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1.
Commun Biol ; 4(1): 193, 2021 02 09.
Artículo en Inglés | MEDLINE | ID: mdl-33564093

RESUMEN

SARS-CoV-2 Nsp15 is a uridine-specific endoribonuclease with C-terminal catalytic domain belonging to the EndoU family that is highly conserved in coronaviruses. As endoribonuclease activity seems to be responsible for the interference with the innate immune response, Nsp15 emerges as an attractive target for therapeutic intervention. Here we report the first structures with bound nucleotides and show how the enzyme specifically recognizes uridine moiety. In addition to a uridine site we present evidence for a second base binding site that can accommodate any base. The structure with a transition state analog, uridine vanadate, confirms interactions key to catalytic mechanisms. In the presence of manganese ions, the enzyme cleaves unpaired RNAs. This acquired knowledge was instrumental in identifying Tipiracil, an FDA approved drug that is used in the treatment of colorectal cancer, as a potential anti-COVID-19 drug. Using crystallography, biochemical, and whole-cell assays, we demonstrate that Tipiracil inhibits SARS-CoV-2 Nsp15 by interacting with the uridine binding pocket in the enzyme's active site. Our findings provide new insights for the development of uracil scaffold-based drugs.


Asunto(s)
Antivirales/farmacología , /virología , Endorribonucleasas/antagonistas & inhibidores , Inhibidores Enzimáticos/farmacología , Pirrolidinas/farmacología , /enzimología , Timina/farmacología , Proteínas no Estructurales Virales/antagonistas & inhibidores , Células A549 , Antivirales/química , Antivirales/farmacocinética , Dominio Catalítico , Cristalografía por Rayos X , Endorribonucleasas/química , Endorribonucleasas/metabolismo , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacocinética , Humanos , Ligandos , Modelos Moleculares , Conformación Proteica , Pirrolidinas/química , Pirrolidinas/farmacocinética , Timina/química , Timina/farmacocinética , Uridina/metabolismo , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/metabolismo
2.
Arch Biochem Biophys ; 700: 108771, 2021 03 30.
Artículo en Inglés | MEDLINE | ID: mdl-33485847

RESUMEN

In the current study, a structure-based virtual screening paradigm was used to screen a small molecular database against the Non-structural protein 15 (Nsp15) endoribonuclease of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 is the causative agent of the recent outbreak of coronavirus disease 2019 (COVID-19) which left the entire world locked down inside the home. A multi-step molecular docking study was performed against antiviral specific compounds (~8722) collected from the Asinex antiviral database. The less or non-interacting molecules were wiped out sequentially in the molecular docking. Further, MM-GBSA based binding free energy was estimated for 26 compounds which shows a high affinity towards the Nsp15. The drug-likeness and pharmacokinetic parameters of all 26 compounds were explored, and five molecules were found to have an acceptable pharmacokinetic profile. Overall, the Glide-XP docking score and Prime-MM-GBSA binding free energy of the selected molecules were explained strong interaction potentiality towards the Nsp15 endoribonuclease. The dynamic behavior of each molecule with Nsp15 was assessed using conventional molecular dynamics (MD) simulation. The MD simulation information was strongly favors the Nsp15 and each identified ligand stability in dynamic condition. Finally, from the MD simulation trajectories, the binding free energy was estimated using the MM-PBSA method. Hence, the proposed final five molecules might be considered as potential Nsp15 modulators for SARS-CoV-2 inhibition.


Asunto(s)
Antivirales/farmacología , /virología , Endorribonucleasas/antagonistas & inhibidores , /enzimología , Proteínas no Estructurales Virales/antagonistas & inhibidores , Antivirales/química , Antivirales/farmacocinética , Bases de Datos de Compuestos Químicos , Evaluación Preclínica de Medicamentos , Endorribonucleasas/química , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacocinética , Inhibidores Enzimáticos/farmacología , Humanos , Técnicas In Vitro , Ligandos , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Estructura Molecular , Interfaz Usuario-Computador , Proteínas no Estructurales Virales/química
3.
Food Chem ; 346: 128933, 2021 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-33418408

RESUMEN

Immensely aggravated situation of COVID-19 has pushed the scientific community towards developing novel therapeutics to fight the pandemic. Small molecules can possibly prevent the spreading infection by targeting specific vital components of the viral genome. Non-structural protein 15 (Nsp15) has emerged as a promising target for such inhibitor molecules. In this investigation, we docked bioactive molecules of tea onto the active site of Nsp15. Based on their docking scores, top three molecules (Barrigenol, Kaempferol, and Myricetin) were selected and their conformational behavior was analyzed via molecular dynamics simulations and MMPBSA calculations. The results indicated that the protein had well adapted the ligands in the binding pocket thereby forming stable complexes. These molecules displayed low binding energy during MMPBSA calculations, substantiating their strong association with Nsp15. The inhibitory potential of these molecules could further be examined by in-vivo and in-vitro investigations to validate their use as inhibitors against Nsp15 of SARS-CoV2.


