RESUMEN
VP30 and VP40 proteins of Ebola and Marburg viruses have been recognized as potential targets for antiviral drug development due to their essential roles in the viral lifecycle. Targeting these proteins could disrupt key stages of the viral replication process, inhibiting the viruses' ability to propagate and cause disease. The current study aims to perform molecular docking and virtual screening on deep-sea fungal metabolites targeting Marburg virus VP40 Dimer, matrix protein VP40 from Ebola virus Sudan, Ebola VP35 Interferon Inhibitory Domain, and VP35 from Marburg virus. The top ten compounds for each protein target were chosen using the glide score. All the compounds obtained indicate a positive binding interaction. Furthermore, AdmetSAR was utilized to investigate the pharmacokinetics of the inhibitors chosen. Gliotoxin was used as a ligand with Marburg virus VP40 Dimer, Austinol with matrix protein VP40 from Ebola virus Sudan, Ozazino-cyclo-(2,3-dihydroxyl-trp-tyr) with Ebola VP35 Interferon Inhibitory Domain, and Dehydroaustinol with VP35 from Marburg virus. MD modeling and MMPBSA studies were used to provide a better understanding of binding behaviors. Pre-clinical experiments can assist validate our in-silico studies and assess whether the molecule can be employed as an anti-viral drug.
Asunto(s)
Antivirales , Ebolavirus , Marburgvirus , Simulación del Acoplamiento Molecular , Ebolavirus/efectos de los fármacos , Ebolavirus/metabolismo , Marburgvirus/efectos de los fármacos , Marburgvirus/metabolismo , Antivirales/farmacología , Antivirales/química , Proteínas de la Matriz Viral/metabolismo , Proteínas de la Matriz Viral/antagonistas & inhibidores , Proteínas de la Matriz Viral/química , Fiebre Hemorrágica Ebola/tratamiento farmacológico , Fiebre Hemorrágica Ebola/virología , Humanos , Simulación por Computador , Simulación de Dinámica Molecular , Proteínas Reguladoras y Accesorias ViralesRESUMEN
The Ebola virus (EBOV) is a lethal pathogen causing hemorrhagic fever syndrome which remains a global health challenge. In the EBOV, two multifunctional proteins, VP35 and VP40, have significant roles in replication, virion assembly, and budding from the cell and have been identified as druggable targets. In this study, we employed in silico methods comprising molecular docking, molecular dynamic simulations, and pharmacological properties to identify prospective drugs for inhibiting VP35 and VP40 proteins from the myxobacterial bioactive natural product repertoire. Cystobactamid 934-2, Cystobactamid 919-1, and Cittilin A bound firmly to VP35. Meanwhile, 2-Hydroxysorangiadenosine, Enhypyrazinone B, and Sorangiadenosine showed strong binding to the matrix protein VP40. Molecular dynamic simulations revealed that, among these compounds, Cystobactamid 919-1 and 2-Hydroxysorangiadenosine had stable interactions with their respective targets. Similarly, molecular mechanics Poisson-Boltzmann surface area (MMPBSA) calculations indicated close-fitting receptor binding with VP35 or VP40. These two compounds also exhibited good pharmacological properties. In conclusion, we identified Cystobactamid 919-1 and 2-Hydroxysorangiadenosine as potential ligands for EBOV that target VP35 and VP40 proteins. These findings signify an essential step in vitro and in vivo to validate their potential for EBOV inhibition.
Asunto(s)
Antivirales , Productos Biológicos , Ebolavirus , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Ebolavirus/efectos de los fármacos , Productos Biológicos/farmacología , Productos Biológicos/química , Antivirales/farmacología , Antivirales/química , Myxococcales/química , Humanos , Proteínas Reguladoras y Accesorias Virales/antagonistas & inhibidores , Proteínas Reguladoras y Accesorias Virales/metabolismo , Proteínas Reguladoras y Accesorias Virales/química , Proteínas de la Matriz Viral/antagonistas & inhibidores , Proteínas de la Matriz Viral/metabolismo , Proteínas de la Matriz Viral/química , Proteínas de la NucleocápsideRESUMEN
SARS-CoV-2 as a positive-sense single-stranded RNA coronavirus caused the global outbreak of COVID-19. The main protease (Mpro) of the virus as the major enzyme processing viral polyproteins contributed to the replication and transcription of SARS-CoV-2 in host cells, and has been characterized as an attractive target in drug discovery. Herein, a set of 1,4-naphthoquinones with juglone skeleton were prepared and evaluated for the inhibitory efficacy against SARS-CoV-2 Mpro. More than half of the tested naphthoquinones could effectively inhibit the target enzyme with an inhibition rate of more than 90% at the concentration of 10 µM. In the structure-activity relationships (SARs) analysis, the characteristics of substituents and their position on juglone core scaffold were recognized as key ingredients for enzyme inhibitory activity. The most active compound, 2-acetyl-8-methoxy-1,4-naphthoquinone (15), which exhibited much higher potency in enzyme inhibitions than shikonin as the positive control, displayed an IC50 value of 72.07 ± 4.84 nM towards Mpro-mediated hydrolysis of the fluorescently labeled peptide. It fit well into the active site cavity of the enzyme by forming hydrogen bonds with adjacent amino acid residues in molecular docking studies. The results from in vitro antiviral activity evaluation demonstrated that the most potent Mpro inhibitor could significantly suppress the replication of SARS-CoV-2 in Vero E6 cells within the low micromolar concentrations, with its EC50 value of about 4.55 µM. It was non-toxic towards the host Vero E6 cells under tested concentrations. The present research work implied that juglone skeleton could be a primary template for the development of potent Mpro inhibitors.
