Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 22.511
Filtrar
1.
Int J Med Mushrooms ; 23(3): 1-14, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33822495

RESUMEN

The most challenging threat facing the global community today is the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite global efforts to develop suitable treatments, very few specific antiviral agents have been suggested and the virus remains a serious global health risk. In vivo animal experiments have demonstrated that bioactive mycochemical constituents of Inonotus obliquus have immunomodulatory, antimicrobial, and antiviral properties. The present study investigates the antiviral potential of I. obliquus terpenoids against COVID-19 using a molecular docking study. The in silico study elucidates the ability of most of the terpenoid components to interact with the receptor-binding domain of SARS-CoV-2 spike glycoprotein with excellent affinity. Additionally, we found that both betulinic acid and inonotusane C could bind and stably interact with the spike protein near the host cell recognition site of angiotensin-converting enzyme 2.


Asunto(s)
/tratamiento farmacológico , Simulación del Acoplamiento Molecular , Glicoproteína de la Espiga del Coronavirus/efectos de los fármacos , Terpenos/farmacología , Concentración 50 Inhibidora , Estructura Molecular , Glicoproteína de la Espiga del Coronavirus/metabolismo , Terpenos/química , Terpenos/metabolismo
2.
Molecules ; 26(6)2021 Mar 23.
Artículo en Inglés | MEDLINE | ID: mdl-33806967

RESUMEN

Bats are unique in their potential to serve as reservoir hosts for intracellular pathogens. Recently, the impact of COVID-19 has relegated bats from biomedical darkness to the frontline of public health as bats are the natural reservoir of many viruses, including SARS-Cov-2. Many bat genomes have been sequenced recently, and sequences coding for antimicrobial peptides are available in the public databases. Here we provide a structural analysis of genome-predicted bat cathelicidins as components of their innate immunity. A total of 32 unique protein sequences were retrieved from the NCBI database. Interestingly, some bat species contained more than one cathelicidin. We examined the conserved cysteines within the cathelin-like domain and the peptide portion of each sequence and revealed phylogenetic relationships and structural dissimilarities. The antibacterial, antifungal, and antiviral activity of peptides was examined using bioinformatic tools. The peptides were modeled and subjected to docking analysis with the region binding domain (RBD) region of the SARS-CoV-2 Spike protein. The appearance of multiple forms of cathelicidins verifies the complex microbial challenges encountered by these species. Learning more about antiviral defenses of bats and how they drive virus evolution will help scientists to investigate the function of antimicrobial peptides in these species.


Asunto(s)
Catelicidinas/química , Catelicidinas/farmacología , Quirópteros/genética , Glicoproteína de la Espiga del Coronavirus/metabolismo , Animales , Antibacterianos/química , Antibacterianos/farmacología , Antifúngicos/química , Antifúngicos/farmacología , Péptidos Catiónicos Antimicrobianos/química , Péptidos Catiónicos Antimicrobianos/farmacología , Antivirales/química , Antivirales/farmacología , Sitios de Unión , Catelicidinas/genética , Catelicidinas/metabolismo , Biología Computacional/métodos , Simulación por Computador , Genoma , Simulación del Acoplamiento Molecular , Filogenia
3.
Pestic Biochem Physiol ; 174: 104811, 2021 May.
Artículo en Inglés | MEDLINE | ID: mdl-33838713

RESUMEN

Isoxazole, nicotinic acid and benzoic acid are important components in many natural products and useful synthons to build macrostructures having valuable biological activities. In continuation of our effort to discover 4-hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) inhibitors and search for active fragments from natural products, a series of substituted aryl-formyl piperidinone derivatives with natural product fragments was rationally designed, synthesized and tested for their herbicidal activity. Compound I-9 was considered the most effective candidate with an IC50 value of 0.260 µM. The molecular docking results showed that the triketone group of compound I-9 forms a bidentate complex with a metal ion, and the benzene ring interacted with Phe424 and Phe381 via π-π stacking, which was similar to the mechanisms of mesotrione. The present work indicates that compound I-9 may serve as a potential lead compound for further development of green HPPD inhibitors.


Asunto(s)
Herbicidas , Inhibidores Enzimáticos/farmacología , Herbicidas/farmacología , Simulación del Acoplamiento Molecular , Estructura Molecular , Relación Estructura-Actividad
4.
J Chem Inf Model ; 61(3): 1402-1411, 2021 03 22.
Artículo en Inglés | MEDLINE | ID: mdl-33655751

RESUMEN

SARS-CoV-2 is a positive-sense RNA virus that requires an RNA-dependent RNA polymerase (RdRp) for replication of its viral genome. Nucleoside analogs such as Remdesivir and ß-d-N4-hydroxycytidine are antiviral candidates and may function as chain terminators or induce viral mutations, thus impairing RdRp function. Recently disclosed Cryo-EM structures of apo, RNA-bound, and inhibitor-bound SARS-CoV-2 RdRp provided insight into the inhibitor-bound structure by capturing the enzyme with its reaction product: Remdesivir covalently bound to the RNA primer strand. To gain a structural understanding of the binding of this and several other nucleoside analogs in the precatalytic state, molecular models were developed that predict the noncovalent interactions to a complex of SARS-CoV-2 RdRp, RNA, and catalytic metal cations. MM-GBSA evaluation of these interactions is consistent with resistance-conferring mutations and existing structure-activity relationship (SAR) data. Therefore, this approach may yield insights into antiviral mechanisms and guide the development of experimental drugs for COVID-19 treatment.


