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1.
Molecules ; 26(5)2021 Feb 24.
Artículo en Inglés | MEDLINE | ID: mdl-33668217

RESUMEN

Protein molecules are inherently dynamic and modulate their interactions with different molecular partners by accessing different tertiary structures under physiological conditions. Elucidating such structures remains challenging. Current momentum in deep learning and the powerful performance of generative adversarial networks (GANs) in complex domains, such as computer vision, inspires us to investigate GANs on their ability to generate physically-realistic protein tertiary structures. The analysis presented here shows that several GAN models fail to capture complex, distal structural patterns present in protein tertiary structures. The study additionally reveals that mechanisms touted as effective in stabilizing the training of a GAN model are not all effective, and that performance based on loss alone may be orthogonal to performance based on the quality of generated datasets. A novel contribution in this study is the demonstration that Wasserstein GAN strikes a good balance and manages to capture both local and distal patterns, thus presenting a first step towards more powerful deep generative models for exploring a possibly very diverse set of structures supporting diverse activities of a protein molecule in the cell.


Asunto(s)
Redes Neurales de la Computación , Proteínas/química , Estructura Terciaria de Proteína
2.
J Phys Chem B ; 125(10): 2533-2550, 2021 03 18.
Artículo en Inglés | MEDLINE | ID: mdl-33657325

RESUMEN

The novel RNA virus, severe acute respiratory syndrome coronavirus II (SARS-CoV-2), is currently the leading cause of mortality in 2020, having led to over 1.6 million deaths and infecting over 75 million people worldwide by December 2020. While vaccination has started and several clinical trials for a number of vaccines are currently underway, there is a pressing need for a cure for those already infected with the virus. Of particular interest in the design of anti-SARS-CoV-2 therapeutics is the human protein angiotensin converting enzyme II (ACE2) to which this virus adheres before entry into the host cell. The SARS-CoV-2 virion binds to cell-surface bound ACE2 via interactions of the spike protein (s-protein) on the viral surface with ACE2. In this paper, we use all-atom molecular dynamics simulations and binding enthalpy calculations to determine the effect that a bound ACE2 active site inhibitor (MLN-4760) would have on the binding affinity of SARS-CoV-2 s-protein with ACE2. Our analysis indicates that the binding enthalpy could be reduced for s-protein adherence to the active site inhibitor-bound ACE2 protein by as much as 1.48-fold as an upper limit. This weakening of binding strength was observed to be due to the destabilization of the interactions between ACE2 residues Glu-35, Glu-37, Tyr-83, Lys-353, and Arg-393 and the SARS-CoV-2 s-protein receptor binding domain (RBD). The conformational changes were shown to lead to weakening of ACE2 interactions with SARS-CoV-2 s-protein, therefore reducing s-protein binding strength. Further, we observed increased conformational lability of the N-terminal helix and a conformational shift of a significant portion of the ACE2 motifs involved in s-protein binding, which may affect the kinetics of the s-protein binding when the small molecule inhibitor is bound to the ACE2 active site. These observations suggest potential new ways for interfering with the SARS-CoV-2 adhesion by modulating ACE2 conformation through distal active site inhibitor binding.


Asunto(s)
/metabolismo , Inhibidores de Proteasas/metabolismo , Glicoproteína de la Espiga del Coronavirus/metabolismo , /antagonistas & inhibidores , Sitios de Unión , /virología , Dominio Catalítico , Diseño de Fármacos , Humanos , Enlace de Hidrógeno , Simulación de Dinámica Molecular , Inhibidores de Proteasas/química , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Estructura Terciaria de Proteína , Bibliotecas de Moléculas Pequeñas/química , Bibliotecas de Moléculas Pequeñas/metabolismo , Glicoproteína de la Espiga del Coronavirus/química , Termodinámica
3.
Methods Mol Biol ; 2266: 239-259, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33759131

RESUMEN

Molecular dynamics simulations can now routinely access the microsecond timescale, making feasible direct sampling of ligand association events. While Markov State Model (MSM) approaches offer a useful framework for analyzing such trajectory data to gain insight into binding mechanisms, accurate modeling of ligand association pathways and kinetics must be done carefully. We describe methods and good practices for constructing MSMs of ligand binding from unbiased trajectory data and discuss how to use time-lagged independent component analysis (tICA) to build informative models, using as an example recent simulation work to model the binding of phenylalanine to the regulatory ACT domain dimer of phenylalanine hydroxylase. We describe a variety of methods for estimating association rates from MSMs and discuss how to distinguish between conformational selection and induced-fit mechanisms using MSMs. In addition, we review some examples of MSMs constructed to elucidate the mechanisms by which p53 transactivation domain (TAD) and related peptides bind the oncoprotein MDM2.