Asunto(s)
Tratamiento Farmacológico de COVID-19 , Naftoquinonas/química , Inhibidores de Proteasas/uso terapéutico , SARS-CoV-2/enzimología , Proteínas de la Matriz Viral/antagonistas & inhibidores , Animales , Sitios de Unión , COVID-19/patología , COVID-19/virología , Dominio Catalítico , Supervivencia Celular/efectos de los fármacos , Chlorocebus aethiops , Diseño de Fármacos , Evaluación Preclínica de Medicamentos , Humanos , Enlace de Hidrógeno , Simulación del Acoplamiento Molecular , Naftoquinonas/metabolismo , Naftoquinonas/farmacología , Naftoquinonas/uso terapéutico , Inhibidores de Proteasas/química , Inhibidores de Proteasas/metabolismo , Inhibidores de Proteasas/farmacología , SARS-CoV-2/aislamiento & purificación , Relación Estructura-Actividad , Células Vero , Proteínas de la Matriz Viral/metabolismoRESUMEN
Seasonal influenza A virus (IAV) infections are among the most important global health problems. FDA-approved antiviral therapies against IAV include neuraminidase inhibitors, M2 inhibitors, and polymerase inhibitor baloxavir. Resistance against adamantanes (amantadine and rimantadine) is widespread as virtually all IAV strains currently circulating in the human population are resistant to adamantanes through the acquisition of the S31N mutation. The neuraminidase inhibitor-resistant strains also contain the M2-S31N mutant, suggesting M2-S31N is a high-profile antiviral drug target. Here we report the development of a novel deuterium-containing M2-S31N inhibitor UAWJ280. UAWJ280 had broad-spectrum antiviral activity against both oseltamivir sensitive and -resistant influenza A strains and had a synergistic antiviral effect in combination with oseltamivir in cell culture. In vivo pharmacokinetic (PK) studies demonstrated that UAWJ280 had favourable PK properties. The in vivo mouse model study showed that UAWJ280 was effective alone or in combination with oseltamivir in improving clinical signs and survival after lethal challenge with an oseltamivir sensitive IAV H1N1 strain. Furthermore, UAWJ280 was also able to ameliorate clinical signs and increase survival when mice were challenged with an oseltamivir-resistant IAV H1N1 strain. In conclusion, we show for the first time that the M2-S31N channel blocker UAWJ280 has in vivo antiviral efficacy in mice that are infected with either oseltamivir sensitive or -resistant IAVs, and it has a synergistic antiviral effect with oseltamivir.
Asunto(s)
Anticuerpos Antivirales/sangre , Antivirales/farmacología , Antivirales/farmacocinética , Deuterio/química , Farmacorresistencia Viral , Virus de la Influenza A/efectos de los fármacos , Oseltamivir/farmacología , Proteínas de la Matriz Viral/antagonistas & inhibidores , Proteínas Viroporinas/antagonistas & inhibidores , Animales , Deuterio/farmacocinética , Deuterio/farmacología , Perros , Humanos , Virus de la Influenza A/clasificación , Células de Riñón Canino Madin Darby , Masculino , Ratones Endogámicos BALB C , Mutación , Infecciones por Orthomyxoviridae/tratamiento farmacológico , Infecciones por Orthomyxoviridae/virología , Relación Estructura-ActividadRESUMEN
Widespread infection due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) has led to a global pandemic. Currently, various approaches are being taken up to develop vaccines and therapeutics to treat SARS-CoV2 infection. Consequently, the S protein has become an important target protein for developing vaccines and therapeutics against SARS-CoV2. However, the highly infective nature of SARS-CoV2 restricts experimentation with the virus to highly secure BSL3 facilities. The availability of fusion-enabled, nonreplicating, and nonbiohazardous mimics of SARS-CoV2 virus fusion, containing the viral S or S and M protein in their native conformation on mammalian cells, can serve as a useful substitute for studying viral fusion for testing various inhibitors of viral fusion. This would avoid the use of the BSL3 facility for fusion studies required to develop therapeutics. In the present study, we have developed SARS-CoV2 virus fusion mimics (SCFMs) using mammalian cells transfected with constructs coding for S or S and M protein. The fusogenic property of the mimic(s) and their interaction with the functional human ACE2 receptors was confirmed experimentally. We have also shown that such mimics can easily be used in an inhibition assay. These mimic(s) can be easily prepared on a large scale, and such SCFMs can serve as an invaluable resource for viral fusion inhibition assays and in vitro screening of antiviral agents, which can be shared/handled between labs/facilities without worrying about any biohazard while working under routine laboratory conditions, avoiding the use of BSL3 laboratory.Abbreviations :SCFM: SARS-CoV2 Virus Fusion Mimic; ACE2: Angiotensin-Converting Enzyme 2; hACE2: Human Angiotensin-Converting enzyme 2; MEF: Mouse Embryonic Fibroblasts; HBSS: Hanks Balanced Salt Solution; FBS: Fetal Bovine Serum.
