1
|
Yan D, Yan B. Viral target and metabolism-based rationale for combined use of recently authorized small molecule COVID-19 medicines: Molnupiravir, nirmatrelvir, and remdesivir. Fundam Clin Pharmacol 2023; 37:726-738. [PMID: 36931725 PMCID: PMC10505250 DOI: 10.1111/fcp.12889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/12/2023] [Accepted: 02/27/2023] [Indexed: 03/19/2023]
Abstract
The COVID-19 pandemic remains a major health concern worldwide, and SARS-CoV-2 is continuously evolving. There is an urgent need to identify new antiviral drugs and develop novel therapeutic strategies. Combined use of newly authorized COVID-19 medicines including molnupiravir, nirmatrelvir, and remdesivir has been actively pursued. Mechanistically, nirmatrelvir inhibits SARS-CoV-2 replication by targeting the viral main protease (Mpro ), a critical enzyme in the processing of the immediately translated coronavirus polyproteins for viral replication. Molnupiravir and remdesivir, on the other hand, inhibit SARS-CoV-2 replication by targeting RNA-dependent RNA-polymerase (RdRp), which is directly responsible for genome replication and production of subgenomic RNAs. Molnupiravir targets RdRp and induces severe viral RNA mutations (genome), commonly referred to as error catastrophe. Remdesivir, in contrast, targets RdRp and causes chain termination and arrests RNA synthesis of the viral genome. In addition, all three medicines undergo extensive metabolism with strong therapeutic significance. Molnupiravir is hydrolytically activated by carboxylesterase-2 (CES2), nirmatrelvir is inactivated by cytochrome P450-based oxidation (e.g., CYP3A4), and remdesivir is hydrolytically activated by CES1 but covalently inhibits CES2. Additionally, remdesivir and nirmatrelvir are oxidized by the same CYP enzymes. The distinct mechanisms of action provide strong rationale for their combined use. On the other hand, these drugs undergo extensive metabolism that determines their therapeutic potential. This review discusses how metabolism pathways and enzymes involved should be carefully considered during their combined use for therapeutic synergy.
Collapse
Affiliation(s)
- Daisy Yan
- Department of Dermatology, Boston University School of Medicine 609 Albany Street Boston, MA 02118
| | - Bingfang Yan
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH 45229
| |
Collapse
|
2
|
Aziz S, Waqas M, Mohanta TK, Halim SA, Iqbal A, Ali A, Khalid A, Abdalla AN, Khan A, Al-Harrasi A. Identifying non-nucleoside inhibitors of RNA-dependent RNA-polymerase of SARS-CoV-2 through per-residue energy decomposition-based pharmacophore modeling, molecular docking, and molecular dynamics simulation. J Infect Public Health 2023; 16:501-519. [PMID: 36801630 PMCID: PMC9927802 DOI: 10.1016/j.jiph.2023.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND AND OBJECTIVE The current coronavirus disease-2019 (COVID-19) pandemic has triggered a worldwide health and economic crisis. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes the disease and completes its life cycle using the RNA-dependent RNA-polymerase (RdRp) enzyme, a prominent target for antivirals. In this study, we have computationally screened ∼690 million compounds from the ZINC20 database and 11,698 small molecule inhibitors from DrugBank to find existing and novel non-nucleoside inhibitors for SARS-CoV-2 RdRp. METHODS Herein, a combination of the structure-based pharmacophore modeling and hybrid virtual screening methods, including per-residue energy decomposition-based pharmacophore screening, molecular docking, pharmacokinetics, and toxicity evaluation were employed to retrieve novel as well as existing RdRp non-nucleoside inhibitors from large chemical databases. Besides, molecular dynamics simulation and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) method were used to investigate the binding stability and calculate the binding free energy of RdRp-inhibitor complexes. RESULTS Based on docking scores and significant binding interactions with crucial residues (Lys553, Arg557, Lys623, Cys815, and Ser816) in the RNA binding site of RdRp, three existing drugs, ZINC285540154, ZINC98208626, ZINC28467879, and five compounds from ZINC20 (ZINC739681614, ZINC1166211307, ZINC611516532, ZINC1602963057, and ZINC1398350200) were selected, and the conformational stability of RdRp due to their binding was confirmed through molecular dynamics simulation. The free energy calculations revealed these compounds possess strong binding affinities for RdRp. In addition, these novel inhibitors exhibited drug-like features, good absorption, distribution, metabolism, and excretion profile and were found to be non-toxic. CONCLUSION The compounds identified in the study by multifold computational strategy can be validated in vitro as potential non-nucleoside inhibitors of SARS-CoV-2 RdRp and holds promise for the discovery of novel drugs against COVID-19 in future.
