RESUMEN
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) represents a significant threat to human health. Despite its similarity to related coronaviruses, there are currently no specific treatments for COVID-19 infection, and therefore there is an urgent need to develop therapies for this and future coronavirus outbreaks. Formation of the cap at the 5' end of viral RNA has been shown to help coronaviruses evade host defenses. Nonstructural protein 14 (nsp14) is responsible for N7-methylation of the cap guanosine in coronaviruses. This enzyme is highly conserved among coronaviruses and is a bifunctional protein with both N7-methyltransferase and 3'-5' exonuclease activities that distinguish nsp14 from its human equivalent. Mutational analysis of SARS-CoV nsp14 highlighted its role in viral replication and translation efficiency of the viral genome. In this paper, we describe the characterization and development of a high-throughput assay for nsp14 utilizing RapidFire technology. The assay has been used to screen a library of 1771 Food and Drug Administration (FDA)-approved drugs. From this, we have validated nitazoxanide as a selective inhibitor of the methyltransferase activity of nsp14. Although modestly active, this compound could serve as a starting point for further optimization.
Asunto(s)
Antivirales/farmacología , Exorribonucleasas/antagonistas & inhibidores , Ensayos Analíticos de Alto Rendimiento , Nitrocompuestos/farmacología , Caperuzas de ARN/antagonistas & inhibidores , ARN Viral/antagonistas & inhibidores , SARS-CoV-2/efectos de los fármacos , Tiazoles/farmacología , Proteínas no Estructurales Virales/antagonistas & inhibidores , Antiparasitarios/química , Antiparasitarios/farmacología , Antivirales/química , COVID-19/virología , Clonación Molecular , Reposicionamiento de Medicamentos , Pruebas de Enzimas , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacología , Escherichia coli/genética , Escherichia coli/metabolismo , Exorribonucleasas/genética , Exorribonucleasas/metabolismo , Expresión Génica , Vectores Genéticos/química , Vectores Genéticos/metabolismo , Humanos , Cinética , Espectrometría de Masas/métodos , Metilación , Nitrocompuestos/química , Medicamentos bajo Prescripción/química , Medicamentos bajo Prescripción/farmacología , Caperuzas de ARN/genética , Caperuzas de ARN/metabolismo , ARN Viral/genética , ARN Viral/metabolismo , Proteínas Recombinantes de Fusión/química , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismo , SARS-CoV-2/enzimología , SARS-CoV-2/genética , Bibliotecas de Moléculas Pequeñas/química , Bibliotecas de Moléculas Pequeñas/farmacología , Tiazoles/química , Proteínas no Estructurales Virales/genética , Proteínas no Estructurales Virales/metabolismo , Replicación Viral/efectos de los fármacosRESUMEN
Docking is in demand for the rational computer aided structure based drug design. A review of docking methods and programs is presented. Different types of docking programs are described. They include docking of non-covalent small ligands, protein-protein docking, supercomputer docking, quantum docking, the new generation of docking programs and the application of docking for covalent inhibitors discovery. Taking into account the threat of COVID-19, we present here a short review of docking applications to the discovery of inhibitors of SARS-CoV and SARS-CoV-2 target proteins, including our own result of the search for inhibitors of SARS-CoV-2 main protease using docking and quantum chemical post-processing. The conclusion is made that docking is extremely important in the fight against COVID-19 during the process of development of antivirus drugs having a direct action on SARS-CoV-2 target proteins.
Asunto(s)
Antivirales/química , Proteasas 3C de Coronavirus/antagonistas & inhibidores , Simulación del Acoplamiento Molecular/métodos , Medicamentos bajo Prescripción/química , Inhibidores de Proteasas/química , SARS-CoV-2/química , Secuencia de Aminoácidos , Antivirales/clasificación , Antivirales/farmacología , Dominio Catalítico , Proteasas 3C de Coronavirus/química , Proteasas 3C de Coronavirus/genética , Proteasas 3C de Coronavirus/metabolismo , Diseño de Fármacos , Reposicionamiento de Medicamentos/métodos , Expresión Génica , Humanos , Medicamentos bajo Prescripción/clasificación , Medicamentos bajo Prescripción/farmacología , Inhibidores de Proteasas/clasificación , Inhibidores de Proteasas/farmacología , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Estructura Secundaria de Proteína , SARS-CoV-2/efectos de los fármacos , SARS-CoV-2/enzimología , Relación Estructura-Actividad , Tratamiento Farmacológico de COVID-19RESUMEN
SARS-CoV-2 is the causative agent for the ongoing COVID19 pandemic, and this virus belongs to the Coronaviridae family. Like other members of this family, the virus possesses a positive-sense single-stranded RNA genome. The genome encodes for the nsp12 protein, which houses the RNA-dependent-RNA polymerase (RdRP) activity responsible for the replication of the viral genome. A homology model of nsp12 was prepared using the structure of the SARS nsp12 (6NUR) as a model. The model was used to carry out in silico screening to identify molecules among natural products, or Food and Drug Administration-approved drugs that can potentially inhibit the activity of nsp12. This exercise showed that vitamin B12 (methylcobalamin) may bind to the active site of the nsp12 protein. A model of the nsp12 in complex with substrate RNA and incoming NTP showed that vitamin B12 binding site overlaps with that of the incoming nucleotide. A comparison of the calculated energies of binding for RNA plus NTP and methylcobalamin suggested that the vitamin may bind to the active site of nsp12 with significant affinity. It is, therefore, possible that methylcobalamin binding may prevent association with RNA and NTP and thus inhibit the RdRP activity of nsp12. Overall, our computational studies suggest that methylcobalamin form of vitamin B12 may serve as an effective inhibitor of the nsp12 protein.
Asunto(s)
Antivirales/farmacología , ARN Polimerasa Dependiente de ARN de Coronavirus/antagonistas & inhibidores , Genoma Viral , SARS-CoV-2/enzimología , Vitamina B 12/farmacología , Secuencia de Aminoácidos , Antivirales/química , Sitios de Unión , ARN Polimerasa Dependiente de ARN de Coronavirus/química , ARN Polimerasa Dependiente de ARN de Coronavirus/genética , ARN Polimerasa Dependiente de ARN de Coronavirus/metabolismo , Ensayos Analíticos de Alto Rendimiento , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Medicamentos bajo Prescripción/química , Medicamentos bajo Prescripción/farmacología , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , SARS-CoV-2/efectos de los fármacos , SARS-CoV-2/genética , Alineación de Secuencia , Homología de Secuencia de Aminoácido , Especificidad por Sustrato , Termodinámica , Interfaz Usuario-Computador , Vitamina B 12/químicaRESUMEN
Patients with COVID-19 are sometimes already being treated for one or more other chronic conditions, especially if they are elderly. Introducing a treatment against COVID-19, either on an outpatient basis or during hospitalization for more severe cases, raises the question of potential drug-drug interactions. Here, we analyzed the potential or proven risk of the co-administration of drugs used for the most common chronic diseases and those currently offered as treatment or undergoing therapeutic trials for COVID-19. Practical recommendations are offered, where possible.