Asunto(s)
Cadenas de Markov , Simulación de Dinámica Molecular , Fenilalanina Hidroxilasa/química , Fenilalanina/química , Proteínas Proto-Oncogénicas c-mdm2/química , Programas Informáticos , Proteína p53 Supresora de Tumor/química , Cinética , Ligandos , Unión Proteica , Dominios Proteicos , Estructura Terciaria de Proteína
4.
Food Chem Toxicol ; 150: 112057, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33592201

RESUMEN

World is familiar with the viral pathogen Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2). The principle working enzymes of SARS CoV-2 have been identified as main proteases 3Cl pro which act as main regulators for SARS infection. The need for therapy is required immediately pertaining to the vulnerable conditions. Protein-ligand studies are imperative for understanding the functioning of biological interactions as they are crucial in providing a hypothetical origin for the design and unearthing of novel drug targets. Phytoconstituents from Glycyrrhiza glabra, earlier reported to be anticancerous in nature were used as repurposed drugs against SARS CoV-2 main protease 3Clpro. We analyzed the molecular interactions of protein-phytocompounds, by AutoDock Vina 4.2 tools. The best interactions of each algorithm were subjected to molecular dynamic (MD) simulations to have an insight of the molecular dynamic mechanisms involved. Selected phytoconstituents gave a good score for binding affinity with the main protease 6LU7 of SARS CoV-2 as compared to the antiviral drugs already being used in the disease therapy. DehydroglyasperinC(-8.7,-8.1,-6.7,-7.1)kcal/mol, Licochalcone D(-8.4,-8.2,-7.1,-7.9) kcal/mol, Liquiritin(-8.6,-9.0,-7.2,-7.8) kcal/mol have showed energy interactions with 3Clpro better than many FDA approved repurposed drugs; Remdesvir, Favipiravir, and Hydroxychloroquine. MD Simulation also corelates our findings for molecular docking studies.


Asunto(s)
Antivirales/farmacología , Glycyrrhiza/química , Extractos Vegetales/farmacología , /efectos de los fármacos , Simulación por Computador , Evaluación Preclínica de Medicamentos/métodos , Simulación de Dinámica Molecular , Estructura Terciaria de Proteína , /enzimología
5.
Eur Rev Med Pharmacol Sci ; 25(3): 1708-1723, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33629340

RESUMEN

OBJECTIVE: Recent pandemic virus SARS-CoV-2 is a global warning for the healthcare system. The spike protein of virus SARS-CoV-2 is significant because of two reasons. Firstly, the spike protein of this virus binds with the human ACE2 (hACE2) receptor. Secondly, it has several antigenic regions that might be targeted for vaccine development. However, the structural analytical data for the spike protein of this virus is not available. MATERIALS AND METHODS: Here, we performed an analysis to understand the structural two subunits of S glycoprotein (S gp) of SARS-CoV-2. Further, an analysis of secondary structure components and the tertiary structure analysis of RBD was carried out. We also performed molecular interaction analysis between S gp of this virus and hACE2 as well as between SARS-CoV S gp and hACE2 to compare the binding properties of these two viruses. RESULTS: We noted that the molecular interaction of SARS-CoV-2 S gp and hACE2 form eleven hydrogen bonds, while the molecular interaction of SARS-CoV S gp and hACE2 receptor form seven hydrogen bonds, indicating that the molecular interaction of SARS-CoV-2 S gp and hACE2 receptor is more stable than SARS-CoV S gp and hACE2 receptor. The pairwise sequence alignment of S gp SARS-CoV and SARS-CoV-2 shows several conserved residues of these two proteins. Besides, conserved pattern analysis of SARS-CoV-2 S gp and hACE2 revealed the presence of several highly conserved regions for these two proteins. The molecular dynamics simulation shows a stable interplay between SARS-CoV-2 S gp with the hACE2 receptor. CONCLUSIONS: The present study might help determine the SARS-CoV-2 virus entrance mechanism into the human cell. Moreover, the understanding of the conserved regions may help in the process of therapeutic development from the infection of the deadly virus.