Asunto(s)
/tratamiento farmacológico , Nucleósidos/análogos & derivados , Nucleósidos/farmacología , ARN Viral/metabolismo , /efectos de los fármacos , Antivirales/química , Antivirales/farmacología , Diseño de Fármacos , Descubrimiento de Drogas , Humanos , Simulación del Acoplamiento Molecular , /metabolismo
5.
PLoS One ; 16(3): e0248553, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33735271

RESUMEN

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is a novel human coronavirus strain (HCoV) was initially reported in December 2019 in Wuhan City, China. This acute infection caused pneumonia-like symptoms and other respiratory tract illness. Its higher transmission and infection rate has successfully enabled it to have a global spread over a matter of small time. One of the major concerns involving the SARS-COV-2 is the mutation rate, which enhances the virus evolution and genome variability, thereby making the design of therapeutics difficult. In this study, we identified the most common haplotypes from the haplotype network. The conserved genes and population level variants were analysed. Non-Structural Protein 10 (NSP10), Nucleoprotein, Papain-like protease (Plpro or NSP3) and 3-Chymotrypsin like protease (3CLpro or NSP5), which were conserved at the highest threshold, were used as drug targets for molecular dynamics simulations. Darifenacin, Nebivolol, Bictegravir, Alvimopan and Irbesartan are among the potential drugs, which are suggested for further pre-clinical and clinical trials. This particular study provides a comprehensive targeting of the conserved genes. We also identified the mutation frequencies across the viral genome.


Asunto(s)
/tratamiento farmacológico , Reposicionamiento de Medicamentos/métodos , /genética , Descubrimiento de Drogas/métodos , Genoma Viral , Humanos , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Tasa de Mutación , /metabolismo , Proteínas Virales/genética , Proteínas Virales/metabolismo
6.
Nat Commun ; 12(1): 1732, 2021 03 19.
Artículo en Inglés | MEDLINE | ID: mdl-33741980

RESUMEN

Macrolides are a class of antibiotics widely used in both medicine and agriculture. Unsurprisingly, as a consequence of their exensive usage a plethora of resistance mechanisms have been encountered in pathogenic bacteria. One of these resistance mechanisms entails the enzymatic cleavage of the macrolides' macrolactone ring by erythromycin esterases (Eres). The most frequently identified Ere enzyme is EreA, which confers resistance to the majority of clinically used macrolides. Despite the role Eres play in macrolide resistance, research into this family enzymes has been sparse. Here, we report the first three-dimensional structures of an erythromycin esterase, EreC. EreC is an extremely close homologue of EreA, displaying more than 90% sequence identity. Two structures of this enzyme, in conjunction with in silico flexible docking studies and previously reported mutagenesis data allowed for the proposal of a detailed catalytic mechanism for the Ere family of enzymes, labeling them as metal-independent hydrolases. Also presented are substrate spectrum assays for different members of the Ere family. The results from these assays together with an examination of residue conservation for the macrolide binding site in Eres, suggests two distinct active site archetypes within the Ere enzyme family.


Asunto(s)
Antibacterianos/química , Farmacorresistencia Bacteriana/efectos de los fármacos , Farmacorresistencia Bacteriana/genética , Esterasas/química , Esterasas/genética , Macrólidos/química , Antibacterianos/farmacología , Bacterias/enzimología , Bacterias/genética , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Sitios de Unión , Hidrolasas de Éster Carboxílico/química , Hidrolasas de Éster Carboxílico/genética , Hidrolasas de Éster Carboxílico/metabolismo , Eritromicina/química , Genes Bacterianos , Macrólidos/farmacología , Simulación del Acoplamiento Molecular , Conformación Proteica , Difracción de Rayos X
7.
Biomed Res Int ; 2021: 1596834, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33728324