Collapse
Affiliation(s)
- Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25000, Pakistan
| | - Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, 2100, Pakistan; Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Aqib Iqbal
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25000, Pakistan; Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan.
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, 2100, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan 45142, Saudi Arabia; Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P. O. Box 2404, Khartoum, Sudan
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
| |
Collapse
|
3
|
Konkolova E, Krejčová K, Eyer L, Hodek J, Zgarbová M, Fořtová A, Jirasek M, Teply F, Reyes-Gutierrez PE, Růžek D, Weber J, Boura E. A Helquat-like Compound as a Potent Inhibitor of Flaviviral and Coronaviral Polymerases. Molecules 2022; 27:molecules27061894. [PMID: 35335258 PMCID: PMC8953834 DOI: 10.3390/molecules27061894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022]
Abstract
Positive-sense single-stranded RNA (+RNA) viruses have proven to be important pathogens that are able to threaten and deeply damage modern societies, as illustrated by the ongoing COVID-19 pandemic. Therefore, compounds active against most or many +RNA viruses are urgently needed. Here, we present PR673, a helquat-like compound that is able to inhibit the replication of SARS-CoV-2 and tick-borne encephalitis virus in cell culture. Using in vitro polymerase assays, we demonstrate that PR673 inhibits RNA synthesis by viral RNA-dependent RNA polymerases (RdRps). Our results illustrate that the development of broad-spectrum non-nucleoside inhibitors of RdRps is feasible.
Collapse
Affiliation(s)
- Eva Konkolova
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Kateřina Krejčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Luděk Eyer
- Laboratory of Emerging Viral Diseases, Veterinary Research Institute, Hudcova 296/70, 62100 Brno, Czech Republic; (L.E.); (A.F.); (D.R.)
| | - Jan Hodek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Michala Zgarbová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Andrea Fořtová
- Laboratory of Emerging Viral Diseases, Veterinary Research Institute, Hudcova 296/70, 62100 Brno, Czech Republic; (L.E.); (A.F.); (D.R.)
| | - Michael Jirasek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Filip Teply
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Paul E. Reyes-Gutierrez
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Daniel Růžek
- Laboratory of Emerging Viral Diseases, Veterinary Research Institute, Hudcova 296/70, 62100 Brno, Czech Republic; (L.E.); (A.F.); (D.R.)
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 37005 Ceske Budejovice, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
- Correspondence:
| |
Collapse
|
4
|
Albentosa-González L, Jimenez de Oya N, Arias A, Clemente-Casares P, Martin-Acebes MÁ, Saiz JC, Sabariegos R, Mas A. Akt Kinase Intervenes in Flavivirus Replication by Interacting with Viral Protein NS5. Viruses 2021; 13:v13050896. [PMID: 34066055 PMCID: PMC8151281 DOI: 10.3390/v13050896] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 12/30/2022] Open
Abstract
Arthropod-borne flaviviruses, such as Zika virus (ZIKV), Usutu virus (USUV), and West Nile virus (WNV), are a growing cause of human illness and death around the world. Presently, no licensed antivirals to control them are available and, therefore, search for broad-spectrum antivirals, including host-directed compounds, is essential. The PI3K/Akt pathway controls essential cellular functions involved in cell metabolism and proliferation. Moreover, Akt has been found to participate in modulating replication in different viruses including the flaviviruses. In this work we studied the interaction of flavivirus NS5 polymerases with the cellular kinase Akt. In vitro NS5 phosphorylation experiments with Akt showed that flavivirus NS5 polymerases are phosphorylated and co-immunoprecipitate by Akt. Polymerase activity assays of Ala- and Glu-generated mutants for the Akt-phosphorylated residues also indicate that Glu mutants of ZIKV and USUV NS5s present a reduced primer-extension activity that was not observed in WNV mutants. Furthermore, treatment with Akt inhibitors (MK-2206, honokiol and ipatasertib) reduced USUV and ZIKV titers in cell culture but, except for honokiol, not WNV. All these findings suggest an important role for Akt in flavivirus replication although with specific differences among viruses and encourage further investigations to examine the PI3K/Akt/mTOR pathway as an antiviral potential target.