Asunto(s)
/química , /química , Glicoproteína de la Espiga del Coronavirus/química , Simulación por Computador , Secuencia Conservada , Glicosilación , Humanos , Enlace de Hidrógeno , Interacciones Hidrofóbicas e Hidrofílicas , Simulación de Dinámica Molecular , Dominios y Motivos de Interacción de Proteínas , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Subunidades de Proteína
6.
PLoS One ; 16(2): e0245072, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33534822

RESUMEN

Middle East respiratory syndrome (MERS-COV), first identified in Saudi Arabia, was caused by a novel strain of coronavirus. Outbreaks were recorded from different regions of the world, especially South Korea and the Middle East, and were correlated with a 35% mortality rate. MERS-COV is a single-stranded, positive RNA virus that reaches the host by binding to the receptor of dipeptidyl-peptides. Because of the unavailability of the vaccine available for the protection from MERS-COV infection, the rapid case detection, isolation, infection prevention has been recommended to combat MERS-COV infection. So, vaccines for the treatment of MERS-COV infection need to be developed urgently. A possible antiviral mechanism for preventing MERS-CoV infection has been considered to be MERS-CoV vaccines that elicit unique T-cell responses. In the present study, we incorporated both molecular docking and immunoinformatic approach to introduce a multiepitope vaccine (MEP) against MERS-CoV by selecting 15 conserved epitopes from seven viral proteins such as three structural proteins (envelope, membrane, and nucleoprotein) and four non-structural proteins (ORF1a, ORF8, ORF3, ORF4a). The epitopes, which were examined for non-homologous to host and antigenicity, were selected on the basis of conservation between T-cell, B-cell, and IFN-γ epitopes. The selected epitopes were then connected to the adjuvant (ß-defensin) at the N-terminal through an AAY linker to increase the immunogenic potential. Structural modelling and physiochemical characteristic were applied to the vaccine construct developed. Afterwards the structure has been successfully docked with antigenic receptor, Toll-like receptor 3 (TLR-3) and in-silico cloning ensures that its expression efficiency is legitimate. Nonetheless the MEP presented needs tests to verify its safety and immunogenic profile.


Asunto(s)
Epítopos/inmunología , Coronavirus del Síndrome Respiratorio de Oriente Medio/metabolismo , Proteoma , Vacunas Virales/inmunología , Secuencia de Aminoácidos , Sitios de Unión , Infecciones por Coronavirus/inmunología , Infecciones por Coronavirus/patología , Infecciones por Coronavirus/prevención & control , Diseño de Fármacos , Epítopos/química , Humanos , Simulación del Acoplamiento Molecular , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Vacunas de Subunidad/química , Vacunas de Subunidad/inmunología , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/inmunología , Proteínas Estructurales Virales/química , Proteínas Estructurales Virales/inmunología , Vacunas Virales/química
7.
BMC Infect Dis ; 21(1): 166, 2021 Feb 10.
Artículo en Inglés | MEDLINE | ID: mdl-33568111