RESUMEN

Background: Coronaviruses (CoVs) are enveloped positive-strand RNA viruses which have club-like spikes at the surface with a unique replication process. Coronaviruses are categorized as major pathogenic viruses causing a variety of diseases in birds and mammals including humans (lethal respiratory dysfunctions). Nowadays, a new strain of coronaviruses is identified and named as SARS-CoV-2. Multiple cases of SARS-CoV-2 attacks are being reported all over the world. SARS-CoV-2 showed high death rate; however, no specific treatment is available against SARS-CoV-2. Methods: In the current study, immunoinformatics approaches were employed to predict the antigenic epitopes against SARS-CoV-2 for the development of the coronavirus vaccine. Cytotoxic T-lymphocyte and B-cell epitopes were predicted for SARS-CoV-2 coronavirus protein. Multiple sequence alignment of three genomes (SARS-CoV, MERS-CoV, and SARS-CoV-2) was used to conserved binding domain analysis. Results: The docking complexes of 4 CTL epitopes with antigenic sites were analyzed followed by binding affinity and binding interaction analyses of top-ranked predicted peptides with MHC-I HLA molecule. The molecular docking (Food and Drug Regulatory Authority library) was performed, and four compounds exhibiting least binding energy were identified. The designed epitopes lead to the molecular docking against MHC-I, and interactional analyses of the selected docked complexes were investigated. In conclusion, four CTL epitopes (GTDLEGNFY, TVNVLAWLY, GSVGFNIDY, and QTFSVLACY) and four FDA-scrutinized compounds exhibited potential targets as peptide vaccines and potential biomolecules against deadly SARS-CoV-2, respectively. A multiepitope vaccine was also designed from different epitopes of coronavirus proteins joined by linkers and led by an adjuvant. Conclusion: Our investigations predicted epitopes and the reported molecules that may have the potential to inhibit the SARS-CoV-2 virus. These findings can be a step towards the development of a peptide-based vaccine or natural compound drug target against SARS-CoV-2.


Asunto(s)
/inmunología , Inmunogenicidad Vacunal/inmunología , Vacunas de Subunidad/inmunología , Secuencia de Aminoácidos , Epítopos de Linfocito B/inmunología , Epítopos de Linfocito T/inmunología , Humanos , Simulación del Acoplamiento Molecular/métodos
8.
Pestic Biochem Physiol ; 173: 104771, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33771249

RESUMEN

A series of novel 1-phenyl-5-amine-4-pyrazole thioether derivatives containing a 1,3,4-oxadiazole moiety was designed and synthesised. In vivo antiviral bioassay results showed that most of the target compounds exhibited excellent inactivation activity against Tobacco mosaic virus (TMV). The EC50 values of the inactivation activities for T2, T7, T9, T24, T25 and T27 were 15.7, 15.7, 15.5, 11.9, 12.5 and 16.5 µg/mL, respectively, which were remarkably superior over that of the commercialised antiviral agent ningnanmycin (40.3 µg/mL). Morphological study using AFM and TEM of TMV treated with T24 showed that T24 could significantly shorten the polymerization length of TMV particles and formed a distinct break on the rod-shaped TMV. Investigations for virus infection efficiency on tobacco leaves demonstrated that infectivity of virion had been reduced obviously upon T24 treatment. Subsequently, a strong interaction between T24 and TMV-CP (Kd = 3.8 µM, score 6.11) was observed through MST experiments. Molecular docking study further revealed that target compounds interact with amino acid residue Glu50 in TMV CP, causing disassembly of virion, shorting the length of the virion and reducing the infectivity of virion, and resulting in high inactivating activity of target compounds. This study provides a new insight for discovery of antiviral compounds through a new action mechanism with a new binding site.


Asunto(s)
Virus del Mosaico del Tabaco , Aminas , Antivirales/farmacología , Simulación del Acoplamiento Molecular , Pirazoles/farmacología , Relación Estructura-Actividad , Sulfuros
9.
Molecules ; 26(5)2021 Feb 24.
Artículo en Inglés | MEDLINE | ID: mdl-33668306

RESUMEN

Irritable bowel syndrome (IBS) is a chronic disease that causes abdominal pain and an imbalance of defecation patterns due to gastrointestinal dysfunction. The cause of IBS remains unclear, but intestinal-brain axis problems and neurotransmitters have been suggested as factors. In this study, chanoclavine, which has a ring structure similar to 5-hydroxytryptamine (5-HT), showed an interaction with the 5-HT3A receptor to regulate IBS. Although its derivatives are known to be involved in neurotransmitter receptors, the molecular physiological mechanism of the interaction between chanoclavine and the 5-HT3A receptor is unknown. Electrophysiological experiments were conducted using a two-electrode voltage-clamp analysis to observe the inhibitory effects of chanoclavine on Xenopus oocytes in which the h5-HT3A receptor was expressed. The co-application of chanoclavine and 5-HT resulted in concentration-dependent, reversible, voltage-independent, and competitive inhibition. The 5-HT3A response induced by 5-HT was blocked by chanoclavine with half-maximal inhibitory response concentration (IC50) values of 107.2 µM. Docking studies suggested that chanoclavine was positioned close F130 and N138 in the 5-HT3A receptor-binding site. The double mutation of F130A and N138A significantly attenuated the interaction of chanoclavine compared to a single mutation or the wild type. These data suggest that F130 and N138 are important sites for ligand binding and activity. Chanoclavine and ergonovine have different effects. Asparagine, the 130th amino acid sequence of the 5-HT3A receptor, and phenylalanine, the 138th, are important in the role of binding chanoclavine, but ergonovine has no interaction with any amino acid sequence of the 5-HT3A receptor. The results of the electrophysiological studies and of in silico simulation showed that chanoclavine has the potential to inhibit the hypergastric stimulation of the gut by inhibiting the stimulation of signal transduction through 5-HT3A receptor stimulation. These findings suggest chanoclavine as a potential antiemetic agent for excessive gut stimulation and offer insight into the mechanisms of 5-HT3A receptor inhibition.


