and Sciences, Washington State University, Vancouver, WA, United States
| | - Forrest Fearington
- College of Arts and Sciences, Washington State University, Vancouver, WA, United States
| | - Tamasen Hayward
- College of Arts and Sciences, Washington State University, Vancouver, WA, United States
| | - Jordan Hill
- College of Arts and Sciences, Washington State University, Vancouver, WA, United States
| | - Olivia Molano
- College of Arts and Sciences, Washington State University, Vancouver, WA, United States
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6
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Liu XH, Cheng T, Liu BY, Chi J, Shu T, Wang T. Structures of the SARS-CoV-2 spike glycoprotein and applications for novel drug development. Front Pharmacol 2022; 13:955648. [PMID: 36016554 PMCID: PMC9395726 DOI: 10.3389/fphar.2022.955648] [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: 05/29/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022] Open
Abstract
COVID-19 caused by SARS-CoV-2 has raised a health crisis worldwide. The high morbidity and mortality associated with COVID-19 and the lack of effective drugs or vaccines for SARS-CoV-2 emphasize the urgent need for standard treatment and prophylaxis of COVID-19. The receptor-binding domain (RBD) of the glycosylated spike protein (S protein) is capable of binding to human angiotensin-converting enzyme 2 (hACE2) and initiating membrane fusion and virus entry. Hence, it is rational to inhibit the RBD activity of the S protein by blocking the RBD interaction with hACE2, which makes the glycosylated S protein a potential target for designing and developing antiviral agents. In this study, the molecular features of the S protein of SARS-CoV-2 are highlighted, such as the structures, functions, and interactions of the S protein and ACE2. Additionally, computational tools developed for the treatment of COVID-19 are provided, for example, algorithms, databases, and relevant programs. Finally, recent advances in the novel development of antivirals against the S protein are summarized, including screening of natural products, drug repurposing and rational design. This study is expected to provide novel insights for the efficient discovery of promising drug candidates against the S protein and contribute to the development of broad-spectrum anti-coronavirus drugs to fight against SARS-CoV-2.
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7
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Gomes JPA, Rocha LDO, Leal CEY, Filho EBDA. Virtual screening of molecular databases for potential inhibitors of the NSP16/NSP10 methyltransferase from SARS-CoV-2. J Mol Struct 2022; 1261:132951. [PMID: 35369609 PMCID: PMC8958854 DOI: 10.1016/j.molstruc.2022.132951] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/22/2022] [Accepted: 03/27/2022] [Indexed: 12/16/2022]
Abstract
COVID-19 is a disease caused by the SARS-CoV-2 virus and represents one of the greatest health problems that humanity faces at the moment. Therefore, efforts have been made with the objective of seeking therapies that could be effective in combating this problematic. In the search for ligands, computational chemistry plays an essential role, since it allows the screening of thousands of molecules on a given target, in order to save time and money for the in vitro or in vivo pharmacological stage. In this paper, we perform a virtual screening by docking looking for potential inhibitors of the NSP16-NSP10 protein dimer (methyltransferase) from SARS-CoV-2, by evaluating a homemade databank of molecules found in plants of the Caatinga Brazilian biome, compounds from ZINC online molecular database, as well as structural analogues of the enzymatic cofactor s-adenosylmethionine (SAM) and a known inhibitor in the literature, sinefungin (SFG), provided at PubChem database. All the evaluated sets presented molecules that deserve attention, highlighting four compounds from ZINC as the most promising ligands. These results contribute to the discovery of new molecular hits, in the search of potential agents against SARS-CoV-2 virus, still unveiling a pathway that can be used in combined therapies.
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Affiliation(s)
- João Pedro Agra Gomes
- College of Pharmacy, Federal University of San Francisco Valley, Petrolina, Pernambuco, Brazil
| | | | | | - Edilson Beserra de Alencar Filho
- College of Pharmacy, Federal University of San Francisco Valley, Petrolina, Pernambuco, Brazil,Postgraduate Program in Biosciences, Federal University of San Francisco Valley, Petrolina, Pernambuco, Brazil,Postgraduate Program in Health and Biological Sciences, Federal University of San Francisco Valley, Petrolina, Pernambuco, Brazil,Corresponding author
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8
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Appraisal of SARS-CoV-2 mutations and their impact on vaccination efficacy: an overview. J Diabetes Metab Disord 2022; 21:1763-1783. [PMID: 35891981 PMCID: PMC9305048 DOI: 10.1007/s40200-022-01002-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/07/2022] [Indexed: 12/02/2022]
Abstract
With the unexpected emergence of the novel 2019 Wuhan coronavirus, the world was faced with a sudden uproar that quickly shifted into a serious life-threatening pandemic. Affecting the lives of the global population and leaving drastic damage in various sections and systems, several measures have been constantly taken to tackle down this crisis. For instance, numerous vaccines have been developed in the past two years, some of which have been granted emergency use, thus providing sufficient immunity to the vaccinated individuals. However, the appearance of newly emerged SARS-CoV-2 variants with accelerated transmission and fatality has led the world towards another pandemic. Having undergone various mutations in genomic and/or amino acid profiles, some of the emerged variants of concern (VOCs) including Alpha, Beta, Gamma, and Delta have displayed immune evasion and pathogenicity even in the vaccinated population, hence raising concerns regarding the efficacy of current vaccines against new VOCs of COVID-19. Therefore, genomic investigations of SARS-CoV-2 mutations are expected to provide valuable insight into the evolution of SARS-CoV-2, while also determining the impact of different mutations on infection severity. This study was constructed with the aim of shining light on recent advances regarding mutations in major COVID-19 VOCs, as well as vaccination efficacy against those VOCs.