Asunto(s)
Antivirales/farmacología , Simulación por Computador , Endorribonucleasas/antagonistas & inhibidores , Extractos Vegetales/farmacología , Té/química , Proteínas no Estructurales Virales/antagonistas & inhibidores , Dominio Catalítico , Endorribonucleasas/química , Endorribonucleasas/metabolismo , Humanos , Ligandos , Simulación de Dinámica Molecular , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/metabolismo
4.
Int J Biol Macromol ; 168: 272-278, 2021 Jan 31.
Artículo en Inglés | MEDLINE | ID: mdl-33309661

RESUMEN

SARS-CoV-2is the causative agent for the ongoing COVID19 pandemic, and this virus belongs to the Coronaviridae family. The nsp14 protein of SARS-CoV-2 houses a 3' to 5' exoribonuclease activity responsible for removing mismatches that arise during genome duplication. A homology model of nsp10-nsp14 complex was used to carry out in silico screening to identify molecules among natural products, or FDA approved drugs that can potentially inhibit the activity of nsp14. This exercise showed that ritonavir might bind to the exoribonuclease active site of the nsp14 protein. A model of the SARS-CoV-2-nsp10-nsp14 complex bound to substrate RNA showed that the ritonavir binding site overlaps with that of the 3' nucleotide of substrate RNA. A comparison of the calculated energies of binding for RNA and ritonavir suggested that the drug may bind to the active site of nsp14 with significant affinity. It is, therefore, possible that ritonavir may prevent association with substrate RNA and thus inhibit the exoribonuclease activity of nsp14. Overall, our computational studies suggest that ritonavir may serve as an effective inhibitor of the nsp14 protein. nsp14 is known to attenuate the inhibitory effect of drugs that function through premature termination of viral genome replication. Hence, ritonavir may potentiate the therapeutic properties of drugs such as remdesivir, favipiravir and ribavirin.


Asunto(s)
Antivirales/farmacología , Exorribonucleasas/antagonistas & inhibidores , Ritonavir/farmacología , Proteínas no Estructurales Virales/antagonistas & inhibidores , Secuencia de Aminoácidos , Antivirales/administración & dosificación , Antivirales/química , Dominio Catalítico , Simulación por Computador , Evaluación Preclínica de Medicamentos , Sinergismo Farmacológico , Quimioterapia Combinada , Exorribonucleasas/química , Exorribonucleasas/genética , Genoma Viral/efectos de los fármacos , Humanos , Simulación de Dinámica Molecular , Pandemias , Ritonavir/administración & dosificación , Ritonavir/química , /fisiología , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/genética , Replicación Viral/efectos de los fármacos
5.
Spectrochim Acta A Mol Biomol Spectrosc ; 244: 118825, 2021 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-32866803

RESUMEN

Novel antiviral active molecule 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro- phenyl)acetamide has been synthesised and characterized by FT-IR and FT-Raman spectra. The equilibrium geometry, natural bond orbital calculations and vibrational assignments have been carried out using density functional B3LYP method with the 6-311G++(d,p) basis set. The complete vibrational assignments for all the vibrational modes have been supported by normal coordinate analysis, force constants and potential energy distributions. A detailed analysis of the intermolecular interactions has been performed based on the Hirshfeld surfaces. Drug likeness has been carried out based on Lipinski's rule and the absorption, distribution, metabolism, excretion and toxicity of the title molecule has been calculated. Antiviral potency of 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro-phenyl) acetamide has been investigated by docking against SARS-CoV-2 protein. The optimized geometry shows near-planarity between the phenyl ring and the pyrimidine ring. Differences in the geometries due to the substitution of the most electronegative fluorine atom and intermolecular contacts due to amino pyrimidine were analyzed. NBO analysis reveals the formation of two strong stable hydrogen bonded N-H···N intermolecular interactions and weak intramolecular interactions C-H···O and N-H···O. The Hirshfeld surfaces and consequently the 2D-fingerprint confirm the nature of intermolecular interactions and their quantitative contributions towards the crystal packing. The red shift in N-H stretching frequency exposed from IR substantiate the formation of N-H···N intermolecular hydrogen bond. Drug likeness and absorption, distribution, metabolism, excretion and toxicity properties analysis gives an idea about the pharmacokinetic properties of the title molecule. The binding energy -8.7 kcal/mol of the nonbonding interaction present a clear view that 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro- phenyl) acetamide can irreversibly interact with SARS-CoV-2 protease.


Asunto(s)
Acetamidas/química , Antivirales/química , Betacoronavirus/efectos de los fármacos , Infecciones por Coronavirus/tratamiento farmacológico , Pandemias , Neumonía Viral/tratamiento farmacológico , Inhibidores de Proteasas/química , Pirimidinas/química , Proteínas no Estructurales Virales/antagonistas & inhibidores , Acetamidas/farmacocinética , Antivirales/farmacocinética , Betacoronavirus/enzimología , Cristalografía por Rayos X , Cisteína Endopeptidasas , Humanos , Modelos Moleculares , Simulación del Acoplamiento Molecular , Estructura Molecular , Dinámicas no Lineales , Inhibidores de Proteasas/farmacocinética , Conformación Proteica , Pirimidinas/farmacocinética , Teoría Cuántica , Espectroscopía Infrarroja por Transformada de Fourier , Espectrometría Raman , Termodinámica , Vibración
6.
J Mol Model ; 26(12): 340, 2020 Nov 12.
Artículo en Inglés | MEDLINE | ID: mdl-33184722