Asunto(s)
Anticuerpos Neutralizantes/farmacología , Contención de Riesgos Biológicos/métodos , SARS-CoV-2/genética , Glicoproteína de la Espiga del Coronavirus/antagonistas & inhibidores , Proteínas de la Matriz Viral/antagonistas & inhibidores , Internalización del Virus/efectos de los fármacos , Enzima Convertidora de Angiotensina 2/genética , Enzima Convertidora de Angiotensina 2/metabolismo , Animales , Chlorocebus aethiops , Embrión de Mamíferos , Fibroblastos/efectos de los fármacos , Fibroblastos/virología , Expresión Génica , Genes Reporteros , Proteínas Fluorescentes Verdes/genética , Proteínas Fluorescentes Verdes/metabolismo , Células HEK293 , Humanos , Proteínas Luminiscentes/genética , Proteínas Luminiscentes/metabolismo , Células MCF-7 , Ratones , Imitación Molecular , Plásmidos/química , Plásmidos/metabolismo , Cultivo Primario de Células , Unión Proteica , Receptores Virales/genética , Receptores Virales/metabolismo , SARS-CoV-2/efectos de los fármacos , SARS-CoV-2/metabolismo , Glicoproteína de la Espiga del Coronavirus/genética , Glicoproteína de la Espiga del Coronavirus/metabolismo , Transfección , Células Vero , Proteínas de la Matriz Viral/genética , Proteínas de la Matriz Viral/metabolismoRESUMEN
In December 2020, the U.K. authorities reported to the World Health Organization (WHO) that a new COVID-19 variant, considered to be a variant under investigation from December 2020 (VUI-202012/01), was identified through viral genomic sequencing. Although several other mutants were previously reported, VUI-202012/01 proved to be about 70% more transmissible. Hence, the usefulness and effectiveness of the newly U.S. Food and Drug Administration (FDA)-approved COVID-19 vaccines against these new variants are doubtfully questioned. As a result of these unexpected mutants from COVID-19 and due to lack of time, much research interest is directed toward assessing secondary metabolites as potential candidates for developing lead pharmaceuticals. In this study, a marine-derived fungus Aspergillus terreus was investigated, affording two butenolide derivatives, butyrolactones I (1) and III (2), a meroterpenoid, terretonin (3), and 4-hydroxy-3-(3-methylbut-2-enyl)benzaldehyde (4). Chemical structures were unambiguously determined based on mass spectrometry and extensive 1D/2D NMR analyses experiments. Compounds (1-4) were assessed for their in vitro anti-inflammatory, antiallergic, and in silico COVID-19 main protease (Mpro) and elastase inhibitory activities. Among the tested compounds, only 1 revealed significant activities comparable to or even more potent than respective standard drugs, which makes butyrolactone I (1) a potential lead entity for developing a new remedy to treat and/or control the currently devastating and deadly effects of COVID-19 pandemic and elastase-related inflammatory complications.
Asunto(s)
4-Butirolactona/análogos & derivados , Antialérgicos/química , Antiinflamatorios/química , Aspergillus/química , SARS-CoV-2/enzimología , Proteínas de la Matriz Viral/antagonistas & inhibidores , 4-Butirolactona/química , 4-Butirolactona/aislamiento & purificación , 4-Butirolactona/metabolismo , Antialérgicos/metabolismo , Antiinflamatorios/metabolismo , Aspergillus/crecimiento & desarrollo , Aspergillus/metabolismo , Sitios de Unión , COVID-19/patología , COVID-19/virología , Dominio Catalítico , Humanos , Elastasa de Leucocito/antagonistas & inhibidores , Elastasa de Leucocito/metabolismo , Espectroscopía de Resonancia Magnética , Conformación Molecular , Simulación del Acoplamiento Molecular , Neutrófilos/enzimología , SARS-CoV-2/aislamiento & purificación , Agua de Mar/microbiología , Proteínas de la Matriz Viral/metabolismoRESUMEN
COVID-19 is a pandemic respiratory disease caused by the SARS-CoV-2 coronavirus. The worldwide epidemiologic data showed higher mortality in males compared to females, suggesting a hypothesis about the protective effect of estrogens against severe disease progression with the ultimate end being patient's death. This article summarizes the current knowledge regarding the potential effect of estrogens and other modulators of estrogen receptors on COVID-19. While estrogen receptor activation shows complex effects on the patient's organism, such as an influence on the cardiovascular/pulmonary/immune system which includes lower production of cytokines responsible for the cytokine storm, the receptor-independent effects directly inhibits viral replication. Furthermore, it inhibits the interaction of IL-6 with its receptor complex. Interestingly, in addition to natural hormones, phytestrogens and even synthetic molecules are able to interact with the estrogen receptor and exhibit some anti-COVID-19 activity. From this point of view, estrogen receptor modulators have the potential to be included in the anti-COVID-19 therapeutic arsenal.