RESUMEN

BACKGROUND: An unexpected dengue outbreak occurred in Hunan Province in 2018. This was the first dengue outbreak in this area of inland China, and 172 cases were reported. METHODS: To verify the causative agent of this outbreak and characterise the viral genes, the genes encoding the structural proteins C/prM/E of viruses isolated from local residents were sequenced followed by mutation and phylogenetic analysis. Recombination, selection pressure, potential secondary structure and three-dimensional structure analyses were also performed. RESULTS: Phylogenetic analysis revealed that all epidemic strains were of the cosmopolitan DENV-2 genotype and were most closely related to the Zhejiang strain (MH010629, 2017) and then the Malaysia strain (KJ806803, 2013). Compared with the sequence of DENV-2SS, 151 base substitutions were found in the sequences of 89 isolates; these substitutions resulted in 20 non-synonymous mutations, of which 17 mutations existed in all samples (two in the capsid protein, six in the prM/M proteins, and nine in the envelope proteins). Moreover, amino acid substitutions at the 602nd (E322:Q → H) and 670th (E390: N → S) amino acids may have enhanced the virulence of the epidemic strains. One new DNA binding site and five new protein binding sites were observed. Two polynucleotide binding sites and seven protein binding sites were lost in the epidemic strains compared with DENV-2SS. Meanwhile, five changes were found in helical regions. Minor changes were observed in helical transmembrane and disordered regions. The 429th amino acid of the E protein switched from a histamine (positively charged) to an asparagine (neutral) in all 89 isolated strains. No recombination events or positive selection pressure sites were observed. To our knowledge, this study is the first to analyse the genetic characteristics of epidemic strains in the first dengue outbreak in Hunan Province in inland China. CONCLUSIONS: The causative agent is likely to come from Zhejiang Province, a neighbouring province where dengue fever broke out in 2017. This study may help clarify the intrinsic geographical relatedness of DENV-2 and contribute to further research on pathogenicity and vaccine development.


Asunto(s)
Virus del Dengue/genética , Dengue/diagnóstico , Proteínas del Envoltorio Viral/genética , Sitios de Unión , Proteínas de la Cápside/química , Proteínas de la Cápside/genética , Proteínas de la Cápside/metabolismo , China/epidemiología , Dengue/epidemiología , Dengue/virología , Virus del Dengue/clasificación , Virus del Dengue/aislamiento & purificación , Brotes de Enfermedades , Genotipo , Humanos , Mutación , Filogenia , Estructura Terciaria de Proteína , ARN Viral/química , ARN Viral/metabolismo , Análisis de Secuencia de ARN , Proteínas del Envoltorio Viral/química , Proteínas no Estructurales Virales/genética , Proteínas no Estructurales Virales/metabolismo
8.
Life Sci ; 271: 119182, 2021 Apr 15.
Artículo en Inglés | MEDLINE | ID: mdl-33577851

RESUMEN

Glitazones are synthetic derivatives of thiazolidinedione, and are designated as oral anti-diabetic agents, primarily acting on peroxisome proliferator-activated receptor-gamma (PPAR-γ) receptors and driving some crucial metabolic pathways linked to glucose and lipid metabolism at transcriptional level. Despite presenting adverse effects, including weight gain, fluid retention, prostate hyperplasia, hyperinsulinemia, and myocardial infarction, they are still preferred in clinical settings due to their utmost efficacy and selectivity. However, these complications kept glitazones restrained for long-term usage. The present review briefly highlights some important synthetic derivatives of thiazolidine2,4-dione and emphasizes the influence of various structural manipulations on their bio-efficacy.


Asunto(s)
Hipoglucemiantes/química , Hipoglucemiantes/metabolismo , Tiazolidinedionas/química , Tiazolidinedionas/metabolismo , Animales , Diabetes Mellitus Tipo 2/tratamiento farmacológico , Diabetes Mellitus Tipo 2/metabolismo , Glucosa/antagonistas & inhibidores , Glucosa/metabolismo , Humanos , Hipoglucemiantes/uso terapéutico , Resistencia a la Insulina/fisiología , PPAR gamma/metabolismo , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Tiazolidinedionas/uso terapéutico
9.
Mol Pharmacol ; 99(4): 266-276, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33436520