Asunto(s)
Ergolinas/farmacología , Receptores de Serotonina 5-HT3/metabolismo , Relación Dosis-Respuesta a Droga , Ergolinas/química , Ergonovina/química , Ergonovina/farmacología , Humanos , Conformación Molecular , Simulación del Acoplamiento Molecular , Serotonina/farmacología , Transducción de Señal/efectos de los fármacos
10.
Molecules ; 26(4)2021 Feb 21.
Artículo en Inglés | MEDLINE | ID: mdl-33670019

RESUMEN

Suramin was initially used to treat African sleeping sickness and has been clinically tested to treat human cancers and HIV infection in the recent years. However, the therapeutic index is low with numerous clinical side-effects, attributed to its diverse interactions with multiple biological macromolecules. Here, we report a novel binding target of suramin, human Raf1 kinase inhibitory protein (hRKIP), which is an important regulatory protein involved in the Ras/Raf1/MEK/ERK (MAPK) signal pathway. Biolayer interference technology showed that suramin had an intermediate affinity for binding hRKIP with a dissociation constant of 23.8 µM. Both nuclear magnetic resonance technology and molecular docking analysis revealed that suramin bound to the conserved ligand-binding pocket of hRKIP, and that residues K113, W173, and Y181 play crucial roles in hRKIP binding suramin. Furthermore, suramin treatment at 160 µM could profoundly increase the ERK phosphorylation level by around 3 times. Our results indicate that suramin binds to hRKIP and prevents hRKIP from binding with hRaf1, thus promoting the MAPK pathway. This work is beneficial to both mechanistically understanding the side-effects of suramin and efficiently improving the clinical applications of suramin.


Asunto(s)
Inhibidores de Proteínas Quinasas/farmacología , Proteínas Proto-Oncogénicas c-raf/antagonistas & inhibidores , Suramina/farmacología , Sitios de Unión/efectos de los fármacos , Células HEK293 , Humanos , Ligandos , Simulación del Acoplamiento Molecular , Inhibidores de Proteínas Quinasas/química , Proteínas Proto-Oncogénicas c-raf/aislamiento & purificación , Proteínas Proto-Oncogénicas c-raf/metabolismo , Suramina/análogos & derivados , Suramina/química
11.
Sci Rep ; 11(1): 5543, 2021 03 10.
Artículo en Inglés | MEDLINE | ID: mdl-33692377

RESUMEN

The COVID-19 caused by the SARS-CoV-2 virus was declared a pandemic disease in March 2020 by the World Health Organization (WHO). Structure-Based Drug Design strategies based on docking methodologies have been widely used for both new drug development and drug repurposing to find effective treatments against this disease. In this work, we present the developments implemented in the DockThor-VS web server to provide a virtual screening (VS) platform with curated structures of potential therapeutic targets from SARS-CoV-2 incorporating genetic information regarding relevant non-synonymous variations. The web server facilitates repurposing VS experiments providing curated libraries of currently available drugs on the market. At present, DockThor-VS provides ready-for-docking 3D structures for wild type and selected mutations for Nsp3 (papain-like, PLpro domain), Nsp5 (Mpro, 3CLpro), Nsp12 (RdRp), Nsp15 (NendoU), N protein, and Spike. We performed VS experiments of FDA-approved drugs considering the therapeutic targets available at the web server to assess the impact of considering different structures and mutations to identify possible new treatments of SARS-CoV-2 infections. The DockThor-VS is freely available at www.dockthor.lncc.br .


Asunto(s)
/tratamiento farmacológico , Diseño de Fármacos , Reposicionamiento de Medicamentos/métodos , Antivirales/farmacología , Humanos , Internet , Simulación del Acoplamiento Molecular/métodos , Pandemias , /patogenicidad
12.
Molecules ; 26(5)2021 Feb 26.
Artículo en Inglés | MEDLINE | ID: mdl-33652639