Asunto(s)
COVID-19/patología , Moduladores de los Receptores de Estrógeno/farmacología , SARS-CoV-2/efectos de los fármacos , Neoplasias de la Mama/complicaciones , Neoplasias de la Mama/tratamiento farmacológico , Neoplasias de la Mama/patología , COVID-19/complicaciones , COVID-19/virología , Moduladores de los Receptores de Estrógeno/metabolismo , Moduladores de los Receptores de Estrógeno/uso terapéutico , Femenino , Humanos , Receptores de Estrógenos/química , Receptores de Estrógenos/metabolismo , SARS-CoV-2/aislamiento & purificación , SARS-CoV-2/fisiología , Proteínas de la Matriz Viral/antagonistas & inhibidores , Proteínas de la Matriz Viral/metabolismo , Internalización del Virus/efectos de los fármacos , Replicación Viral/efectos de los fármacosRESUMEN
The development of new antiviral drugs against SARS-CoV-2 is a valuable long-term strategy to protect the global population from the COVID-19 pandemic complementary to the vaccination. Considering this, the viral main protease (Mpro) is among the most promising molecular targets in light of its importance during the viral replication cycle. The natural flavonoid quercetin 1 has been recently reported to be a potent Mpro inhibitor in vitro, and we explored the effect produced by the introduction of organoselenium functionalities in this scaffold. In particular, we report here a new synthetic method to prepare previously inaccessible C-8 seleno-quercetin derivatives. By screening a small library of flavonols and flavone derivatives, we observed that some compounds inhibit the protease activity in vitro. For the first time, we demonstrate that quercetin (1) and 8-(p-tolylselenyl)quercetin (2d) block SARS-CoV-2 replication in infected cells at non-toxic concentrations, with an IC50 of 192 µM and 8 µM, respectively. Based on docking experiments driven by experimental evidence, we propose a non-covalent mechanism for Mpro inhibition in which a hydrogen bond between the selenium atom and Gln189 residue in the catalytic pocket could explain the higher Mpro activity of 2d and, as a result, its better antiviral profile.
Asunto(s)
Antivirales/química , Quercetina/química , SARS-CoV-2/metabolismo , Selenio/química , Proteínas de la Matriz Viral/antagonistas & inhibidores , Animales , Antivirales/metabolismo , Antivirales/farmacología , Sitios de Unión , COVID-19/patología , COVID-19/virología , Dominio Catalítico , Chlorocebus aethiops , Humanos , Enlace de Hidrógeno , Simulación del Acoplamiento Molecular , Inhibidores de Proteasas/química , Inhibidores de Proteasas/metabolismo , Inhibidores de Proteasas/farmacología , Quercetina/metabolismo , Quercetina/farmacología , SARS-CoV-2/aislamiento & purificación , Selenio/metabolismo , Células Vero , Proteínas de la Matriz Viral/metabolismo , Replicación Viral/efectos de los fármacosRESUMEN
Designing covalent inhibitors is increasingly important, although it remains challenging. Here, we present covalentizer, a computational pipeline for identifying irreversible inhibitors based on structures of targets with non-covalent binders. Through covalent docking of tailored focused libraries, we identify candidates that can bind covalently to a nearby cysteine while preserving the interactions of the original molecule. We found â¼11,000 cysteines proximal to a ligand across 8,386 complexes in the PDB. Of these, the protocol identified 1,553 structures with covalent predictions. In a prospective evaluation, five out of nine predicted covalent kinase inhibitors showed half-maximal inhibitory concentration (IC50) values between 155 nM and 4.5 µM. Application against an existing SARS-CoV Mpro reversible inhibitor led to an acrylamide inhibitor series with low micromolar IC50 values against SARS-CoV-2 Mpro. The docking was validated by 12 co-crystal structures. Together these examples hint at the vast number of covalent inhibitors accessible through our protocol.
Asunto(s)
Diseño de Fármacos , Inhibidores de Proteínas Quinasas/química , SARS-CoV-2/enzimología , Proteínas de la Matriz Viral/antagonistas & inhibidores , Acrilamida/química , Acrilamida/metabolismo , Sitios de Unión , COVID-19/patología , COVID-19/virología , Dominio Catalítico , Biología Computacional/métodos , Bases de Datos de Proteínas , Humanos , Concentración 50 Inhibidora , Simulación del Acoplamiento Molecular , Inhibidores de Proteínas Quinasas/metabolismo , SARS-CoV-2/aislamiento & purificación , Proteínas de la Matriz Viral/metabolismoRESUMEN
The COVID-19 pandemic caused by the SARS-CoV-2 has mobilized scientific attention in search of a treatment. The cysteine-proteases, main protease (Mpro) and papain-like protease (PLpro) are important targets for antiviral drugs. In this work, we simulate the interactions between the Mpro and PLpro with Ebselen, its metabolites and derivatives with the aim of finding molecules that can potentially inhibit these enzymes. The docking data demonstrate that there are two main interactions between the thiol (-SH) group of Cys (from the protease active sites) and the electrophilic centers of the organoselenium molecules, i. e. the interaction with the carbonyl group (O=C SH) and the interaction with the Se moiety (Se SH). Both interactions may lead to an adduct formation and enzyme inhibition. Density Functional Theory (DFT) calculations with Ebselen indicate that the energetics of the thiol nucleophilic attack is more favorable on Se than on the carbonyl group, which is in accordance with experimental data (Jin etâ al. Nature, 2020, 582, 289-293). Therefore, organoselenium molecules should be further explored as inhibitors of the SARS-CoV-2 proteases. Furthermore, we suggest that some metabolites of Ebselen (e. g. Ebselen diselenide and methylebselenoxide) and derivatives ethaselen and ebsulfur should be tested inâ vitro as inhibitors of virus replication and its proteases.