Collapse
Affiliation(s)
- Laura Albentosa-González
- Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (L.A.-G.); (A.A.); (P.C.-C.)
| | - Nereida Jimenez de Oya
- ZOOVIR, Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28040 Madrid, Spain; (N.J.d.O.); (M.Á.M.-A.); (J.C.S.)
| | - Armando Arias
- Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (L.A.-G.); (A.A.); (P.C.-C.)
- Unidad de Biomedicina UCLM-CSIC, 02008 Albacete, Spain
- Escuela Técnica Superior de Ingenieros Agrónomos, Universidad de Castilla-La Mancha, 02071 Albacete, Spain
| | - Pilar Clemente-Casares
- Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (L.A.-G.); (A.A.); (P.C.-C.)
- Unidad de Biomedicina UCLM-CSIC, 02008 Albacete, Spain
- Facultad de Farmacia, Universidad de Castilla-La Mancha, 02008 Albacete, Spain
| | - Miguel Ángel Martin-Acebes
- ZOOVIR, Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28040 Madrid, Spain; (N.J.d.O.); (M.Á.M.-A.); (J.C.S.)
| | - Juan Carlos Saiz
- ZOOVIR, Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28040 Madrid, Spain; (N.J.d.O.); (M.Á.M.-A.); (J.C.S.)
| | - Rosario Sabariegos
- Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (L.A.-G.); (A.A.); (P.C.-C.)
- Unidad de Biomedicina UCLM-CSIC, 02008 Albacete, Spain
- Facultad de Medicina, Universidad de Castilla-La Mancha, 02008 Albacete, Spain
- Correspondence: (R.S.); (A.M.)
| | - Antonio Mas
- Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (L.A.-G.); (A.A.); (P.C.-C.)
- Unidad de Biomedicina UCLM-CSIC, 02008 Albacete, Spain
- Facultad de Farmacia, Universidad de Castilla-La Mancha, 02008 Albacete, Spain
- Correspondence: (R.S.); (A.M.)
| |
Collapse
|
5
|
Albentosa-González L, Sabariegos R, Arias A, Clemente-Casares P, Mas A. Akt Interacts with Usutu Virus Polymerase, and Its Activity Modulates Viral Replication. Pathogens 2021; 10:244. [PMID: 33672588 DOI: 10.3390/pathogens10020244] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/09/2021] [Accepted: 02/18/2021] [Indexed: 12/17/2022] Open
Abstract
Usutu virus (USUV) is a flavivirus that mainly infects wild birds through the bite of Culex mosquitoes. Recent outbreaks have been associated with an increased number of cases in humans. Despite being a growing source of public health concerns, there is yet insufficient data on the virus or host cell targets for infection control. In this work we have investigated whether the cellular kinase Akt and USUV polymerase NS5 interact and co-localize in a cell. To this aim, we performed co-immunoprecipitation (Co-IP) assays, followed by confocal microscopy analyses. We further tested whether NS5 is a phosphorylation substrate of Akt in vitro. Finally, to examine its role in viral replication, we chemically silenced Akt with three inhibitors (MK-2206, honokiol and ipatasertib). We found that both proteins are localized (confocal) and pulled down (Co-IP) together when expressed in different cell lines, supporting the fact that they are interacting partners. This possibility was further sustained by data showing that NS5 is phosphorylated by Akt. Treatment of USUV-infected cells with Akt-specific inhibitors led to decreases in virus titers (>10-fold). Our results suggest an important role for Akt in virus replication and stimulate further investigations to examine the PI3K/Akt/mTOR pathway as an antiviral target.