RESUMEN

Hepatitis C is affecting millions of people around the globe annually, which leads to death in very high numbers. After many years of research, hepatitis C virus (HCV) remains a serious threat to the human population and needs proper management. The in silico approach in the drug discovery process is an efficient method in identifying inhibitors for various diseases. In our study, the interaction between Epigallocatechin-3-gallate, a component of green tea, and envelope glycoprotein E2 of HCV is evaluated. Epigallocatechin-3-gallate is the most promising polyphenol approved through cell culture analysis that can inhibit the entry of HCV. Therefore, various in silico techniques have been employed to find out other potential inhibitors that can behave as EGCG. Thus, the homology modelling of E2 protein was performed. The potential lead molecules were predicted using ligand-based as well as structure-based virtual screening methods. The compounds obtained were then screened through PyRx. The drugs obtained were ranked based on their binding affinities. Furthermore, the docking of the topmost drugs was performed by AutoDock Vina, while its 2D interactions were plotted in LigPlot+. The lead compound mms02387687 (2-[[5-[(4-ethylphenoxy) methyl]-4-prop-2-enyl-1,2,4-triazol-3-yl] sulfanyl]-N-[3(trifluoromethyl) phenyl] acetamide) was ranked on top, and we believe it can serve as a drug against HCV in the future, owing to experimental validation.


Asunto(s)
Catequina/análogos & derivados , Hepacivirus/efectos de los fármacos , Hepatitis C/tratamiento farmacológico , Proteínas del Envoltorio Viral/genética , Antivirales/química , Antivirales/farmacología , Catequina/química , Catequina/farmacología , Hepacivirus/genética , Hepacivirus/patogenicidad , Hepatitis C/virología , Humanos , Ligandos , Simulación del Acoplamiento Molecular , Polifenoles/química , Polifenoles/farmacología , Té/química , Proteínas del Envoltorio Viral/antagonistas & inhibidores , Internalización del Virus/efectos de los fármacos
13.
Molecules ; 26(5)2021 Feb 26.
Artículo en Inglés | MEDLINE | ID: mdl-33652837

RESUMEN

In search of anti-inflammatory compounds, novel scaffolds containing isonicotinoyl motif were synthesized via an efficient strategy. The compounds were screened for their in vitro anti-inflammatory activity. Remarkably high activities were observed for isonicotinates 5-6 and 8a-8b. The compound 5 exhibits an exceptional IC50 value (1.42 ± 0.1 µg/mL) with 95.9% inhibition at 25 µg/mL, which is eight folds better than the standard drug ibuprofen (11.2 ± 1.9 µg/mL). To gain an insight into the mode of action of anti-inflammatory compounds, molecular docking studies were also performed. Decisively, further development and fine tuning of these isonicotinates based scaffolds for the treatment of various aberrations is still a wide-open field of research.


Asunto(s)
Antiinflamatorios no Esteroideos/síntesis química , Inflamación/tratamiento farmacológico , Ácidos Isonicotínicos/síntesis química , Especies Reactivas de Oxígeno/antagonistas & inhibidores , Antiinflamatorios no Esteroideos/química , Antiinflamatorios no Esteroideos/farmacología , Inhibidores de la Ciclooxigenasa 2/síntesis química , Inhibidores de la Ciclooxigenasa 2/química , Inhibidores de la Ciclooxigenasa 2/farmacología , Humanos , Ibuprofeno/química , Ácidos Isonicotínicos/química , Ácidos Isonicotínicos/farmacología , Simulación del Acoplamiento Molecular , Especies Reactivas de Oxígeno/química , Relación Estructura-Actividad
14.
Molecules ; 26(5)2021 Feb 26.
Artículo en Inglés | MEDLINE | ID: mdl-33652925

RESUMEN

Two new minor Amaryllidaceae alkaloids were isolated from Hippeastrum × hybridum cv. Ferrari and Narcissus pseudonarcissus cv. Carlton. The chemical structures were identified by various spectroscopic (one- and two-dimensional (1D and 2D) NMR, circular dichroism (CD), high-resolution mass spectrometry (HRMS) and by comparison with literature data of similar compounds. Both isolated alkaloids were screened for their human acetylcholinesterase (hAChE) and butyrylcholinesterase (hBuChE) inhibition activity. One of the new compounds, a heterodimer alkaloid of narcikachnine-type, named narciabduliine (2), showed balanced inhibition potency for both studied enzymes, with IC50 values of 3.29 ± 0.73 µM for hAChE and 3.44 ± 0.02 µM for hBuChE. The accommodation of 2 into the active sites of respective enzymes was predicted using molecular modeling simulation.