Asunto(s)
Azoles/farmacología , Tratamiento Farmacológico de COVID-19 , Proteasas Similares a la Papaína de Coronavirus/metabolismo , Compuestos de Organoselenio/farmacología , Inhibidores de Proteasas/farmacología , SARS-CoV-2/efectos de los fármacos , Proteínas de la Matriz Viral/metabolismo , Antivirales/química , Antivirales/metabolismo , Antivirales/farmacología , Azoles/química , Azoles/metabolismo , COVID-19/metabolismo , Dominio Catalítico/efectos de los fármacos , Proteasas Similares a la Papaína de Coronavirus/antagonistas & inhibidores , Descubrimiento de Drogas , Humanos , Isoindoles , Simulación del Acoplamiento Molecular , Compuestos de Organoselenio/química , Compuestos de Organoselenio/metabolismo , Inhibidores de Proteasas/química , Inhibidores de Proteasas/metabolismo , Proteínas de la Matriz Viral/antagonistas & inhibidoresRESUMEN
Nowadays, over 200 countries face a wellbeing emergency because of epidemiological disease COVID-19 caused by the SARS-CoV-2 virus. It will cause a very high effect on the world's economy and the worldwide health sector. The present work is an investigation of the newly synthesized 4-benzyl-1-(2,4,6-trimethyl-benzyl)-piperidine (M1BZP) molecule's inhibitory potential against important protein targets of SARS-CoV-2 using computational approaches. M1BZP crystallizes in monoclinic type with P1211 space group. For the title compound M1BZP, spectroscopic characterization like 1H NMR, 13C NMR, FTIR, were carried out. The geometry of the compound had been optimized by the DFT method and its results were compared with the X-ray diffraction data. The calculated energies for the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO) showed the stability and reactivity of the title compound. Intermolecular interactions in the crystal network were determined using Hirshfeld surface analyses. The molecular electrostatic potential (MEP) picture was drawn using the same level of theory to visualize the chemical reactivity and charge distribution on the molecule. Molecular docking study performed for the synthesized compound revealed an efficient interaction with the COVID-19 protease and resulted in good activities. We hope the present study would help workers in the field to develop potential vaccines and therapeutics against the novel coronavirus. Virtual ADME studies were carried out as well and a relationship between biological, electronic, and physicochemical qualifications of the target compound was determined. Toxicity prediction by computational technique for the title compound was also carried out.
Asunto(s)
Antivirales/metabolismo , Piperidinas/química , SARS-CoV-2/metabolismo , Glicoproteína de la Espiga del Coronavirus/antagonistas & inhibidores , Adenosina Monofosfato/análogos & derivados , Adenosina Monofosfato/química , Adenosina Monofosfato/metabolismo , Alanina/análogos & derivados , Alanina/química , Alanina/metabolismo , Antivirales/síntesis química , Antivirales/química , Sitios de Unión , COVID-19/patología , COVID-19/virología , Cristalografía por Rayos X , Teoría Funcional de la Densidad , Semivida , Humanos , Conformación Molecular , Simulación del Acoplamiento Molecular , Piperidinas/síntesis química , Piperidinas/metabolismo , SARS-CoV-2/aislamiento & purificación , Glicoproteína de la Espiga del Coronavirus/metabolismo , Proteínas de la Matriz Viral/antagonistas & inhibidores , Proteínas de la Matriz Viral/metabolismoRESUMEN
The emerging COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised a global catastrophe. To date, there is no specific antiviral drug available to combat this virus, except the vaccine. In this study, the main protease (Mpro) required for SARS-CoV-2 viral replication was expressed and purified. Thirty-six compounds were tested as inhibitors of SARS-CoV-2 Mpro by fluorescence resonance energy transfer (FRET) technique. The half-maximal inhibitory concentration (IC50) values of Ebselen and Ebsulfur analogs were obtained to be in the range of 0.074-0.91 µM. Notably, the molecules containing furane substituent displayed higher inhibition against Mpro, followed by Ebselen 1i (IC50 = 0.074 µM) and Ebsulfur 2k (IC50 = 0.11 µM). The action mechanism of 1i and 2k were characterized by enzyme kinetics, pre-incubation and jump dilution assays, as well as fluorescent labeling experiments, which suggested that both compounds covalently and irreversibly bind to Mpro, while molecular docking suggested that 2k formed an SS bond with the Cys145 at the enzymatic active site. This study provides two very potent scaffolds Ebsulfur and Ebselen for the development of covalent inhibitors of Mpro to combat COVID-19.