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9
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Aghamirza Moghim Aliabadi H, Eivazzadeh‐Keihan R, Beig Parikhani A, Fattahi Mehraban S, Maleki A, Fereshteh S, Bazaz M, Zolriasatein A, Bozorgnia B, Rahmati S, Saberi F, Yousefi Najafabadi Z, Damough S, Mohseni S, Salehzadeh H, Khakyzadeh V, Madanchi H, Kardar GA, Zarrintaj P, Saeb MR, Mozafari M. COVID-19: A systematic review and update on prevention, diagnosis, and treatment. MedComm (Beijing) 2022; 3:e115. [PMID: 35281790 PMCID: PMC8906461 DOI: 10.1002/mco2.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/18/2021] [Accepted: 12/19/2021] [Indexed: 01/09/2023] Open
Abstract
Since the rapid onset of the COVID-19 or SARS-CoV-2 pandemic in the world in 2019, extensive studies have been conducted to unveil the behavior and emission pattern of the virus in order to determine the best ways to diagnosis of virus and thereof formulate effective drugs or vaccines to combat the disease. The emergence of novel diagnostic and therapeutic techniques considering the multiplicity of reports from one side and contradictions in assessments from the other side necessitates instantaneous updates on the progress of clinical investigations. There is also growing public anxiety from time to time mutation of COVID-19, as reflected in considerable mortality and transmission, respectively, from delta and Omicron variants. We comprehensively review and summarize different aspects of prevention, diagnosis, and treatment of COVID-19. First, biological characteristics of COVID-19 were explained from diagnosis standpoint. Thereafter, the preclinical animal models of COVID-19 were discussed to frame the symptoms and clinical effects of COVID-19 from patient to patient with treatment strategies and in-silico/computational biology. Finally, the opportunities and challenges of nanoscience/nanotechnology in identification, diagnosis, and treatment of COVID-19 were discussed. This review covers almost all SARS-CoV-2-related topics extensively to deepen the understanding of the latest achievements (last updated on January 11, 2022).
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Affiliation(s)
- Hooman Aghamirza Moghim Aliabadi
- Protein Chemistry LaboratoryDepartment of Medical BiotechnologyBiotechnology Research CenterPasteur Institute of IranTehranIran
- Advance Chemical Studies LaboratoryFaculty of ChemistryK. N. Toosi UniversityTehranIran
| | | | - Arezoo Beig Parikhani
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | | | - Ali Maleki
- Department of ChemistryIran University of Science and TechnologyTehranIran
| | | | - Masoume Bazaz
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | | | | | - Saman Rahmati
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | - Fatemeh Saberi
- Department of Medical BiotechnologySchool of Advanced Technologies in MedicineShahid Beheshti University of Medical SciencesTehranIran
| | - Zeinab Yousefi Najafabadi
- Department of Medical BiotechnologySchool of Advanced Technologies in MedicineTehran University of Medical SciencesTehranIran
- ImmunologyAsthma & Allergy Research InstituteTehran University of Medical SciencesTehranIran
| | - Shadi Damough
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | - Sara Mohseni
- Non‐metallic Materials Research GroupNiroo Research InstituteTehranIran
| | | | - Vahid Khakyzadeh
- Department of ChemistryK. N. Toosi University of TechnologyTehranIran
| | - Hamid Madanchi
- School of MedicineSemnan University of Medical SciencesSemnanIran
- Drug Design and Bioinformatics UnitDepartment of Medical BiotechnologyBiotechnology Research CenterPasteur Institute of IranTehranIran
| | - Gholam Ali Kardar
- Department of Medical BiotechnologySchool of Advanced Technologies in MedicineTehran University of Medical SciencesTehranIran
- ImmunologyAsthma & Allergy Research InstituteTehran University of Medical SciencesTehranIran
| | - Payam Zarrintaj
- School of Chemical EngineeringOklahoma State UniversityStillwaterOklahomaUSA
| | - Mohammad Reza Saeb
- Department of Polymer TechnologyFaculty of ChemistryGdańsk University of TechnologyGdańskPoland
| | - Masoud Mozafari
- Department of Tissue Engineering & Regenerative MedicineIran University of Medical SciencesTehranIran
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10