Asunto(s)
Alcaloides/química , Alcaloides de Amaryllidaceae/química , Inhibidores de la Colinesterasa/química , Colinesterasas/ultraestructura , Alcaloides/farmacología , Enfermedad de Alzheimer , Alcaloides de Amaryllidaceae/farmacología , Butirilcolinesterasa/química , Butirilcolinesterasa/ultraestructura , Dominio Catalítico/efectos de los fármacos , Inhibidores de la Colinesterasa/farmacología , Colinesterasas/química , Dicroismo Circular , Humanos , Simulación del Acoplamiento Molecular , Estructura Molecular , Relación Estructura-Actividad
15.
Aging (Albany NY) ; 13(5): 6258-6272, 2021 03 07.
Artículo en Inglés | MEDLINE | ID: mdl-33678621

RESUMEN

It has been confirmed that the new coronavirus SARS-CoV-2 caused the global pandemic of coronavirus disease 2019 (COVID-19). Studies have found that 3-chymotrypsin-like protease (3CLpro) is an essential enzyme for virus replication, and could be used as a potential target to inhibit SARS-CoV-2. In this work, 3CLpro was used as the target to complete the high-throughput virtual screening of the FDA-approved drugs, and Indinavir and other 10 drugs with high docking scores for 3CLpro were obtained. Studies on the binding pattern of 3CLpro and Indinavir found that Indinavir could form the stable hydrogen bond (H-bond) interactions with the catalytic dyad residues His41-Cys145. Binding free energy study found that Indinavir had high binding affinity with 3CLpro. Subsequently, molecular dynamics simulations were performed on the 3CLpro and 3CLpro-Indinavir systems, respectively. The post-dynamic analyses showed that the conformational state of the 3CLpro-Indinavir system transformed significantly and the system tended to be more stable. Moreover, analyses of the residue interaction network (RIN) and H-bond occupancy revealed that the residue-residue interaction at the catalytic site of 3CLpro was significantly enhanced after binding with Indinavir, which in turn inactivated the protein. In short, through this research, we hope to provide more valuable clues against COVID-19.


Asunto(s)
/tratamiento farmacológico , /enzimología , /farmacología , /virología , /metabolismo , Aprobación de Drogas , Descubrimiento de Drogas , Evaluación Preclínica de Medicamentos , Ensayos Analíticos de Alto Rendimiento , Humanos , Indinavir/química , Indinavir/farmacología , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , /efectos de los fármacos , /química
16.
Drug Des Devel Ther ; 15: 1111-1133, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33737804

RESUMEN

Purpose: SARS-CoV-2 engages human ACE2 through its spike (S) protein receptor binding domain (RBD) to enter the host cell. Recent computational studies have reported that withanone and withaferin A, phytochemicals found in Withania somnifera, target viral main protease (MPro) and host transmembrane TMPRSS2, and glucose related protein 78 (GRP78), respectively, implicating their potential as viral entry inhibitors. Absence of specific treatment against SARS-CoV-2 infection has encouraged exploration of phytochemicals as potential antivirals. Aim: This study aimed at in silico exploration, along with in vitro and in vivo validation of antiviral efficacy of the phytochemical withanone. Methods: Through molecular docking, molecular dynamic (MD) simulation and electrostatic energy calculation the plausible biochemical interactions between withanone and the ACE2-RBD complex were investigated. These in silico observations were biochemically validated by ELISA-based assays. Withanone-enriched extract from W. somnifera was tested for its ability to ameliorate clinically relevant pathological features, modelled in humanized zebrafish through SARS-CoV-2 recombinant spike (S) protein induction. Results: Withanone bound efficiently at the interacting interface of the ACE2-RBD complex and destabilized it energetically. The electrostatic component of binding free energies of the complex was significantly decreased. The two intrachain salt bridge interactions (K31-E35) and the interchain long-range ion-pair (K31-E484), at the ACE2-RBD interface were completely abolished by withanone, in the 50 ns simulation. In vitro binding assay experimentally validated that withanone efficiently inhibited (IC50=0.33 ng/mL) the interaction between ACE2 and RBD, in a dose-dependent manner. A withanone-enriched extract, without any co-extracted withaferin A, was prepared from W. somnifera leaves. This enriched extract was found to be efficient in ameliorating human-like pathological responses induced in humanized zebrafish by SARS-CoV-2 recombinant spike (S) protein. Conclusion: In conclusion, this study provided experimental validation for computational insight into the potential of withanone as a potent inhibitor of SARS-CoV-2 coronavirus entry into the host cells.


Asunto(s)
/metabolismo , Antivirales/farmacología , /efectos de los fármacos , Glicoproteína de la Espiga del Coronavirus/metabolismo , Withania , Witanólidos/farmacología , Células A549 , Animales , Antivirales/química , Antivirales/aislamiento & purificación , /virología , Modelos Animales de Enfermedad , Femenino , Interacciones Huésped-Patógeno , Humanos , Masculino , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Dominios y Motivos de Interacción de Proteínas , /patogenicidad , Glicoproteína de la Espiga del Coronavirus/química , Electricidad Estática , Relación Estructura-Actividad , Internalización del Virus/efectos de los fármacos , Withania/química , Witanólidos/química , Witanólidos/aislamiento & purificación , Pez Cebra
17.
Int J Nanomedicine ; 16: 1789-1804, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33688191