Asunto(s)
Antivirales/metabolismo , Azoles/metabolismo , Compuestos de Organoselenio/metabolismo , SARS-CoV-2/metabolismo , Compuestos de Azufre/metabolismo , Proteínas de la Matriz Viral/metabolismo , Antivirales/química , Antivirales/uso terapéutico , Azoles/química , Azoles/uso terapéutico , Sitios de Unión , COVID-19/patología , COVID-19/virología , Dominio Catalítico , Transferencia Resonante de Energía de Fluorescencia , Humanos , Concentración 50 Inhibidora , Isoindoles , Cinética , Simulación del Acoplamiento Molecular , Compuestos de Organoselenio/química , Compuestos de Organoselenio/uso terapéutico , SARS-CoV-2/aislamiento & purificación , Relación Estructura-Actividad , Compuestos de Azufre/química , Compuestos de Azufre/uso terapéutico , Proteínas de la Matriz Viral/antagonistas & inhibidores , Proteínas de la Matriz Viral/genética , Tratamiento Farmacológico de COVID-19RESUMEN
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for the COVID-19 pandemic, which generated more than 1.82 million deaths in 2020 alone, in addition to 83.8 million infections. Currently, there is no antiviral medication to treat COVID-19. In the search for drug leads, marine-derived metabolites are reported here as prospective SARS-CoV-2 inhibitors. Two hundred and twenty-seven terpene natural products isolated from the biodiverse Red-Sea ecosystem were screened for inhibitor activity against the SARS-CoV-2 main protease (Mpro) using molecular docking and molecular dynamics (MD) simulations combined with molecular mechanics/generalized Born surface area binding energy calculations. On the basis of in silico analyses, six terpenes demonstrated high potency as Mpro inhibitors with ΔGbinding ≤ -40.0 kcal/mol. The stability and binding affinity of the most potent metabolite, erylosides B, were compared to the human immunodeficiency virus protease inhibitor, lopinavir. Erylosides B showed greater binding affinity towards SARS-CoV-2 Mpro than lopinavir over 100 ns with ΔGbinding values of -51.9 vs. -33.6 kcal/mol, respectively. Protein-protein interactions indicate that erylosides B biochemical signaling shares gene components that mediate severe acute respiratory syndrome diseases, including the cytokine- and immune-signaling components BCL2L1, IL2, and PRKC. Pathway enrichment analysis and Boolean network modeling were performed towards a deep dissection and mining of the erylosides B target-function interactions. The current study identifies erylosides B as a promising anti-COVID-19 drug lead that warrants further in vitro and in vivo testing.
Asunto(s)
Invertebrados/química , SARS-CoV-2/metabolismo , Terpenos/química , Proteínas de la Matriz Viral/antagonistas & inhibidores , Animales , Sitios de Unión , COVID-19/virología , Humanos , Enlace de Hidrógeno , Invertebrados/metabolismo , Lopinavir/química , Lopinavir/metabolismo , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Inhibidores de Proteasas/química , Inhibidores de Proteasas/aislamiento & purificación , Inhibidores de Proteasas/uso terapéutico , Unión Proteica , SARS-CoV-2/aislamiento & purificación , Terpenos/aislamiento & purificación , Terpenos/metabolismo , Terpenos/uso terapéutico , Termodinámica , Proteínas de la Matriz Viral/metabolismo , Tratamiento Farmacológico de COVID-19RESUMEN
The catalytic reaction in SARS-CoV-2 main protease is activated by a proton transfer (PT) from Cys145 to His41. The same PT is likely also required for the covalent binding of some inhibitors. Here we use a multiscale computational approach to investigate the PT thermodynamics in the apo enzyme and in complex with two potent inhibitors, N3 and the α-ketoamide 13b. We show that with the inhibitors the free energy cost to reach the charge-separated state of the active-site dyad is lower, with N3 inducing the most significant reduction. We also show that a few key sites (including specific water molecules) significantly enhance or reduce the thermodynamic feasibility of the PT reaction, with selective desolvation of the active site playing a crucial role. The approach presented is a cost-effective procedure to identify the enzyme regions that control the activation of the catalytic reaction and is thus also useful to guide the design of inhibitors.
Asunto(s)
Diseño de Fármacos , Inhibidores de Proteasas/química , SARS-CoV-2/enzimología , Proteínas de la Matriz Viral/antagonistas & inhibidores , Antivirales/química , Antivirales/metabolismo , Biocatálisis , COVID-19/patología , COVID-19/virología , Dominio Catalítico , Humanos , Simulación de Dinámica Molecular , Inhibidores de Proteasas/metabolismo , Protones , Teoría Cuántica , SARS-CoV-2/aislamiento & purificación , Termodinámica , Proteínas de la Matriz Viral/metabolismoRESUMEN
The 2019 novel coronavirus pandemic caused by SARS-CoV-2 remains a serious health threat to humans and there is an urgent need to develop therapeutics against this deadly virus. Recent scientific evidences have suggested that the main protease (Mpro) enzyme in SARS-CoV-2 can be an ideal drug target due to its crucial role in the viral replication and transcription processes. Therefore, there are ongoing research efforts to identify drug candidates against SARS-CoV-2 Mpro that resulted in hundreds of X-ray crystal structures of ligand-bound Mpro complexes in the Protein Data Bank (PDB) describing the interactions of different fragment chemotypes within different sites of the Mpro. In this work, we performed rigorous molecular dynamics (MD) simulation of 62 reversible ligand-Mpro complexes in the PDB to gain mechanistic insights about their interactions at the atomic level. Using a total of over 3 µs long MD trajectories, we characterized different pockets in the apo Mpro structure, and analyzed the dynamic interactions and binding affinity of ligands within those pockets. Our results identified the key residues that stabilize the ligands in the catalytic sites and other pockets of Mpro. Our analyses unraveled the role of a lateral pocket in the catalytic site in Mpro that is critical for enhancing the ligand binding to the enzyme. We also highlighted the important contribution from HIS163 in the lateral pocket towards ligand binding and affinity against Mpro through computational mutation analyses. Further, we revealed the effects of explicit water molecules and Mpro dimerization in the ligand association with the target. Thus, comprehensive molecular-level insights gained from this work can be useful to identify or design potent small molecule inhibitors against SARS-CoV-2 Mpro.