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Paula HSC, Santiago SB, Araújo LA, Pedroso CF, Marinho TA, Gonçalves IAJ, Santos TAP, Pinheiro RS, Oliveira GA, Batista KA. An overview on the current available treatment for COVID-19 and the impact of antibiotic administration during the pandemic. Braz J Med Biol Res 2021; 55:e11631. [PMID: 34909910 PMCID: PMC8851906 DOI: 10.1590/1414-431x2021e11631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has caused several problems in healthcare systems around the world, as to date, there is no effective and specific treatment against all forms of COVID-19. Currently, drugs with therapeutic potential are being tested, including antiviral, anti-inflammatory, anti-malarial, immunotherapy, and antibiotics. Although antibiotics have no direct effect on viral infections, they are often used against secondary bacterial infections, or even as empiric treatment to reduce viral load, infection, and replication of coronaviruses. However, there are many concerns about this therapeutic approach as it may accelerate and/or increase the long-term rates of antimicrobial resistance (AMR). We focused this overview on exploring candidate drugs for COVID-19 therapy, including antibiotics, considering the lack of specific treatment and that it is unclear whether the widespread use of antibiotics in the treatment of COVID-19 has implications for the emergence and transmission of multidrug-resistant bacteria.
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Affiliation(s)
- H S C Paula
- Departamento de Áreas Acadêmicas, Instituto Federal de Educação, Ciência e Tecnologia de Goiás, Campus Goiânia Oeste, Goiânia, GO, Brasil
| | - S B Santiago
- Departamento de Áreas Acadêmicas, Instituto Federal de Educação, Ciência e Tecnologia de Goiás, Campus Goiânia Oeste, Goiânia, GO, Brasil
| | - L A Araújo
- Departamento de Áreas Acadêmicas, Instituto Federal de Educação, Ciência e Tecnologia de Goiás, Campus Goiânia Oeste, Goiânia, GO, Brasil
| | - C F Pedroso
- Departamento de Áreas Acadêmicas, Instituto Federal de Educação, Ciência e Tecnologia de Goiás, Campus Goiânia Oeste, Goiânia, GO, Brasil
| | - T A Marinho
- Departamento de Áreas Acadêmicas, Instituto Federal de Educação, Ciência e Tecnologia de Goiás, Campus Goiânia Oeste, Goiânia, GO, Brasil
| | - I A J Gonçalves
- Departamento de Áreas Acadêmicas, Instituto Federal de Educação, Ciência e Tecnologia de Goiás, Campus Goiânia Oeste, Goiânia, GO, Brasil
| | - T A P Santos
- Departamento de Áreas Acadêmicas, Instituto Federal de Educação, Ciência e Tecnologia de Goiás, Campus Goiânia Oeste, Goiânia, GO, Brasil
| | - R S Pinheiro
- Departamento de Áreas Acadêmicas, Instituto Federal de Educação, Ciência e Tecnologia de Goiás, Campus Goiânia Oeste, Goiânia, GO, Brasil
| | - G A Oliveira
- Instituto Federal de Educação, Ciência e Tecnologia de Goiás, Campus Valparaíso, Valparaíso, GO, Brasil
| | - K A Batista
- Departamento de Áreas Acadêmicas, Instituto Federal de Educação, Ciência e Tecnologia de Goiás, Campus Goiânia Oeste, Goiânia, GO, Brasil
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11
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Screening of Potential Indonesia Herbal Compounds Based on Multi-Label Classification for 2019 Coronavirus Disease. BIG DATA AND COGNITIVE COMPUTING 2021. [DOI: 10.3390/bdcc5040075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Coronavirus disease 2019 pandemic spreads rapidly and requires an acceleration in the process of drug discovery. Drug repurposing can help accelerate the drug discovery process by identifying new efficacy for approved drugs, and it is considered an efficient and economical approach. Research in drug repurposing can be done by observing the interactions of drug compounds with protein related to a disease (DTI), then predicting the new drug-target interactions. This study conducted multilabel DTI prediction using the stack autoencoder-deep neural network (SAE-DNN) algorithm. Compound features were extracted using PubChem fingerprint, daylight fingerprint, MACCS fingerprint, and circular fingerprint. The results showed that the SAE-DNN model was able to predict DTI in COVID-19 cases with good performance. The SAE-DNN model with a circular fingerprint dataset produced the best average metrics with an accuracy of 0.831, recall of 0.918, precision of 0.888, and F-measure of 0.89. Herbal compounds prediction results using the SAE-DNN model with the circular, daylight, and PubChem fingerprint dataset resulted in 92, 65, and 79 herbal compounds contained in herbal plants in Indonesia respectively.