RESUMEN

Among targets selected for studies aimed at identifying potential inhibitors against COVID-19, SARS-CoV2 main proteinase (Mpro) is highlighted. Mpro is indispensable for virus replication and is a promising target of potential inhibitors of COVID-19. Recently, monomeric SARS-CoV2 Mpro, drug repurposing, and docking methods have facilitated the identification of several potential inhibitors. Results were refined through the assessment of dimeric SARS-CoV2 Mpro, which represents the functional state of enzyme. Docking and molecular dynamics (MD) simulations combined with molecular mechanics/generalized Born surface area (MM/GBSA) studies indicated that dimeric Mpro most significantly impacts binding affinity tendency compared with the monomeric state, which suggests that dimeric state is most useful when performing studies aimed at identifying drugs targeting Mpro. In this study, we extend previous research by performing docking and MD simulation studies coupled with an MM/GBSA approach to assess binding of dimeric SARS-CoV2 Mpro to 12 FDA-approved drugs (darunavir, indinavir, saquinavir, tipranavir, diosmin, hesperidin, rutin, raltegravir, velpatasvir, ledipasvir, rosuvastatin, and bortezomib), which were identified as the best candidates for the treatment of COVID-19 in some previous dockings studies involving monomeric SARS-CoV2 Mpro. This analysis identified saquinavir as a potent inhibitor of dimeric SARS-CoV2 Mpro; therefore, the compound may have clinical utility against COVID-19. Graphical abstract.


Asunto(s)
Antivirales/farmacología , Betacoronavirus/efectos de los fármacos , Infecciones por Coronavirus/tratamiento farmacológico , Neumonía Viral/tratamiento farmacológico , Inhibidores de Proteasas/farmacología , Saquinavir/farmacología , Proteínas no Estructurales Virales/antagonistas & inhibidores , Antivirales/química , Betacoronavirus/enzimología , Infecciones por Coronavirus/virología , Cisteína Endopeptidasas , Reposicionamiento de Medicamentos , Humanos , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Pandemias , Neumonía Viral/virología , Inhibidores de Proteasas/química , Multimerización de Proteína , Saquinavir/química
7.
J Mol Model ; 26(12): 341, 2020 Nov 16.
Artículo en Inglés | MEDLINE | ID: mdl-33200284

RESUMEN

HER-2 type breast cancer is one of the most aggressive malignancies found in women. Tucatinib is recently developed and approved as a potential medicine to fight this disease. In this manuscript, we present the gross structural features of this compound and its reactivity and wave function properties using computational simulations. Density functional theory was used to optimise the ground state geometry of the molecule and molecular docking was used to predict biological activity. As the electrons interact with electromagnetic radiations, electronic excitations between different energy levels are analysed in detail using time-dependent density functional theory. Various intermolecular and intermolecular interactions are analysed and reaction sites for attacking electrophiles and nucleophiles identified. Information entropy calculations show that the compound is inherently stable. Docking with COVID-19 proteins show docking score of - 9.42, - 8.93, - 8.45 and - 8.32 kcal/mol respectively indicating high interaction between the drug and proteins. Hence, this is an ideal candidate to study repurposing of existing drugs to combat the pandemic.


Asunto(s)
Antineoplásicos/química , Antivirales/química , Betacoronavirus/química , Electrones , Oxazoles/química , Inhibidores de Proteasas/química , Piridinas/química , Quinazolinas/química , Proteínas no Estructurales Virales/antagonistas & inhibidores , Antineoplásicos/metabolismo , Antivirales/metabolismo , Betacoronavirus/enzimología , Sitios de Unión , Cisteína Endopeptidasas/química , Cisteína Endopeptidasas/metabolismo , Reposicionamiento de Medicamentos , Humanos , Enlace de Hidrógeno , Interacciones Hidrofóbicas e Hidrofílicas , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Oxazoles/metabolismo , Inhibidores de Proteasas/metabolismo , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Estructura Secundaria de Proteína , Piridinas/metabolismo , Teoría Cuántica , Quinazolinas/metabolismo , Termodinámica , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/metabolismo
8.
BMC Res Notes ; 13(1): 527, 2020 Nov 11.
Artículo en Inglés | MEDLINE | ID: mdl-33176880

RESUMEN

OBJECTIVES: The aim of this study was to use Ligand-based pharmacophore modelling approach for four established antiviral drugs, namely remdesivir, lopinavir, ritonavir and hydroxychloroquine for COVID-19 inhibitors as training sets. In this study Twenty vanillin derivatives together with monolaurin and tetrodotoxin were used as test sets to evaluate as potential SARS-CoV-2 inhibitors. The Structure-based pharmacophore modelling approach was also performed using 5RE6, 5REX and 5RFZ in order to analyse the binding site and ligand-protein complex interactions. RESULTS: The pharmacophore modelling mode of 5RE6 displayed two Hydrogen Bond Acceptors (HBA) and one Hydrophobic (HY) interaction. Besides, the pharmacophore model of 5REX showed two HBA and two HY interactions. Finally, the pharmacophore model of 5RFZ showed three HBA and one HY interaction. Based on ligand-based approach, 20 Schiff-based vanillin derivatives, showed strong MPro inhibition activity. This was due to their good alignment and common features to PDB-5RE6. Similarly, monolaurin and tetrodotoxin displayed some significant activity against SARS-CoV-2. From structure-based approach, vanillin derivatives (1) to (12) displayed some potent MPro inhibition against SARS-CoV-2. Favipiravir, chloroquine and hydroxychloroquine also showed some significant MPro inhibition.