Asunto(s)
Simulación de Dinámica Molecular , Inhibidores de Proteasas/química , SARS-CoV-2/metabolismo , Proteínas de la Matriz Viral/antagonistas & inhibidores , Sitios de Unión , COVID-19/patología , COVID-19/virología , Dominio Catalítico , Bases de Datos de Proteínas , Humanos , Ligandos , Mutagénesis Sitio-Dirigida , Análisis de Componente Principal , Inhibidores de Proteasas/metabolismo , SARS-CoV-2/aislamiento & purificación , Termodinámica , Proteínas de la Matriz Viral/metabolismoRESUMEN
COVID-19, the disease caused by the newly discovered coronavirus-SARS-CoV-2, has created a global health, social, and economic crisis. As of mid-January 2021, there are over 90 million confirmed cases and more than 2 million reported deaths due to COVID-19. Currently, there are very limited therapeutics for the treatment or prevention of COVID-19. For this reason, it is important to find drug targets that will lead to the development of safe and effective therapeutics against the disease. The main protease (Mpro) of the virus is an attractive target for the development of effective antiviral therapeutics because it is required for proteolytic cleavage of viral polyproteins. Furthermore, the Mpro has no human homologues, so drugs designed to bind to this target directly have less risk for off-target effects. Recently, several high-resolution crystallographic structures of the Mpro in complex with inhibitors have been determined-to guide drug development and to spur efforts in structure-based drug design. One of the primary objectives of modern structure-based drug design is the accurate prediction of receptor-ligand binding affinities for rational drug design and discovery. Here, we perform rigorous alchemical absolute binding free energy calculations and QM/MM calculations to give insight into the total binding energy of two recently crystallized inhibitors of SARS-CoV-2 Mpro, namely, N3 and α-ketoamide 13b. The total binding energy consists of both covalent and non-covalent binding components since both compounds are covalent inhibitors of the Mpro. Our results indicate that the covalent and non-covalent binding free energy contributions of both inhibitors to the Mpro target differ significantly. The N3 inhibitor has more favourable non-covalent interactions, particularly hydrogen bonding, in the binding site of the Mpro than the α-ketoamide inhibitor. Also, the Gibbs energy of reaction for the Mpro-N3 covalent adduct is greater than the Gibbs reaction energy for the Mpro-α-ketoamide covalent adduct. These differences in the covalent and non-covalent binding free energy contributions for both inhibitors could be a plausible explanation for their in vitro differences in antiviral activity. Our findings are consistent with the reversible and irreversible character of both inhibitors as reported by experiment and highlight the importance of both covalent and non-covalent binding free energy contributions to the absolute binding affinity of a covalent inhibitor towards its target. This information could prove useful in the rational design, discovery, and evaluation of potent SARS-CoV-2 Mpro inhibitors for targeted antiviral therapy.
Asunto(s)
Peptidomiméticos/química , Inhibidores de Proteasas/química , SARS-CoV-2/enzimología , Proteínas de la Matriz Viral/antagonistas & inhibidores , Amidas/química , Amidas/metabolismo , Sitios de Unión , COVID-19/patología , COVID-19/virología , Dominio Catalítico , Diseño de Fármacos , Humanos , Concentración de Iones de Hidrógeno , Cinética , Ligandos , Simulación de Dinámica Molecular , Peptidomiméticos/metabolismo , Inhibidores de Proteasas/metabolismo , Teoría Cuántica , SARS-CoV-2/aislamiento & purificación , Termodinámica , Proteínas de la Matriz Viral/metabolismoRESUMEN
Considering the urgent need for novel therapeutics in ongoing COVID-19 pandemic, drug repurposing approach might offer rapid solutions comparing to de novo drug design. In this study, we designed an integrative in silico drug repurposing approach for rapid selection of potential candidates against SARS-CoV-2 Main Protease (Mpro ). To screen FDA-approved drugs, we implemented structure-based molecular modelling techniques, physiologically-based pharmacokinetic (PBPK) modelling of drugs disposition and data mining analysis of drug-gene-COVID-19 association. Through presented approach, we selected the most promising FDA approved drugs for further COVID-19 drug development campaigns and analysed them in context of available experimental data. To the best of our knowledge, this is unique in silico study which integrates structure-based molecular modeling of Mpro inhibitors with predictions of their tissue disposition, drug-gene-COVID-19 associations and prediction of pleiotropic effects of selected candidates.