RESUMEN

Background: SARS-COVID-2 has recently been one of the most life-threatening problems which urgently needs new therapeutic antiviral agents, especially those of herbal origin. Purpose: The study aimed to load acaciin (ACA) into the new self-assembled nanofibers (NFs) followed by investigating their possible antiviral effect against bovine coronavirus (BCV) as a surrogate model for SARS-COV-2. Methods: ACA was identified using 1H-NMR and DEPT-Q 13C-NMR spectroscopy, the molecular docking study was performed using Autodock 4 and a modification of the traditional solvent injection method was applied for the synthesis of the biodegradable NFs. Different characterization techniques were used to inspect the formation of the NFs, which is followed by antiviral investigation against BCV as well as MTT assay using MDBK cells. Results: Core/shell NFs, ranging between 80-330 nm with tiny thorn-like branches, were formed which attained an enhanced encapsulation efficiency (97.5 ± 0.53%, P<0.05) and a dual controlled release (a burst release of 65% at 1 h and a sustained release up to >24 h). The antiviral investigation of the formed NFs revealed a significant inhibition of 98.88 ± 0.16% (P<0.05) with IC50 of 12.6 µM against BCV cells. Conclusion: The results introduced a new, time/cost-saving strategy for the synthesis of biodegradable NFs without the need for electric current or hazardous cross-linking agents. Moreover, it provided an innovative avenue for the discovery of drugs of herbal origin for the fight against SARS-CoV-2 infection.


Asunto(s)
Coronavirus Bovino/efectos de los fármacos , Glicósidos/farmacología , Nanofibras/química , /efectos de los fármacos , Antivirales/química , Antivirales/farmacología , /virología , Línea Celular , Glicósidos/química , Glicósidos/aislamiento & purificación , Glicósidos/uso terapéutico , Humanos , Ligandos , Modelos Biológicos , Simulación del Acoplamiento Molecular , Nanofibras/ultraestructura , Solventes , Rayos Ultravioleta
18.
Life Sci ; 274: 119325, 2021 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-33713665

RESUMEN

AIMS: The emergence of antibiotic tolerance was a tricky problem in the treatment of chronic Pseudomonas aeruginosa-infected cystic fibrosis and burn victims. The quorum sensing (QS) inhibitor may serve as a new tactic for the bacterial resistance by inhibiting the biofilm formation and the production of virulence factors. This study explored the potential of luteolin as a QS inhibitor against P. aeruginosa and the molecular mechanism involved. MAIN METHODS: Crystal violet staining, CLSM observation, and SEM analysis were carried out to assess the effect of luteolin on biofilm formation. The motility assays and the production of virulence factors were determined to evaluate the QS-inhibitory activity of luteolin. Acyl-homoserine lactone, RT-PCR, and molecular docking assays were conducted to explain its anti-QS mechanisms. KEY FINDINGS: The biofilm formation, the production of virulence factors, and the motility of P. aeruginosa could be efficiently inhibited by luteolin. Luteolin could also attenuate the accumulation of the QS-signaling molecules N-(3-oxododecanoyl)-L-homoserine lactone (OdDHL) and N-butanoyl-L-homoserine lactone (BHL) (P < 0.01) and downregulate the transcription levels of QS genes (lasR, lasI, rhlR, and rhlI) (P < 0.01). Molecular docking analysis indicated that luteolin had a greater docking affinity with LasR regulator protein compared with OdDHL. SIGNIFICANCE: This study is important as it reports the molecular mechanisms involved in the anti-biofilm formation activity of luteolin against P. aeruginosa. This study also indicated that luteolin could be helpful when used for the treatment of clinical drug-resistant infections of P. aeruginosa.


Asunto(s)
Proteínas Bacterianas/metabolismo , Biopelículas/efectos de los fármacos , Regulación Bacteriana de la Expresión Génica , Luteolina/farmacología , Infecciones por Pseudomonas/tratamiento farmacológico , Pseudomonas aeruginosa/efectos de los fármacos , Percepción de Quorum/efectos de los fármacos , Transactivadores/metabolismo , 4-Butirolactona/análogos & derivados , 4-Butirolactona/antagonistas & inhibidores , Biopelículas/crecimiento & desarrollo , Homoserina/análogos & derivados , Homoserina/antagonistas & inhibidores , Humanos , Simulación del Acoplamiento Molecular , Infecciones por Pseudomonas/microbiología , Pseudomonas aeruginosa/aislamiento & purificación , Factores de Virulencia
19.
Eur Rev Med Pharmacol Sci ; 25(5): 2435-2448, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33755983