Asunto(s)
Antivirales/farmacología , Betacoronavirus/efectos de los fármacos , Cloroquina/farmacología , Inhibidores de Cisteína Proteinasa/farmacología , Proteínas no Estructurales Virales/antagonistas & inhibidores , Amidas/química , Amidas/farmacología , Antivirales/química , Benzaldehídos/química , Cloroquina/química , Simulación por Computador , Cisteína Endopeptidasas , Inhibidores de Cisteína Proteinasa/química , Humanos , Hidroxicloroquina/química , Hidroxicloroquina/farmacología , Lauratos/química , Lauratos/farmacología , Pruebas de Sensibilidad Microbiana , Modelos Moleculares , Monoglicéridos/química , Monoglicéridos/farmacología , Pirazinas/química , Pirazinas/farmacología , Relación Estructura-Actividad , Tetrodotoxina/química , Tetrodotoxina/farmacología
9.
Sci Rep ; 10(1): 19125, 2020 11 05.
Artículo en Inglés | MEDLINE | ID: mdl-33154404

RESUMEN

The current outbreak of Covid-19 infection due to SARS-CoV-2, a virus from the coronavirus family, has become a major threat to human healthcare. The virus has already infected more than 44 M people and the number of deaths reported has reached more than 1.1 M which may be attributed to lack of medicine. The traditional drug discovery approach involves many years of rigorous research and development and demands for a huge investment which cannot be adopted for the ongoing pandemic infection. Rather we need a swift and cost-effective approach to inhibit and control the viral infection. With the help of computational screening approaches and by choosing appropriate chemical space, it is possible to identify lead drug-like compounds for Covid-19. In this study, we have used the Drugbank database to screen compounds against the most important viral targets namely 3C-like protease (3CLpro), papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp) and the spike (S) protein. These targets play a major role in the replication/transcription and host cell recognition, therefore, are vital for the viral reproduction and spread of infection. As the structure based computational screening approaches are more reliable, we used the crystal structures for 3C-like main protease and spike protein. For the remaining targets, we used the structures based on homology modeling. Further, we employed two scoring methods based on binding free energies implemented in AutoDock Vina and molecular mechanics-generalized Born surface area approach. Based on these results, we propose drug cocktails active against the three viral targets namely 3CLpro, PLpro and RdRp. Interestingly, one of the identified compounds in this study i.e. Baloxavir marboxil has been under clinical trial for the treatment of Covid-19 infection. In addition, we have identified a few compounds such as Phthalocyanine, Tadalafil, Lonafarnib, Nilotinib, Dihydroergotamine, R-428 which can bind to all three targets simultaneously and can serve as multi-targeting drugs. Our study also included calculation of binding energies for various compounds currently under drug trials. Among these compounds, it is found that Remdesivir binds to targets, 3CLpro and RdRp with high binding affinity. Moreover, Baricitinib and Umifenovir were found to have superior target-specific binding while Darunavir is found to be a potential multi-targeting drug. As far as we know this is the first study where the compounds from the Drugbank database are screened against four vital targets of SARS-CoV-2 and illustrates that the computational screening using a double scoring approach can yield potential drug-like compounds against Covid-19 infection.


Asunto(s)
Infecciones por Coronavirus/tratamiento farmacológico , Bases de Datos Farmacéuticas , Evaluación Preclínica de Medicamentos/métodos , Terapia Molecular Dirigida , Neumonía Viral/tratamiento farmacológico , Análisis Costo-Beneficio , Cisteína Endopeptidasas/química , Cisteína Endopeptidasas/metabolismo , Evaluación Preclínica de Medicamentos/economía , Humanos , Simulación del Acoplamiento Molecular , Pandemias , Conformación Proteica , Proteínas no Estructurales Virales/antagonistas & inhibidores , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/metabolismo
10.
Nat Commun ; 11(1): 5877, 2020 11 18.
Artículo en Inglés | MEDLINE | ID: mdl-33208735

RESUMEN

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (Mpro) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 Å resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 Å resolution and in its product bound state at 2.0 Å resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on Mpro inhibition.