Asunto(s)
Antivirales/farmacología , Tratamiento Farmacológico de COVID-19 , Reposicionamiento de Medicamentos/métodos , Inhibidores de Proteasas/farmacología , SARS-CoV-2/enzimología , Proteínas de la Matriz Viral/antagonistas & inhibidores , Antivirales/química , Simulación por Computador , Diseño de Fármacos , Humanos , Simulación del Acoplamiento Molecular , Inhibidores de Proteasas/química , SARS-CoV-2/efectos de los fármacos , Proteínas de la Matriz Viral/metabolismoRESUMEN
As a member of the Orthomyxoviridae family of viruses, influenza viruses (IVs) are known causative agents of respiratory infection in vertebrates. They remain a major global threat responsible for the most virulent diseases and global pandemics in humans. The virulence of IVs and the consequential high morbidity and mortality of IV infections are primarily attributed to the high mutation rates in the IVs' genome coupled with the numerous genomic segments, which give rise to antiviral resistant and vaccine evading strains. Current therapeutic options include vaccines and small molecule inhibitors, which therapeutically target various catalytic processes in IVs. However, the periodic emergence of new IV strains necessitates the continuous development of novel anti-influenza therapeutic options. The crux of this review highlights the recent studies on the biology of influenza viruses, focusing on the structure, function, and mechanism of action of the M2 channel and neuraminidase as therapeutic targets. We further provide an update on the development of new M2 channel and neuraminidase inhibitors as an alternative to existing anti-influenza therapy. We conclude by highlighting therapeutic strategies that could be explored further towards the design of novel anti-influenza inhibitors with the ability to inhibit resistant strains.
Asunto(s)
Gripe Humana/tratamiento farmacológico , Orthomyxoviridae/efectos de los fármacos , Infecciones del Sistema Respiratorio/tratamiento farmacológico , Proteínas de la Matriz Viral/genética , Farmacorresistencia Viral/efectos de los fármacos , Inhibidores Enzimáticos/uso terapéutico , Humanos , Gripe Humana/virología , Neuraminidasa/antagonistas & inhibidores , Neuraminidasa/genética , Orthomyxoviridae/genética , Infecciones del Sistema Respiratorio/patología , Infecciones del Sistema Respiratorio/virología , Proteínas de la Matriz Viral/antagonistas & inhibidoresRESUMEN
Protein-protein interactions (PPIs) play a critical role in living cells and represent promising targets for the drug discovery and life sciences communities. However, lateral transmembrane PPIs are difficult targets for small-molecule inhibitor development given less structural information is known and fewer ligand discovery methods have been explored compared to soluble proteins. In this study, the interactions of the transmembrane domain 5 (TMD-5) of latent membrane protein 1 (LMP-1) of Epstein-Barr virus (EBV) were disrupted by pentamidine derivatives to curb the committed step of EBV infection. A pentamidine derivative 2 with a 7-atom di-amide linker had the best activity whilst switching the amide regiochemistry in the linker influenced membrane permeability and abolished anti TMD-5 activity. Molecular dynamics simulations were performed to understand the interaction between pentamidine derivatives and TMD-5, and to rationalise the observed structure-activity relationships. This study explicitly demonstrated that the interaction of small molecule with lipid should be considered alongside interaction with the protein target when designing small molecules targeting the PPIs of TMDs. In all, this study provides proof of concept for the rational design of small molecules targeting transmembrane PPIs.
Asunto(s)
Pentamidina/farmacología , Bibliotecas de Moléculas Pequeñas/farmacología , Proteínas de la Matriz Viral/antagonistas & inhibidores , Animales , Supervivencia Celular/efectos de los fármacos , Células Cultivadas , Perros , Relación Dosis-Respuesta a Droga , Modelos Moleculares , Estructura Molecular , Pentamidina/química , Bibliotecas de Moléculas Pequeñas/química , Relación Estructura-Actividad , Proteínas de la Matriz Viral/metabolismoRESUMEN
Nasopharyngeal cancer (NPC), endemic in Southeast Asia, lacks effective diagnostic and therapeutic strategies. Even in high-income countries the 5-year survival rate for stage IV NPC is less than 40%. Here we report high somatostatin receptor 2 (SSTR2) expression in multiple clinical cohorts comprising 402 primary, locally recurrent and metastatic NPCs. We show that SSTR2 expression is induced by the Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1) via the NF-κB pathway. Using cell-based and preclinical rodent models, we demonstrate the therapeutic potential of SSTR2 targeting using a cytotoxic drug conjugate, PEN-221, which is found to be superior to FDA-approved SSTR2-binding cytostatic agents. Furthermore, we reveal significant correlation of SSTR expression with increased rates of survival and report in vivo uptake of the SSTR2-binding 68Ga-DOTA-peptide radioconjugate in PET-CT scanning in a clinical trial of NPC patients (NCT03670342). These findings reveal a key role in EBV-associated NPC for SSTR2 in infection, imaging, targeted therapy and survival.