RESUMEN

Benzbromarone (BBR), a potent uricosuric agent for the management of gout, is known to cause fatal fulminant hepatitis. Although the mechanism of BBR-induced idiosyncratic hepatotoxicity remains unelucidated, cytochrome P450 enzyme-mediated bioactivation of BBR to electrophilic reactive metabolites is commonly regarded as a key molecular initiating event. However, apart from causing aberrant toxicities, reactive metabolites may result in mechanism-based inactivation (MBI) of cytochrome P450. Here, we investigated and confirmed that BBR inactivated CYP3A4 in a time-, concentration-, and NADPH-dependent manner with K I, k inact, and partition ratio of 11.61 µM, 0.10 minutes-1, and 110, respectively. Coincubation with ketoconazole, a competitive inhibitor of CYP3A4, attenuated the MBI of CYP3A4 by BBR, whereas the presence of glutathione and catalase did not confer such protection. The lack of substantial recovery of enzyme activity postdialysis and after oxidation with potassium ferricyanide, combined with the absence of a Soret peak in spectral difference scans, implied that MBI of CYP3A4 by BBR did not occur through the formation of quasi-irreversible metabolite-intermediate complexes. Analysis of the reduced CO-difference spectrum revealed an ∼44% reduction in ferrous-CO binding and hinted that inactivation is mediated via irreversible covalent adduction to both the prosthetic heme moiety and the apoprotein. Finally, our in silico covalent docking analysis further suggested the modulation of substrate binding to CYP3A4 via the covalent adduction of epoxide-derived reactive intermediates of BBR to two key cysteine residues (Cys239 and Cys58) vicinal to the entrance of the orthosteric binding site. SIGNIFICANCE STATEMENT: Although the bioactivation of benzbromarone (BBR) to reactive metabolites has been well characterized, its potential to cause mechanism-based inactivation (MBI) of cytochrome P450 has not been fully investigated. This study reports the MBI of CYP3A4 by BBR via irreversible covalent adduction and develops a unique covalent docking methodology to predict the structural molecular determinants underpinning the inactivation for the first time. These findings lay the groundwork for future investigation of clinically relevant drug-drug interactions implicating BBR and mechanisms of BBR-induced idiosyncratic hepatotoxicity.


Asunto(s)
Benzbromarona/farmacología , Citocromo P-450 CYP3A/química , Citocromo P-450 CYP3A/metabolismo , Simulación del Acoplamiento Molecular/métodos , Relación Dosis-Respuesta a Droga , Humanos , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Especies Reactivas de Oxígeno/antagonistas & inhibidores , Especies Reactivas de Oxígeno/metabolismo , Uricosúricos/farmacología
10.
Trends Microbiol ; 29(3): 195-203, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33446406

RESUMEN

Camelid-derived and synthetic single-domain antibodies (sdAbs) are emerging as potent weapons against the novel coronavirus, SARS-CoV-2. sdAbs are small, compact, thermostable immunoglobulin elements capable of binding targets with subnanomolar affinities. By leveraging the power of phage- and yeast surface-display technologies, rare sdAbs can be isolated from highly diverse and complex antibody libraries. Once in hand, sdAbs can be engineered to improve binding affinity, avidity, target specificities, and biodistribution. In this Opinion piece we highlight a series of sophisticated studies describing the identification of ultrapotent sdAbs directed against the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein. We discuss the possible applications of these antibodies in the global fight against COVID-19.


Asunto(s)
Anticuerpos Antivirales/química , Anticuerpos Antivirales/inmunología , Anticuerpos de Dominio Único/química , Anticuerpos de Dominio Único/inmunología , Glicoproteína de la Espiga del Coronavirus/inmunología , Humanos , Estructura Terciaria de Proteína , Biología Sintética/métodos
11.
PLoS Pathog ; 17(1): e1009246, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33493182

RESUMEN

Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) infects cells by binding to the host cell receptor ACE2 and undergoing virus-host membrane fusion. Fusion is triggered by the protease TMPRSS2, which processes the viral Spike (S) protein to reveal the fusion peptide. SARS-CoV-2 has evolved a multibasic site at the S1-S2 boundary, which is thought to be cleaved by furin in order to prime S protein for TMPRSS2 processing. Here we show that CRISPR-Cas9 knockout of furin reduces, but does not prevent, the production of infectious SARS-CoV-2 virus. Comparing S processing in furin knockout cells to multibasic site mutants reveals that while loss of furin substantially reduces S1-S2 cleavage it does not prevent it. SARS-CoV-2 S protein also mediates cell-cell fusion, potentially allowing virus to spread virion-independently. We show that loss of furin in either donor or acceptor cells reduces, but does not prevent, TMPRSS2-dependent cell-cell fusion, unlike mutation of the multibasic site that completely prevents syncytia formation. Our results show that while furin promotes both SARS-CoV-2 infectivity and cell-cell spread it is not essential, suggesting furin inhibitors may reduce but not abolish viral spread.