Collapse
|
6
|
Pormohammad A, Monych NK, Turner RJ. Zinc and SARS‑CoV‑2: A molecular modeling study of Zn interactions with RNA‑dependent RNA‑polymerase and 3C‑like proteinase enzymes. Int J Mol Med 2021; 47:326-334. [PMID: 33236142 PMCID: PMC7723401 DOI: 10.3892/ijmm.2020.4790] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/13/2020] [Indexed: 11/09/2022] Open
Abstract
RNA‑dependent RNA‑polymerase (RdRp) and 3C‑like proteinase (3CLpro) are two main enzymes that play a key role in the replication of SARS‑CoV‑2. Zinc (Zn) has strong immunogenic properties and is known to bind to a number of proteins, modulating their activities. Zn also has a history of use in viral infection control. Thus, the present study models potential Zn binding to RdRp and the 3CLpro. Through molecular modeling, the Zn binding sites in the aforementioned two important enzymes of viral replication were found to be conserved between severe acute respiratory syndrome (SARS)‑coronavirus (CoV) and SARS‑CoV‑2. The location of these sites may influence the enzymatic activity of 3CLpro and RdRp in coronavirus disease 2019 (COVID‑19). Since Zn has established immune health benefits, is readily available, non‑expensive and a safe food supplement, with the comparisons presented here between SARS‑CoV and COVID‑19, the present study proposes that Zn could help ameliorate the disease process of COVID‑19 infection.
Collapse
Affiliation(s)
- Ali Pormohammad
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N4V8, Canada
| | - Nadia K. Monych
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N4V8, Canada
| | - Raymond J. Turner
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N4V8, Canada
| |
Collapse
|
7
|
Alexpandi R, De Mesquita JF, Pandian SK, Ravi AV. Quinolines-Based SARS-CoV-2 3CLpro and RdRp Inhibitors and Spike-RBD-ACE2 Inhibitor for Drug-Repurposing Against COVID-19: An in silico Analysis. Front Microbiol 2020; 11:1796. [PMID: 32793181 PMCID: PMC7390959 DOI: 10.3389/fmicb.2020.01796] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/09/2020] [Indexed: 01/20/2023] Open
Abstract
The novel coronavirus SARS-CoV-2 disease “COVID-19” emerged in China and rapidly spread to other countries; due to its rapid worldwide spread, the WHO has declared this as a global emergency. As there is no specific treatment prescribed to treat COVID-19, the seeking of suitable therapeutics among existing drugs seems valuable. The structure availability of coronavirus macromolecules has encouraged the finding of conceivable anti-SARS-CoV-2 therapeutics through in silico analysis. The results reveal that quinoline,1,2,3,4-tetrahydro-1-[(2-phenylcyclopropyl)sulfonyl]-trans-(8CI) and saquinavir strongly interact with the active site (Cys-His catalytic dyad), thereby are predicted to hinder the activity of SARS-CoV-2 3CLpro. Out of 113 quinoline-drugs, elvitegravir and oxolinic acid are able to interact with the NTP entry-channel and thus interfere with the RNA-directed 5′-3′ polymerase activity of SARS-CoV-2 RdRp. The bioactivity-prediction results also validate the outcome of the docking study. Moreover, as SARS-CoV-2 Spike-glycoprotein uses human ACE2-receptor for viral entry, targeting the Spike-RBD-ACE2 has been viewed as a promising strategy to control the infection. The result shows rilapladib is the only quinoline that can interrupt the Spike-RBD-ACE2 complex. In conclusion, owing to their ability to target functional macromolecules of SARS-CoV-2, along with positive ADMET properties, quinoline,1,2,3,4-tetrahydro-1-[(2-phenylcyclopropyl)sulfonyl]-trans-(8CI), saquinavir, elvitegravir, oxolinic acid, and rilapladib are suggested for the treatment of COVID-19.