Asunto(s)
Betacoronavirus/enzimología , Cisteína Endopeptidasas/química , Proteínas no Estructurales Virales/química , Betacoronavirus/química , Sitios de Unión , Dominio Catalítico , Cristalografía por Rayos X , Cisteína Endopeptidasas/genética , Cisteína Endopeptidasas/metabolismo , Dimerización , Humanos , Modelos Moleculares , Mutación , Inhibidores de Proteasas/metabolismo , Conformación Proteica , Especificidad por Sustrato , Proteínas no Estructurales Virales/antagonistas & inhibidores , Proteínas no Estructurales Virales/genética , Proteínas no Estructurales Virales/metabolismo
11.
Int J Mol Sci ; 21(21)2020 Oct 30.
Artículo en Inglés | MEDLINE | ID: mdl-33142980

RESUMEN

For the last decade, porcine epidemic diarrhea virus (PEDV) variant strains have caused severe damage to the global pig industry. Until now, no effective antivirals have been developed for the therapeutic treatment of PEDV infection. In the present study, we found that quercetin significantly suppressed PEDV infection at noncytotoxic concentrations. A molecular docking study indicated that quercetin might bind the active site and binding pocket of PEDV 3C-like protease (3CLpro). Surface plasmon resonance (SPR) analysis revealed that quercetin exhibited a binding affinity to PEDV 3CLpro. Based on the results of the fluorescence resonance energy transfer (FRET) assay, quercetin was proven to exert an inhibitory effect on PEDV 3CLpro. Since coronavirus 3CLpro is an important drug target and participates in the viral replication process, quercetin should be developed as a novel drug in the control of PEDV infection.


Asunto(s)
Antivirales/farmacología , Infecciones por Coronavirus/veterinaria , Virus de la Diarrea Epidémica Porcina/efectos de los fármacos , Quercetina/farmacología , Enfermedades de los Porcinos/tratamiento farmacológico , Proteínas no Estructurales Virales/antagonistas & inhibidores , Replicación Viral , Animales , Antivirales/uso terapéutico , Infecciones por Coronavirus/tratamiento farmacológico , Cisteína Endopeptidasas , Virus de la Diarrea Epidémica Porcina/fisiología , Quercetina/uso terapéutico , Porcinos
12.
Proc Natl Acad Sci U S A ; 117(44): 27381-27387, 2020 11 03.
Artículo en Inglés | MEDLINE | ID: mdl-33051297

RESUMEN

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global crisis. There is no therapeutic treatment specific for COVID-19. It is highly desirable to identify potential antiviral agents against SARS-CoV-2 from existing drugs available for other diseases and thus repurpose them for treatment of COVID-19. In general, a drug repurposing effort for treatment of a new disease, such as COVID-19, usually starts from a virtual screening of existing drugs, followed by experimental validation, but the actual hit rate is generally rather low with traditional computational methods. Here we report a virtual screening approach with accelerated free energy perturbation-based absolute binding free energy (FEP-ABFE) predictions and its use in identifying drugs targeting SARS-CoV-2 main protease (Mpro). The accurate FEP-ABFE predictions were based on the use of a restraint energy distribution (RED) function, making the practical FEP-ABFE-based virtual screening of the existing drug library possible. As a result, out of 25 drugs predicted, 15 were confirmed as potent inhibitors of SARS-CoV-2 Mpro The most potent one is dipyridamole (inhibitory constant Ki = 0.04 µM) which has shown promising therapeutic effects in subsequently conducted clinical studies for treatment of patients with COVID-19. Additionally, hydroxychloroquine (Ki = 0.36 µM) and chloroquine (Ki = 0.56 µM) were also found to potently inhibit SARS-CoV-2 Mpro We anticipate that the FEP-ABFE prediction-based virtual screening approach will be useful in many other drug repurposing or discovery efforts.


Asunto(s)
Antivirales/farmacología , Betacoronavirus/efectos de los fármacos , Reposicionamiento de Medicamentos , Inhibidores de Proteasas/farmacología , Proteínas no Estructurales Virales/antagonistas & inhibidores , Cloroquina/farmacología , Infecciones por Coronavirus/tratamiento farmacológico , Cisteína Endopeptidasas , Dipiridamol/farmacología , Humanos , Hidroxicloroquina/farmacología , Simulación del Acoplamiento Molecular , Estructura Molecular , Pandemias , Neumonía Viral/tratamiento farmacológico
13.
J Phys Chem Lett ; 11(21): 9144-9151, 2020 Nov 05.
Artículo en Inglés | MEDLINE | ID: mdl-33052685

RESUMEN

The raging COVID-19 pandemic caused by SARS-CoV-2 has infected tens of millions of people and killed several hundred thousand patients worldwide. Currently, there are no effective drugs or vaccines available for treating coronavirus infections. In this study, we have focused on the SARS-CoV-2 helicase (Nsp13), which is critical for viral replication and the most conserved nonstructural protein within the coronavirus family. Using homology modeling that couples published electron-density with molecular dynamics (MD)-based structural refinements, we generated structural models of the SARS-CoV-2 helicase in its apo- and ATP/RNA-bound conformations. We performed virtual screening of ∼970 000 chemical compounds against the ATP-binding site to identify potential inhibitors. Herein, we report docking hits of approved human drugs targeting the ATP-binding site. Importantly, two of our top drug hits have significant activity in inhibiting purified recombinant SARS-CoV-2 helicase, providing hope that these drugs can be potentially repurposed for the treatment of COVID-19.