Asunto(s)
Fusión Celular , Furina/genética , Glicoproteína de la Espiga del Coronavirus/química , Internalización del Virus , Animales , Sistemas CRISPR-Cas , Chlorocebus aethiops , Técnicas de Inactivación de Genes , Células HEK293 , Humanos , Estructura Terciaria de Proteína , Serina Endopeptidasas , Células Vero
12.
Viruses ; 13(2)2021 01 22.
Artículo en Inglés | MEDLINE | ID: mdl-33499226

RESUMEN

Cadherin Related Family Member 3 (CDHR3) is the identified and required cellular receptor for all virus isolates in the rhinovirus-C species (RV-C). Cryo-EM determinations recently resolved the atomic structure of RV-C15a, and subsequently, a complex of this virus bound to CDHR3 extracellular domain 1 (EC1), the N-terminal portion of this receptor responsible for virus interactions. The EC1 binds to a hypervariable sequence footprint on the virus surface, near the 3-fold axis of icosahedral symmetry. The key contacts involve discontinuous residues from 3 viral proteins, VP1, VP2 and VP3. That single cryo-EM EC1 structure, however, could not resolve whether the virus-receptor interface was structurally adaptable to accommodate multiple virus sequences. We now report the solution NMR determination of CDHR3 EC1, showing that this protein, in fact, is mostly inflexible, particularly in the virus-binding face. The new, higher resolution dataset identifies 3 cis-Pro residues in important loop regions, where they can influence both rigidity and overall protein conformation. The data also provide clarification about the residues involved in essential calcium ion binding, and a potential CDHR3 surface groove feature that may be involved in native protein interactions with cellular partners.


Asunto(s)
Cadherinas/química , Enterovirus/química , Proteínas de la Membrana/química , Enterovirus/clasificación , Infecciones por Enterovirus/virología , Humanos , Modelos Moleculares , Resonancia Magnética Nuclear Biomolecular , Conformación Proteica , Estructura Terciaria de Proteína , Proteínas Virales/química , Acoplamiento Viral
13.
Sci Rep ; 11(1): 1529, 2021 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-33452303

RESUMEN

The genetic variations among individuals are one of the notable factors determining disease severity and drug response. Nowadays, COVID-19 pandemic has been adversely affecting many aspects of human life. We used the Tehran Cardio-Metabolic Genetic Study (TCGS) data that is an ongoing genetic study including the whole-genome sequencing of 1200 individuals and chip genotyping of more than 15,000 participants. Here, the effect of ACE2 variations by focusing on the receptor-binding site of SARS-CoV-2 and ACE2 cleavage by TMPRSS2 protease were investigated through simulations study. After analyzing TCGS data, 570 genetic variations on the ACE2 gene, including single nucleotide polymorphisms (SNP) and insertion/deletion (INDEL) were detected. Interestingly, two observed missense variants, K26R and S331F, which only the first one was previously reported, can reduce the receptor affinity for the viral Spike protein. Moreover, our bioinformatics simulation of 3D structures and docking of proteins explains important details of ACE2-Spike and ACE2-TMPRSS2 interactions, especially the critical role of Arg652 of ACE2 for protease function of TMPRSS2 was uncovered. As our results show that the genetic variation of ACE2 can at least influence the affinity of this receptor to its partners, we need to consider the genetic variations on ACE2 as well as other genes in the pathways that contribute to the pathogenesis of COVID-19 for designing efficient drugs and vaccines.