Collapse
Affiliation(s)
- Rajaiah Alexpandi
- Department of Biotechnology, School of Biological Sciences, Science Campus, Alagappa University, Karaikudi, India
| | - Joelma Freire De Mesquita
- Laboratory of Bioinformatics and Computational Biology, Department of Genetics and Molecular Biology, Federal University of Rio de Janeiro State (UNIRIO), Rio de Janeiro, Brazil
| | - Shunmugiah Karutha Pandian
- Department of Biotechnology, School of Biological Sciences, Science Campus, Alagappa University, Karaikudi, India
| | - Arumugam Veera Ravi
- Department of Biotechnology, School of Biological Sciences, Science Campus, Alagappa University, Karaikudi, India
| |
Collapse
|
8
|
Calligari P, Bobone S, Ricci G, Bocedi A. Molecular Investigation of SARS-CoV-2 Proteins and Their Interactions with Antiviral Drugs. Viruses 2020; 12:v12040445. [PMID: 32295237 PMCID: PMC7232184 DOI: 10.3390/v12040445] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/27/2020] [Accepted: 04/13/2020] [Indexed: 12/12/2022] Open
Abstract
A new Coronavirus strain, named SARS-CoV-2, suddenly emerged in early December 2019. SARS-CoV-2 resulted in being dramatically infectious, with thousands of people infected. In this scenario, and without effective vaccines available, the importance of an immediate tool to support patients and against viral diffusion becomes evident. In this study, we exploit the molecular docking approach to analyze the affinity between different viral proteins and several inhibitors, originally developed for other viral infections. Our data show that, in some cases, a relevant binding can be detected. These findings support the hypothesis to develop new antiviral agents against COVID-19, on the basis of already established therapies.
Collapse
Affiliation(s)
| | | | | | - Alessio Bocedi
- Correspondence: ; Tel.: +39-067-259-4353; Fax: +39-067-259-4328
| |
Collapse
|
9
|
Albentosa-González L, Clemente-Casares P, Sabariegos R, Mas A. Polymerase Activity, Protein-Protein Interaction, and Cellular Localization of the Usutu Virus NS5 Protein. Antimicrob Agents Chemother 2019; 64:e01573-19. [PMID: 31685463 DOI: 10.1128/AAC.01573-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/23/2019] [Indexed: 12/31/2022] Open
Abstract
Usutu virus (USUV) has become increasingly relevant in recent years, with large outbreaks that sporadically have affected humans being reported in wildlife. Similarly to the rest of flaviviruses, USUV contains a positive-sense single-stranded RNA genome which is replicated by the activity of nonstructural protein 5 (NS5). USUV NS5 shows high sequence identity with the remaining viruses in this genus. This permitted us to identify the predicted methyltransferase domain and the RNA-dependent RNA polymerase domain (RdRpD). Owing to their high degree of conservation, viral polymerases are considered priority targets for the development of antiviral compounds. In the present study, we cloned and expressed the entire NS5 and the RdRpD in a heterologous system and used purified preparations for protein characterizations. We determined the optimal reaction conditions by investigating how variations in different physicochemical parameters, such as buffer concentration, temperature, and pH, affect RNA polymerization activity. We also found that USUV polymerase, but not the full-length NS5, exhibits cooperative activity in the synthesis of RNA and that the RdRp activity is not inhibited by sofosbuvir. To further examine the characteristics of USUV polymerase in a more specifically biological context, we have expressed NS5 and the RdRpD in eukaryotic cells and analyzed their subcellular location. NS5 is predominantly found in the cytoplasm; a significant proportion is directed to the nucleus, and this translocation involves nuclear location signals (NLS) located at least between the MTase and RdRpD domains.