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12
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Bernardi M, Ghaani MR, Bayazeid O. Phenylethanoid glycosides as a possible COVID-19 protease inhibitor: a virtual screening approach. J Mol Model 2021; 27:341. [PMID: 34731296 PMCID: PMC8565174 DOI: 10.1007/s00894-021-04963-2] [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: 01/27/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022]
Abstract
From the beginning of pandemic, more than 240 million people have been infected with a death rate higher than 2%. Indeed, the current exit strategy involving the spreading of vaccines must be combined with progress in effective treatment development. This scenario is sadly supported by the vaccine's immune activation time and the inequalities in the global immunization schedule. Bringing the crises under control means providing the world population with accessible and impactful new therapeutics. We screened a natural product library that contains a unique collection of 2370 natural products into the binding site of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro). According to the docking score and to the interaction at the active site, three phenylethanoid glycosides (forsythiaside A, isoacteoside, and verbascoside) were selected. In order to provide better insight into the atomistic interaction and test the impact of the three selected compounds at the binding site, we resorted to a half microsecond-long molecular dynamics simulation. As a result, we are showing that forsythiaside A is the most stable molecule and it is likely to possess the highest inhibitory effect against SARS-CoV-2 Mpro. Phenylethanoid glycosides also have been reported to have both protease and kinase activity. This kinase inhibitory activity is very beneficial in fighting viruses inside the body as kinases are required for viral entry, metabolism, and/or reproduction. The dual activity (kinase/protease) of phenylethanoid glycosides makes them very promising anit-COVID-19 agents.
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Affiliation(s)
- Mario Bernardi
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
- Department of Pharmacognosy, Faculty of Pharmacy, Hacettepe University, Ankara, 06100, Turkey
| | - Mohammad Reza Ghaani
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Omer Bayazeid
- Department of Pharmacognosy, Faculty of Pharmacy, Hacettepe University, Ankara, 06100, Turkey.
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Liu J, Yang W, Liu Y, Lu C, Ruan L, Zhao C, Huo R, Shen X, Miao Q, Lv W, Li H, Shi H, Hu L, Yang Z, Zhang L, Wang B, Dong G, Xian Y, Li B, Zhou Z, Xu C, Chen Y, Bian Y, Guo J, Yang J, Wang J, Qi W, Chen S, Chen Y, Yan B, Wang W, Li J, Xie X, Xu M, Jiang J, Wang G, Cong X, Zhu H, Shi J, Leng L, Li D, Guo L, Huang L. Combination of Hua Shi Bai Du granule (Q-14) and standard care in the treatment of patients with coronavirus disease 2019 (COVID-19): A single-center, open-label, randomized controlled trial. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 91:153671. [PMID: 34425471 PMCID: PMC8285932 DOI: 10.1016/j.phymed.2021.153671] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 06/08/2021] [Accepted: 07/13/2021] [Indexed: 05/15/2023]
Abstract
OBJECTIVE To evaluate the efficacy and safety of Hua Shi Bai Du Granule (Q-14) plus standard care compared with standard care alone in adults with coronavirus disease (COVID-19). STUDY DESIGN A single-center, open-label, randomized controlled trial. SETTING Wuhan Jinyintan Hospital, Wuhan, China, February 27 to March 27, 2020. PARTICIPANTS A total of 204 patients with laboratory-confirmed COVID-19 were randomized into the treatment group and control group, consisting of 102 patients in each group. INTERVENTIONS In the treatment group, Q-14 was administered at 10 g (granules) twice daily for 14 days, plus standard care. In the control group, patients were provided standard care alone for 14 days. MAIN OUTCOME MEASURE The primary outcome was the conversion time for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral assay. Adverse events were analyzed in the safety population. RESULTS Among the 204 patients, 195 were analyzed according to the intention-to-treat principle. A total of 149 patients (71 vs. 78 in the treatment and control groups, respectively) tested negative via the SARS-CoV-2 viral assay. There was no statistical significance in the conversion time between the treatment group and control group (Full analysis set: Median [interquartile range]: 10.00 [9.00-11.00] vs. 10.00 [9.00-11.00]; Mean rank: 67.92 vs. 81.44; P = 0.051). The recovery time for fever was shorter in the treatment group than in the control group. The disappearance rate of symptoms like cough, fatigue, and chest discomfort was significantly higher in the treatment group. In chest computed tomography (CT) examinations, the overall evaluation of chest CT examination after treatment compared with baseline showed that more patients improved in the treatment group. There were no significant differences in the other outcomes. CONCLUSION The combination of Q-14 and standard care for COVID-19 was useful for the improvement of symptoms (such as fever, cough, fatigue, and chest discomfort), but did not result in a significantly higher probability of negative conversion in the SARS-CoV-2 viral assay. No serious adverse events were observed. TRIAL REGISTRATION ChiCTR2000030288.