Asunto(s)
Antivirales/química , Betacoronavirus/enzimología , ARN Helicasas/antagonistas & inhibidores , Proteínas no Estructurales Virales/antagonistas & inhibidores , Adenosina Trifosfato/química , Adenosina Trifosfato/metabolismo , Secuencia de Aminoácidos , Antivirales/metabolismo , Antivirales/uso terapéutico , Betacoronavirus/aislamiento & purificación , Sitios de Unión , Infecciones por Coronavirus/tratamiento farmacológico , Infecciones por Coronavirus/virología , Humanos , Interacciones Hidrofóbicas e Hidrofílicas , Simulación de Dinámica Molecular , Pandemias , Neumonía Viral/tratamiento farmacológico , Neumonía Viral/virología , Estructura Terciaria de Proteína , ARN Helicasas/química , ARN Helicasas/metabolismo , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/metabolismo
14.
J Chem Theory Comput ; 16(11): 7160-7172, 2020 Nov 10.
Artículo en Inglés | MEDLINE | ID: mdl-33090785

RESUMEN

In the context of drug-receptor binding affinity calculations using molecular dynamics techniques, we implemented a combination of Hamiltonian replica exchange (HREM) and a novel nonequilibrium alchemical methodology, called virtual double-system single-box, with increased accuracy, precision, and efficiency with respect to the standard nonequilibrium approaches. The method has been applied for the determination of absolute binding free energies of 16 newly designed noncovalent ligands of the main protease (3CLpro) of SARS-CoV-2. The core structures of 3CLpro ligands were previously identified using a multimodal structure-based ligand design in combination with docking techniques. The calculated binding free energies for four additional ligands with known activity (either for SARS-CoV or SARS-CoV-2 main protease) are also reported. The nature of binding in the 3CLpro active site and the involved residues besides the CYS-HYS catalytic dyad have been thoroughly characterized by enhanced sampling simulations of the bound state. We have identified several noncongeneric compounds with predicted low micromolar activity for 3CLpro inhibition, which may constitute possible lead compounds for the development of antiviral agents in Covid-19 treatment.


Asunto(s)
Betacoronavirus/enzimología , Cisteína Endopeptidasas/metabolismo , Proteínas no Estructurales Virales/metabolismo , Antivirales/farmacología , Antivirales/uso terapéutico , Infecciones por Coronavirus/tratamiento farmacológico , Infecciones por Coronavirus/virología , Humanos , Ligandos , Simulación del Acoplamiento Molecular , Pandemias , Neumonía Viral/tratamiento farmacológico , Neumonía Viral/virología , Inhibidores de Proteasas/farmacología , Inhibidores de Proteasas/uso terapéutico , Unión Proteica , Interfaz Usuario-Computador , Proteínas no Estructurales Virales/antagonistas & inhibidores
15.
Molecules ; 25(19)2020 Oct 06.
Artículo en Inglés | MEDLINE | ID: mdl-33036293

RESUMEN

A novel series of some hydrazones bearing thiazole moiety were generated via solvent-drop grinding of thiazole carbohydrazide 2 with various carbonyl compounds. Also, dehydrative-cyclocondensation of 2 with active methylene compounds or anhydrides gave the respective pyarzole or pyrazine derivatives. The structures of the newly synthesized compounds were established based on spectroscopic evidences and their alternative syntheses. Additionally, the anti-viral activity of all the products was tested against SARS-CoV-2 main protease (Mpro) using molecular docking combined with molecular dynamics simulation (MDS). The average binding affinities of the compounds 3a, 3b, and 3c (-8.1 ± 0.33 kcal/mol, -8.0 ± 0.35 kcal/mol, and -8.2 ± 0.21 kcal/mol, respectively) are better than that of the positive control Nelfinavir (-6.9 ± 0.51 kcal/mol). This shows the possibility of these three compounds to effectively bind to SARS-CoV-2 Mpro and hence, contradict the virus lifecycle.


Asunto(s)
Antivirales/síntesis química , Betacoronavirus/enzimología , Hidrazonas/síntesis química , Inhibidores de Proteasas/síntesis química , Pirazinas/síntesis química , Pirazoles/síntesis química , Proteínas no Estructurales Virales/antagonistas & inhibidores , Antivirales/farmacología , Betacoronavirus/química , Betacoronavirus/efectos de los fármacos , Sitios de Unión , Infecciones por Coronavirus/tratamiento farmacológico , Cisteína Endopeptidasas/química , Cisteína Endopeptidasas/metabolismo , Descubrimiento de Drogas , Humanos , Hidrazonas/farmacología , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Pandemias , Neumonía Viral/tratamiento farmacológico , Inhibidores de Proteasas/farmacología , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Pirazinas/farmacología , Pirazoles/farmacología , Termodinámica , Interfaz Usuario-Computador , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/metabolismo
16.
J Mol Graph Model ; 101: 107758, 2020 12.
Artículo en Inglés | MEDLINE | ID: mdl-33007575

RESUMEN

A novel strain of coronavirus, namely, SARS-CoV-2 identified in Wuhan city of China in December 2019, continues to spread at a rapid rate worldwide. There are no specific therapies available and investigations regarding the treatment of this disease are still lacking. In order to identify a novel potent inhibitor, we performed blind docking studies on the main virus protease Mpro with eight approved drugs belonging to four pharmacological classes such as: anti-malarial, anti-bacterial, anti-infective and anti-histamine. Among the eight studied compounds, Lymecycline and Mizolastine appear as potential inhibitors of this protease. When docked against Mpro crystal structure, these two compounds revealed a minimum binding energy of -8.87 and -8.71 kcal/mol with 168 and 256 binding modes detected in the binding substrate pocket, respectively. Further, to study the interaction mechanism and conformational dynamics of protein-ligand complexes, Molecular dynamic simulation and MM/PBSA binding free calculations were performed. Our results showed that both Lymecycline and Mizolastine bind in the active site. And exhibited good binding affinities towards target protein. Moreover, the ADMET analysis also indicated drug-likeness properties. Thus it is suggested that the identified compounds can inhibit Chymotrypsin-like protease (3CLpro) of SARS-CoV-2.