Collapse
|
10
|
Ramharack P, Devnarain N, Shunmugam L, Soliman MES. Navigating Research Toward the Re-emerging Nipah Virus- A New Piece to the Puzzle. Curr Pharm Des 2019; 25:1392-1401. [PMID: 31258065 DOI: 10.2174/1381612825666190620104203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/22/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND The recent Nipah virus (NiV) outbreak in India has caused a state of chaos, with potential to become the next international pandemic. There is still a great deal to learn about NiV for the development of a potent treatment against it. The NiV non-structural proteins play important roles in the lifecycle of the virus, with the RNA-dependent RNA-polymerase (RdRp) being a vital component in viral replication. In this study, we not only provide a comprehensive overview of all the literature concerning NiV, we also propose a model of the NiV RdRp and screen for potential inhibitors of the viral enzyme. METHODS In this study, computational tools were utilized in the design of a NiV RdRp homology model. The active site of RdRp was then identified and potential inhibitors of the protein were discovered with the use of pharmacophore-based screening. RESULTS Ramachandran plot analysis revealed a favourable model. Upon binding of nucleoside analog, 4'- Azidocytidine, active site residues Trp1714 and Ser1713 took part in stabilizing hydrogen bonds, while Thr1716, Ser1478, Ser1476 and Glu1465 contributed to hydrophobic interactions. Pharmacophore based screening yielded 18 hits, of which ZINC00085930 demonstrated the most optimal binding energy (-8.1 kcal/mol), validating its use for further analysis as an inhibitor of NiV. CONCLUSION In this study we provide a critical guide, elucidating on the in silico requirements of the drug design and discovery process against NiV. This material lays a foundation for future research into the design and development of drugs that inhibit NiV.
Collapse
Affiliation(s)
- Pritika Ramharack
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Nikita Devnarain
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Letitia Shunmugam
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| |
Collapse
|
11
|
da Costa AC, Luchs A, Milagres FAP, Komninakis SV, Gill DE, Lobato MCABS, Brustulin R, das Chagas RT, Abrão MFNDS, Soares CVDA, Deng X, Sabino EC, Delwart E, Leal É. Recombination Located over 2A-2B Junction Ribosome Frameshifting Region of Saffold Cardiovirus. Viruses 2018; 10:E520. [PMID: 30249971 DOI: 10.3390/v10100520] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/26/2018] [Accepted: 09/04/2018] [Indexed: 01/15/2023] Open
Abstract
Here we report the nearly full-length genome of a recombinant Saffold virus strain (SAFV-BR-193) isolated from a child with acute gastroenteritis. Evolutionary analysis performed using all available near-full length Saffold picornavirus genomes showed that the breakpoint found in the Brazilian strain (SAFV-BR-193) is indeed a recombination hotspot. Notably, this hotspot is located just one nucleotide after the ribosomal frameshift GGUUUUU motif in the SAFV genome. Empirical studies will be necessary to determine if this motif also affects the binding affinity of RNA-dependent RNA-polymerase (RdRp) and therefore increases the changes of RdRp swap between molecules during the synthesis of viral genomes.
Collapse
|
12
|
Abstract
INTRODUCTION In the United States, respiratory syncytial virus (RSV) is responsible for the majority of infant hospitalizations resulting from viral infections, as well as a leading source of pneumonia and bronchiolitis in young children and the elderly. In the absence of vaccine prophylaxis or an effective antiviral for improved disease management, the development of novel anti-RSV therapeutics is critical. Several advanced drug development campaigns of the past decade have focused on blocking viral infection. These efforts have returned a chemically distinct panel of small-molecule RSV entry inhibitors, but binding sites and molecular mechanism of action appeared to share a common mechanism, resulting in comprehensive cross-resistance and calling for alternative druggable targets such as viral RNA-dependent RNA-polymerase complex. Areas Covered: In this review, the authors discuss the current status of the mechanism of action of RSV entry inhibitors. They also provide the recent structural insight into the organization of the polymerase complex that have revealed novel drug targets sites, and outline a path towards the discovery of next-generation RSV therapeutics. Expert opinion: Considering the tremendous progress experienced in our structural understanding of RSV biology in recent years and encouraging early results of a nucleoside analog inhibitor in clinical trials, there is high prospect that new generations of much needed effective anti-RSV therapeutics will become available for clinical use in the foreseeable future.
Collapse
Affiliation(s)
- Robert Cox
- Institute for Biomedical Sciences, Georgia State University, 100 Piedmont Av, Atlanta, Georgia 30303-3222 USA
| | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, 100 Piedmont Av, Atlanta, Georgia 30303-3222 USA
| |
Collapse
|