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Affiliation(s)
- Jia Liu
- China Academy of Chinese Medical Sciences Institute of Basic Research in Clinical Medicine, Beijing, China
| | - Wei Yang
- China Academy of Chinese Medical Sciences Institute of Basic Research in Clinical Medicine, Beijing, China
| | - Yue Liu
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Cheng Lu
- China Academy of Chinese Medical Sciences Institute of Basic Research in Clinical Medicine, Beijing, China
| | | | - Chen Zhao
- China Academy of Chinese Medical Sciences Institute of Basic Research in Clinical Medicine, Beijing, China
| | - Ruili Huo
- China Academy of Chinese Medical Sciences, Beijing, China
| | - Xin Shen
- China Academy of Chinese Medical Sciences Institute of Chinese Materia Medica, Beijing, China
| | - Qing Miao
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Wenliang Lv
- China Academy of Chinese Medical Sciences Guanganmen Hospital, Beijing, China
| | - Hao Li
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Huaxin Shi
- China Academy of Chinese Medical Sciences, Beijing, China
| | - Lijie Hu
- China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhixu Yang
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Li Zhang
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Bing Wang
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Guoju Dong
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Yongyue Xian
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Bin Li
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Zhenqi Zhou
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Chunyan Xu
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Yingying Chen
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Yongjun Bian
- China Academy of Chinese Medical Sciences Guanganmen Hospital, Beijing, China
| | - Jing Guo
- China Academy of Chinese Medical Sciences Guanganmen Hospital, Beijing, China
| | - Jinliang Yang
- China Academy of Chinese Medical Sciences Guanganmen Hospital, Beijing, China
| | - Jian Wang
- China Academy of Chinese Medical Sciences Guanganmen Hospital, Beijing, China
| | - Wensheng Qi
- China Academy of Chinese Medical Sciences Guanganmen Hospital, Beijing, China
| | - Suping Chen
- China Academy of Chinese Medical Sciences Guanganmen Hospital, Beijing, China
| | - Yang Chen
- China Academy of Chinese Medical Sciences Guanganmen Hospital, Beijing, China
| | - Bei Yan
- China Academy of Chinese Medical Sciences Guanganmen Hospital, Beijing, China
| | - Wei Wang
- China Academy of Chinese Medical Sciences Guanganmen Hospital, Beijing, China
| | - Jing Li
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Xiaolei Xie
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Ming Xu
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Jianxin Jiang
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Gang Wang
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Xiaodong Cong
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Haoning Zhu
- China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Jiaheng Shi
- China Academy of Chinese Medical Sciences Guanganmen Hospital, Beijing, China
| | - Luxing Leng
- China Academy of Chinese Medical Sciences Guanganmen Hospital, Beijing, China
| | - Dongxu Li
- China Academy of Chinese Medical Sciences Guanganmen Hospital, Beijing, China
| | - Lanping Guo
- China Academy of Chinese Medical Sciences Chinese Materia Medica Resource Center, Beijing, China
| | - Luqi Huang
- China Academy of Chinese Medical Sciences, Beijing, China; China Center for Evidence-based Medicine of Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China.