Asunto(s)
Cisteína Endopeptidasas/química , Inhibidores de Proteasas/química , Inhibidores de Proteasas/farmacología , Proteínas no Estructurales Virales/antagonistas & inhibidores , Proteínas no Estructurales Virales/química , Animales , Antibacterianos/química , Antivirales/química , Antivirales/farmacocinética , Antivirales/farmacología , Sitios de Unión , Simulación por Computador , Cisteína Endopeptidasas/metabolismo , Bases de Datos Farmacéuticas , Aprobación de Drogas , Reposicionamiento de Medicamentos , Antagonistas de los Receptores Histamínicos/química , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Inhibidores de Proteasas/farmacocinética , Proteínas no Estructurales Virales/metabolismo
17.
Comput Biol Med ; 126: 104046, 2020 11.
Artículo en Inglés | MEDLINE | ID: mdl-33065388

RESUMEN

Coronavirus Disease 2019 (COVID-19) is an infectious illness caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), originally identified in Wuhan, China (December 2019) and has since expanded into a pandemic. Here, we investigate metabolites present in several common spices as possible inhibitors of COVID-19. Specifically, 32 compounds isolated from 14 cooking seasonings were examined as inhibitors for SARS-CoV-2 main protease (Mpro), which is required for viral multiplication. Using a drug discovery approach to identify possible antiviral leads, in silico molecular docking studies were performed. Docking calculations revealed a high potency of salvianolic acid A and curcumin as Mpro inhibitors with binding energies of -9.7 and -9.2 kcal/mol, respectively. Binding mode analysis demonstrated the ability of salvianolic acid A and curcumin to form nine and six hydrogen bonds, respectively with amino acids proximal to Mpro's active site. Stabilities and binding affinities of the two identified natural spices were calculated over 40 ns molecular dynamics simulations and compared to an antiviral protease inhibitor (lopinavir). Molecular mechanics-generalized Born surface area energy calculations revealed greater salvianolic acid A affinity for the enzyme over curcumin and lopinavir with energies of -44.8, -34.2 and -34.8 kcal/mol, respectively. Using a STRING database, protein-protein interactions were identified for salvianolic acid A included the biochemical signaling genes ACE, MAPK14 and ESR1; and for curcumin, EGFR and TNF. This study establishes salvianolic acid A as an in silico natural product inhibitor against the SARS-CoV-2 main protease and provides a promising inhibitor lead for in vitro enzyme testing.


Asunto(s)
Betacoronavirus/enzimología , Ácidos Cafeicos/química , Infecciones por Coronavirus/tratamiento farmacológico , Curcumina/química , Cisteína Endopeptidasas , Descubrimiento de Drogas , Lactatos/química , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Neumonía Viral/tratamiento farmacológico , Inhibidores de Proteasas/química , Proteínas no Estructurales Virales , Ácidos Cafeicos/uso terapéutico , Infecciones por Coronavirus/enzimología , Curcumina/uso terapéutico , Cisteína Endopeptidasas/química , Humanos , Lactatos/uso terapéutico , Pandemias , Neumonía Viral/enzimología , Inhibidores de Proteasas/uso terapéutico , Termodinámica , Proteínas no Estructurales Virales/antagonistas & inhibidores , Proteínas no Estructurales Virales/química
18.
Molecules ; 25(20)2020 Oct 13.
Artículo en Inglés | MEDLINE | ID: mdl-33066278

RESUMEN

The global SARS-CoV-2 pandemic started late 2019 and currently continues unabated. The lag-time for developing vaccines means it is of paramount importance to be able to quickly develop and repurpose therapeutic drugs. Protein-based biosensors allow screening to be performed using routine molecular laboratory equipment without a need for expensive chemical reagents. Here we present a biosensor for the 3-chymotrypsin-like cysteine protease from SARS-CoV-2, comprising a FRET-capable pair of fluorescent proteins held in proximity by a protease cleavable linker. We demonstrate the utility of this biosensor for inhibitor discovery by screening 1280 compounds from the Library of Pharmaceutically Active Compounds collection. The screening identified 65 inhibitors, with the 20 most active exhibiting sub-micromolar inhibition of 3CLpro in follow-up EC50 assays. The top hits included several compounds not previously identified as 3CLpro inhibitors, in particular five members of a family of aporphine alkaloids that offer promise as new antiviral drug leads.