RESUMEN

OBJECTIVE: Since no effective therapy exists, we aimed to test existing HIV antivirals for combination treatment of Coronavirus disease 19 (COVID-19). MATERIALS AND METHODS: The crystal structures of SARS-CoV-2 main protein (Mpro) (PDB ID: 6Y2F) and SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) (PDB ID: 7BV2) both available from Protein Data Bank were used in the study. Automated Docking by using blind and standard method both on Mpro and RdRp bound to the modified template-primer RNA was performed with AutoDock 4.2.6 program suite. Lamarckian genetic algorithm (LGA) was used for structures docking. All inhibitors were docked with all bonds completely free to rotate. RESULTS: Our molecular docking findings suggest that lopinavir, ritonavir, darunavir, and atazanavir activated interactions with the key binding sites of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) protease with a better inhibition constant (Ki) for lopinavir, ritonavir, and darunavir. Furthermore, we evidenced the ability of remdesivir, tenofovir, emtricitabine, and lamivudine to be incorporated in SARS-CoV-2 RdRp in the same protein pocket where poses the corresponding natural nucleoside substrates with comparable Ki and activating similar interactions. In principle, the four antiviral nucleotides might be used effectively against SARS-CoV-2. CONCLUSIONS: The combination of a protease inhibitor and two nucleoside analogues, drugs widely used to treat HIV infection, could be evaluated in clinical trials for the treatment of COVID-19.


Asunto(s)
Antivirales/farmacología , Quimioterapia Combinada/métodos , Nucleósidos/uso terapéutico , Inhibidores de Proteasas/uso terapéutico , Adenosina Monofosfato/análogos & derivados , Alanina/análogos & derivados , Sulfato de Atazanavir , Darunavir , Combinación de Medicamentos , Intervención Médica Temprana , Emtricitabina , Humanos , Lamivudine , Lopinavir , Simulación del Acoplamiento Molecular , Ritonavir
20.
mBio ; 12(2)2021 03 30.
Artículo en Inglés | MEDLINE | ID: mdl-33785634

RESUMEN

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently emerged virus that causes coronavirus infectious disease 2019 (COVID-19). SARS-CoV-2 spike protein, like SARS-CoV-1, uses the angiotensin converting enzyme 2 (ACE2) as a cellular receptor to initiate infection. Compounds that interfere with the SARS-CoV-2 spike protein receptor binding domain protein (RBD)-ACE2 receptor interaction may function as entry inhibitors. Here, we used a dual strategy of molecular docking and surface plasmon resonance (SPR) screening of compound libraries to identify those that bind to human ACE2 or the SARS-CoV-2 spike protein receptor binding domain (RBD). Molecular modeling screening interrogated 57,641 compounds and focused on the region of ACE2 that is engaged by RBD of the SARS-CoV-2 spike glycoprotein and vice versa. SPR screening used immobilized human ACE2 and SARS-CoV-2 Spike protein to evaluate the binding of these proteins to a library of 3,141 compounds. These combined screens identified compounds from these libraries that bind at KD (equilibrium dissociation constant) <3 µM affinity to their respective targets, 17 for ACE2 and 6 for SARS-CoV-2 RBD. Twelve ACE2 binders and six of the RBD binders compete with the RBD-ACE2 interaction in an SPR-based competition assay. These compounds included registered drugs and dyes used in biomedical applications. A Vero-E6 cell-based SARS-CoV-2 infection assay was used to evaluate infection blockade by candidate entry inhibitors. Three compounds demonstrated dose-dependent antiviral in vitro potency-Evans blue, sodium lifitegrast, and lumacaftor. This study has identified potential drugs for repurposing as SARS-CoV-2 entry inhibitors or as chemical scaffolds for drug development.IMPORTANCE SARS-CoV-2, the causative agent of COVID-19, has caused more than 60 million cases worldwide with almost 1.5 million deaths as of November 2020. Repurposing existing drugs is the most rapid path to clinical intervention for emerging diseases. Using an in silico screen of 57,641 compounds and a biophysical screen of 3,141 compounds, we identified 22 compounds that bound to either the angiotensin converting enzyme 2 (ACE2) and/or the SARS-CoV-2 spike protein receptor binding domain (SARS-CoV-2 spike protein RBD). Nine of these drugs were identified by both screening methods. Three of the identified compounds, Evans blue, sodium lifitegrast, and lumacaftor, were found to inhibit viral replication in a Vero-E6 cell-based SARS-CoV-2 infection assay and may have utility as repurposed therapeutics. All 22 identified compounds provide scaffolds for the development of new chemical entities for the treatment of COVID-19.


Asunto(s)
/metabolismo , Antivirales/farmacología , Glicoproteína de la Espiga del Coronavirus/metabolismo , Acoplamiento Viral/efectos de los fármacos , Replicación Viral/efectos de los fármacos , Aminopiridinas/farmacología , Animales , Benzodioxoles/farmacología , Línea Celular , Chlorocebus aethiops , Evaluación Preclínica de Medicamentos , Reposicionamiento de Medicamentos , Azul de Evans/farmacología , Humanos , Simulación del Acoplamiento Molecular , Fenilalanina/análogos & derivados , Fenilalanina/farmacología , Unión Proteica/efectos de los fármacos , /fisiología , Sulfonas/farmacología , Resonancia por Plasmón de Superficie , Células Vero
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA
...