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14
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Asiedu SO, Kwofie SK, Broni E, Wilson MD. Computational Identification of Potential Anti-Inflammatory Natural Compounds Targeting the p38 Mitogen-Activated Protein Kinase (MAPK): Implications for COVID-19-Induced Cytokine Storm. Biomolecules 2021; 11:653. [PMID: 33946644 PMCID: PMC8146027 DOI: 10.3390/biom11050653] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Severely ill coronavirus disease 2019 (COVID-19) patients show elevated concentrations of pro-inflammatory cytokines, a situation commonly known as a cytokine storm. The p38 MAPK receptor is considered a plausible therapeutic target because of its involvement in the platelet activation processes leading to inflammation. This study aimed to identify potential natural product-derived inhibitory molecules against the p38α MAPK receptor to mitigate the eliciting of pro-inflammatory cytokines using computational techniques. The 3D X-ray structure of the receptor with PDB ID 3ZS5 was energy minimized using GROMACS and used for molecular docking via AutoDock Vina. The molecular docking was validated with an acceptable area under the curve (AUC) of 0.704, which was computed from the receiver operating characteristic (ROC) curve. A compendium of 38,271 natural products originating from Africa and China together with eleven known p38 MAPK inhibitors were screened against the receptor. Four potential lead compounds ZINC1691180, ZINC5519433, ZINC4520996 and ZINC5733756 were identified. The compounds formed strong intermolecular bonds with critical residues Val38, Ala51, Lys53, Thr106, Leu108, Met109 and Phe169. Additionally, they exhibited appreciably low binding energies which were corroborated via molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations. The compounds were also predicted to have plausible pharmacological profiles with insignificant toxicity. The molecules were also predicted to be anti-inflammatory, kinase inhibitors, antiviral, platelet aggregation inhibitors, and immunosuppressive, with probable activity (Pa) greater than probable inactivity (Pi). ZINC5733756 is structurally similar to estradiol with a Tanimoto coefficient value of 0.73, which exhibits anti-inflammatory activity by targeting the activation of Nrf2. Similarly, ZINC1691180 has been reported to elicit anti-inflammatory activity in vitro. The compounds may serve as scaffolds for the design of potential biotherapeutic molecules against the cytokine storm associated with COVID-19.
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Affiliation(s)
- Seth O. Asiedu
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra P.O. Box LG 581, Ghana; (S.O.A); (M.D.W)
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana;
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana;
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra P.O. Box LG 581, Ghana; (S.O.A); (M.D.W)
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA
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15
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Kumar V, Parate S, Yoon S, Lee G, Lee KW. Computational Simulations Identified Marine-Derived Natural Bioactive Compounds as Replication Inhibitors of SARS-CoV-2. Front Microbiol 2021; 12:647295. [PMID: 33967984 PMCID: PMC8097174 DOI: 10.3389/fmicb.2021.647295] [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: 12/29/2020] [Accepted: 02/25/2021] [Indexed: 01/18/2023] Open
Abstract
The rapid spread of COVID-19, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a worldwide health emergency. Unfortunately, to date, a very small number of remedies have been to be found effective against SARS-CoV-2 infection. Therefore, further research is required to achieve a lasting solution against this deadly disease. Repurposing available drugs and evaluating natural product inhibitors against target proteins of SARS-CoV-2 could be an effective approach to accelerate drug discovery and development. With this strategy in mind, we derived Marine Natural Products (MNP)-based drug-like small molecules and evaluated them against three major target proteins of the SARS-CoV-2 virus replication cycle. A drug-like database from MNP library was generated using Lipinski's rule of five and ADMET descriptors. A total of 2,033 compounds were obtained and were subsequently subjected to molecular docking with 3CLpro, PLpro, and RdRp. The docking analyses revealed that a total of 14 compounds displayed better docking scores than the reference compounds and have significant molecular interactions with the active site residues of SARS-CoV-2 virus targeted proteins. Furthermore, the stability of docking-derived complexes was analyzed using molecular dynamics simulations and binding free energy calculations. The analyses revealed two hit compounds against each targeted protein displaying stable behavior, binding affinity, and molecular interactions. Our investigation identified two hit compounds against each targeted proteins displaying stable behavior, higher binding affinity and key residual molecular interactions, with good in silico pharmacokinetic properties, therefore can be considered for further in vitro studies.
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Affiliation(s)
- Vikas Kumar
- Division of Life Sciences, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science, Gyeongsang National University, Jinju, South Korea
| | - Shraddha Parate
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), Jinju, South Korea
| | - Sanghwa Yoon
- Division of Life Sciences, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science, Gyeongsang National University, Jinju, South Korea
| | - Gihwan Lee
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), Jinju, South Korea
| | - Keun Woo Lee
- Division of Life Sciences, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science, Gyeongsang National University, Jinju, South Korea
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16
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Shoemark DK, Colenso CK, Toelzer C, Gupta K, Sessions RB, Davidson AD, Berger I, Schaffitzel C, Spencer J, Mulholland AJ. Molecular Simulations suggest Vitamins, Retinoids and Steroids as Ligands of the Free Fatty Acid Pocket of the SARS-CoV-2 Spike Protein*. Angew Chem Int Ed Engl 2021; 60:7098-7110. [PMID: 33469977 PMCID: PMC8013358 DOI: 10.1002/anie.202015639] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/18/2020] [Indexed: 12/15/2022]
Abstract
We investigate binding of linoleate and other potential ligands to the recently discovered fatty acid binding site in the SARS-CoV-2 spike protein, using docking and molecular dynamics simulations. Simulations suggest that linoleate and dexamethasone stabilize the locked spike conformation, thus reducing the opportunity for ACE2 interaction. In contrast, cholesterol may expose the receptor-binding domain by destabilizing the closed structure, preferentially binding to a different site in the hinge region of the open structure. We docked a library of FDA-approved drugs to the fatty acid site using an approach that reproduces the structure of the linoleate complex. Docking identifies steroids (including dexamethasone and vitamin D); retinoids (some known to be active in vitro, and vitamin A); and vitamin K as potential ligands that may stabilize the closed conformation. The SARS-CoV-2 spike fatty acid site may bind a diverse array of ligands, including dietary components, and therefore provides a promising target for therapeutics or prophylaxis.