Asunto(s)
Betacoronavirus/efectos de los fármacos , Técnicas Biosensibles/métodos , Infecciones por Coronavirus/tratamiento farmacológico , Transferencia Resonante de Energía de Fluorescencia/métodos , Neumonía Viral/tratamiento farmacológico , Inhibidores de Proteasas/química , Inhibidores de Proteasas/farmacología , Proteínas no Estructurales Virales/antagonistas & inhibidores , Betacoronavirus/enzimología , Betacoronavirus/aislamiento & purificación , Infecciones por Coronavirus/virología , Cisteína Endopeptidasas , Ensayos Analíticos de Alto Rendimiento , Humanos , Pandemias , Neumonía Viral/virología
19.
Sci Adv ; 6(42)2020 10.
Artículo en Inglés | MEDLINE | ID: mdl-33067239

RESUMEN

Viral papain-like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library and performed comprehensive activity profiling of SARS-CoV-2 PLpro. On the scaffold of the best hits from positional scanning, we designed optimal fluorogenic substrates and irreversible inhibitors with a high degree of selectivity for SARS PLpro. We determined crystal structures of two of these inhibitors in complex with SARS-CoV-2 PLpro that reveals their inhibitory mechanisms and provides a molecular basis for the observed substrate specificity profiles. Last, we demonstrate that SARS-CoV-2 PLpro harbors deISGylating activity similar to SARSCoV-1 PLpro but its ability to hydrolyze K48-linked Ub chains is diminished, which our sequence and structure analysis provides a basis for. Together, this work has revealed the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repurposing.


Asunto(s)
Betacoronavirus/enzimología , Diseño de Fármacos , Inhibidores de Proteasas/química , Proteínas no Estructurales Virales/antagonistas & inhibidores , Secuencia de Aminoácidos , Betacoronavirus/aislamiento & purificación , Sitios de Unión , Dominio Catalítico , Infecciones por Coronavirus/patología , Infecciones por Coronavirus/virología , Cristalografía por Rayos X , Cisteína Endopeptidasas/genética , Cisteína Endopeptidasas/metabolismo , Humanos , Cinética , Simulación de Dinámica Molecular , Oligopéptidos/química , Oligopéptidos/metabolismo , Pandemias , Neumonía Viral/patología , Neumonía Viral/virología , Inhibidores de Proteasas/metabolismo , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/química , Proteínas Recombinantes/aislamiento & purificación , Especificidad por Sustrato , Ubiquitinas/metabolismo , Proteínas no Estructurales Virales/genética , Proteínas no Estructurales Virales/metabolismo
20.
Sci Rep ; 10(1): 16577, 2020 10 06.
Artículo en Inglés | MEDLINE | ID: mdl-33024223

RESUMEN

SARS-CoV-2 is responsible for COVID-19, resulting in the largest pandemic in over a hundred years. After examining the molecular structures and activities of hepatitis C viral inhibitors and comparing hepatitis C virus and coronavirus replication, we previously postulated that the FDA-approved hepatitis C drug EPCLUSA (Sofosbuvir/Velpatasvir) might inhibit SARS-CoV-2. We subsequently demonstrated that Sofosbuvir triphosphate is incorporated by the relatively low fidelity SARS-CoV and SARS-CoV-2 RNA-dependent RNA polymerases (RdRps), serving as an immediate polymerase reaction terminator, but not by a host-like high fidelity DNA polymerase. Other investigators have since demonstrated the ability of Sofosbuvir to inhibit SARS-CoV-2 replication in lung and brain cells; additionally, COVID-19 clinical trials with EPCLUSA and with Sofosbuvir plus Daclatasvir have been initiated in several countries. SARS-CoV-2 has an exonuclease-based proofreader to maintain the viral genome integrity. Any effective antiviral targeting the SARS-CoV-2 RdRp must display a certain level of resistance to this proofreading activity. We report here that Sofosbuvir terminated RNA resists removal by the exonuclease to a substantially higher extent than RNA terminated by Remdesivir, another drug being used as a COVID-19 therapeutic. These results offer a molecular basis supporting the current use of Sofosbuvir in combination with other drugs in COVID-19 clinical trials.


Asunto(s)
Adenosina Monofosfato/análogos & derivados , Alanina/análogos & derivados , Antivirales/farmacología , Betacoronavirus/efectos de los fármacos , Infecciones por Coronavirus/tratamiento farmacológico , Exonucleasas/metabolismo , Neumonía Viral/tratamiento farmacológico , Profármacos/farmacología , ARN Viral/efectos de los fármacos , Sofosbuvir/farmacología , Adenosina Monofosfato/química , Adenosina Monofosfato/farmacología , Adenosina Monofosfato/uso terapéutico , Alanina/química , Alanina/farmacología , Alanina/uso terapéutico , Antivirales/química , Antivirales/uso terapéutico , Betacoronavirus/enzimología , Infecciones por Coronavirus/virología , Descubrimiento de Drogas/métodos , Reposicionamiento de Medicamentos/métodos , Hepacivirus/efectos de los fármacos , Hepacivirus/enzimología , Hepatitis C/tratamiento farmacológico , Hepatitis C/virología , Humanos , Pandemias , Neumonía Viral/virología , Profármacos/uso terapéutico , ARN Viral/química , ARN Viral/metabolismo , /metabolismo , Sofosbuvir/química , Sofosbuvir/uso terapéutico , Proteínas no Estructurales Virales/antagonistas & inhibidores , Proteínas no Estructurales Virales/metabolismo , Replicación Viral/efectos de los fármacos
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