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Affiliation(s)
- Deborah K. Shoemark
- School of BiochemistryUniversity of Bristol1 Tankard's CloseBristolBS8 1TDUK
- Bristol Synthetic Biology Centre BrisSynBio24 Tyndall AveBristolBS8 1TQUK
| | - Charlotte K. Colenso
- School of Cellular and Molecular Medicine, Biomedical Sciences BuildingUniversity of BristolBristolBS8 1TDUK
| | - Christine Toelzer
- School of BiochemistryUniversity of Bristol1 Tankard's CloseBristolBS8 1TDUK
- Bristol Synthetic Biology Centre BrisSynBio24 Tyndall AveBristolBS8 1TQUK
| | - Kapil Gupta
- School of BiochemistryUniversity of Bristol1 Tankard's CloseBristolBS8 1TDUK
- Bristol Synthetic Biology Centre BrisSynBio24 Tyndall AveBristolBS8 1TQUK
| | - Richard B. Sessions
- School of BiochemistryUniversity of Bristol1 Tankard's CloseBristolBS8 1TDUK
| | - Andrew D. Davidson
- School of Cellular and Molecular Medicine, Biomedical Sciences BuildingUniversity of BristolBristolBS8 1TDUK
| | - Imre Berger
- School of BiochemistryUniversity of Bristol1 Tankard's CloseBristolBS8 1TDUK
- Bristol Synthetic Biology Centre BrisSynBio24 Tyndall AveBristolBS8 1TQUK
- Max Planck Bristol Centre for Minimal BiologyCantock's CloseBristolBS8 1TSUK
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | - Christiane Schaffitzel
- School of BiochemistryUniversity of Bristol1 Tankard's CloseBristolBS8 1TDUK
- Bristol Synthetic Biology Centre BrisSynBio24 Tyndall AveBristolBS8 1TQUK
| | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences BuildingUniversity of BristolBristolBS8 1TDUK
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17
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Shoemark DK, Colenso CK, Toelzer C, Gupta K, Sessions RB, Davidson AD, Berger I, Schaffitzel C, Spencer J, Mulholland AJ. Molecular Simulations suggest Vitamins, Retinoids and Steroids as Ligands of the Free Fatty Acid Pocket of the SARS‐CoV‐2 Spike Protein**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Deborah K. Shoemark
- School of Biochemistry University of Bristol 1 Tankard's Close Bristol BS8 1TD UK
- Bristol Synthetic Biology Centre BrisSynBio 24 Tyndall Ave Bristol BS8 1TQ UK
| | - Charlotte K. Colenso
- School of Cellular and Molecular Medicine, Biomedical Sciences Building University of Bristol Bristol BS8 1TD UK
| | - Christine Toelzer
- School of Biochemistry University of Bristol 1 Tankard's Close Bristol BS8 1TD UK
- Bristol Synthetic Biology Centre BrisSynBio 24 Tyndall Ave Bristol BS8 1TQ UK
| | - Kapil Gupta
- School of Biochemistry University of Bristol 1 Tankard's Close Bristol BS8 1TD UK
- Bristol Synthetic Biology Centre BrisSynBio 24 Tyndall Ave Bristol BS8 1TQ UK
| | - Richard B. Sessions
- School of Biochemistry University of Bristol 1 Tankard's Close Bristol BS8 1TD UK
| | - Andrew D. Davidson
- School of Cellular and Molecular Medicine, Biomedical Sciences Building University of Bristol Bristol BS8 1TD UK
| | - Imre Berger
- School of Biochemistry University of Bristol 1 Tankard's Close Bristol BS8 1TD UK
- Bristol Synthetic Biology Centre BrisSynBio 24 Tyndall Ave Bristol BS8 1TQ UK
- Max Planck Bristol Centre for Minimal Biology Cantock's Close Bristol BS8 1TS UK
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | - Christiane Schaffitzel
- School of Biochemistry University of Bristol 1 Tankard's Close Bristol BS8 1TD UK
- Bristol Synthetic Biology Centre BrisSynBio 24 Tyndall Ave Bristol BS8 1TQ UK
| | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building University of Bristol Bristol BS8 1TD UK
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18
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Rabaan AA, Al-Ahmed SH, Sah R, Tiwari R, Yatoo MI, Patel SK, Pathak M, Malik YS, Dhama K, Singh KP, Bonilla-Aldana DK, Haque S, Martinez-Pulgarin DF, Rodriguez-Morales AJ, Leblebicioglu H. SARS-CoV-2/COVID-19 and advances in developing potential therapeutics and vaccines to counter this emerging pandemic. Ann Clin Microbiol Antimicrob 2020; 19:40. [PMID: 32878641 PMCID: PMC7464065 DOI: 10.1186/s12941-020-00384-w] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/27/2020] [Indexed: 12/15/2022] Open
Abstract
A novel coronavirus (SARS-CoV-2), causing an emerging coronavirus disease (COVID-19), first detected in Wuhan City, Hubei Province, China, which has taken a catastrophic turn with high toll rates in China and subsequently spreading across the globe. The rapid spread of this virus to more than 210 countries while affecting more than 25 million people and causing more than 843,000 human deaths, it has resulted in a pandemic situation in the world. The SARS-CoV-2 virus belongs to the genus Betacoronavirus, like MERS-CoV and SARS-CoV, all of which originated in bats. It is highly contagious, causing symptoms like fever, dyspnea, asthenia and pneumonia, thrombocytopenia, and the severely infected patients succumb to the disease. Coronaviruses (CoVs) among all known RNA viruses have the largest genomes ranging from 26 to 32 kb in length. Extensive research has been conducted to understand the molecular basis of the SARS-CoV-2 infection and evolution, develop effective therapeutics, antiviral drugs, and vaccines, and to design rapid and confirmatory viral diagnostics as well as adopt appropriate prevention and control strategies. To date, August 30, 2020, no effective, proven therapeutic antibodies or specific drugs, and vaccines have turned up. In this review article, we describe the underlying molecular organization and phylogenetic analysis of the coronaviruses, including the SARS-CoV-2, and recent advances in diagnosis and vaccine development in brief and focusing mainly on developing potential therapeutic options that can be explored to manage this pandemic virus infection, which would help in valid countering of COVID-19.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Shamsah H Al-Ahmed
- Specialty Paediatric Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Ranjit Sah
- Department of Microbiology, Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, 281001, India
| | - Mohd Iqbal Yatoo
- Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Shailesh Kumar Patel
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India
| | - Mamta Pathak
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India.
| | - Karam Pal Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India
| | - D Katterine Bonilla-Aldana
- Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda, Colombia
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Dayron F Martinez-Pulgarin
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia.
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Americas, Pereira, Risaralda, Colombia.
- School of Medicine, Universidad Privada Franz Tamayo (UNIFRANZ), Cochabamba, Bolivia.
| | - Hakan Leblebicioglu
- Department of Infectious Diseases, Samsun VM Medicalpark Hospital, Samsun, Turkey
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19
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De Vita S, Chini MG, Lauro G, Bifulco G. Accelerating the repurposing of FDA-approved drugs against coronavirus disease-19 (COVID-19). RSC Adv 2020; 10:40867-40875. [PMID: 35519188 PMCID: PMC9057693 DOI: 10.1039/d0ra09010g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 11/02/2020] [Indexed: 12/24/2022] Open
Abstract
The recent release of the main protein structures belonging to SARS CoV-2, responsible for the coronavirus disease-19 (COVID-19), strongly pushed for identifying valuable drug treatments. With this aim, we show a repurposing study on FDA-approved drugs applying a new computational protocol and introducing a novel parameter called IVSratio. Starting with a virtual screening against three SARS CoV-2 targets (main protease, papain-like protease, spike protein), the top-ranked molecules were reassessed combining the Inverse Virtual Screening novel approach and MM-GBSA calculations. Applying this protocol, a list of drugs was identified against the three investigated targets. Also, the top-ranked selected compounds on each target (rutin vs. main protease, velpatasvir vs. papain-like protease, lomitapide vs. spike protein) were further tested with molecular dynamics simulations to confirm the promising binding modes, obtaining encouraging results such as high stability of the complex during the simulation and a good protein–ligand interaction network involving some important residues of each target. Moreover, the recent outcomes highlighting the inhibitory activity of quercetin, a natural compound strictly related to rutin, on the SARS-CoV-2 main protease, strengthened the applicability of the proposed workflow. New computational protocol applied to a repurposing campaign against SARS-CoV-2.![]()
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Affiliation(s)
- Simona De Vita
- Department of Pharmacy
- University of Salerno
- Fisciano 84084
- Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory
- University of Molise
- 86090 Pesche (IS)
- Italy
| | - Gianluigi Lauro
- Department of Pharmacy
- University of Salerno
- Fisciano 84084
- Italy
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