Asunto(s)
/genética , /patología , /química , Sitios de Unión , /virología , Susceptibilidad a Enfermedades , Expresión Génica , Genotipo , Humanos , Mutación INDEL , Irán , Simulación del Acoplamiento Molecular , Mutación Missense , Polimorfismo de Nucleótido Simple , Unión Proteica , Estructura Terciaria de Proteína , /metabolismo , Serina Endopeptidasas/química , Serina Endopeptidasas/metabolismo , Glicoproteína de la Espiga del Coronavirus/química , Glicoproteína de la Espiga del Coronavirus/metabolismo , Secuenciación Completa del Genoma
14.
J Med Chem ; 64(1): 890-904, 2021 01 14.
Artículo en Inglés | MEDLINE | ID: mdl-33372782

RESUMEN

The sigma 1 receptor (S1R) is a molecular chaperone protein located in the endoplasmic reticulum and plasma membranes and has been shown to play important roles in various pathological disorders including pain and, as recently discovered, COVID-19. Employing structure- and QSAR-based drug design strategies, we rationally designed, synthesized, and biologically evaluated a series of novel triazole-based S1R antagonists. Compound 10 exhibited potent binding affinity for S1R, high selectivity over S2R and 87 other human targets, acceptable in vitro metabolic stability, slow clearance in liver microsomes, and excellent blood-brain barrier permeability in rats. Further in vivo studies in rats showed that 10 exhibited negligible acute toxicity in the rotarod test and statistically significant analgesic effects in the formalin test for acute inflammatory pain and paclitaxel-induced neuropathic pain models during cancer chemotherapy. These encouraging results promote further development of our triazole-based S1R antagonists as novel treatments for pain of different etiologies.


Asunto(s)
Manejo del Dolor/métodos , Receptores sigma/antagonistas & inhibidores , Triazoles/química , Animales , Sitios de Unión , Barrera Hematoencefálica/metabolismo , Diseño de Fármacos , Cobayas , Semivida , Humanos , Microsomas Hepáticos/metabolismo , Simulación de Dinámica Molecular , Neuralgia/inducido químicamente , Neuralgia/tratamiento farmacológico , Estructura Terciaria de Proteína , Relación Estructura-Actividad Cuantitativa , Ratas , Receptores sigma/metabolismo , Triazoles/metabolismo , Triazoles/uso terapéutico
15.
Food Chem ; 334: 127508, 2021 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-32711265

RESUMEN

Quercetin, a potential polyphenolic which possesses several biological effects. The influenza virus polymerase basic 2 (PB2) subunit of RNA polymerase responsible for replication, degree of virus conservation and active target site for designing specific antivirals. The quercetin derivatives downloaded from PubChem were screened using PyRX software configured with Vina Wizard, targeted on cap-binding site of the PB2 of influenza viral RNA polymerase. Among the PubChem library (total 97,585,747 compounds), 410 quercetin derivatives were screened using molecular docking (affinity: <-9.0 kcal) for their drug-likeness and in vitro cytopathic effect by Sulforhodamine B (SRB) assay. Among all quercetin derivatives, quercetin 3'-glucuronide (Q3G) showed strongest binding affinity towards cap-binding site of the PB2 subunit with -9.6 kcal of binding affinity and 0.00054 mM of Ki value, while quercetin 3'-glucuronide (Q7G) was presented highest anti-influenza activity with 2.10 ± 0.05 of IC50 on influenza A/PR/8/34 virus and non-cytotoxic effect as CC50 > 100 µg/mL.


Asunto(s)
Antivirales/farmacología , Virus de la Influenza A/efectos de los fármacos , Quercetina/análogos & derivados , Animales , Antivirales/química , Antivirales/metabolismo , Sitios de Unión , Supervivencia Celular/efectos de los fármacos , ARN Polimerasas Dirigidas por ADN/química , ARN Polimerasas Dirigidas por ADN/metabolismo , Perros , Humanos , Virus de la Influenza A/enzimología , Influenzavirus B/efectos de los fármacos , Células de Riñón Canino Madin Darby , Simulación del Acoplamiento Molecular , Estructura Terciaria de Proteína , Subunidades de Proteína/química , Subunidades de Proteína/metabolismo , Quercetina/química , Quercetina/metabolismo , Quercetina/farmacología , Termodinámica
16.
Methods Mol Biol ; 2231: 179-200, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33289894

RESUMEN

Bioinformatic analysis of functionally diverse superfamilies can help to study the structure-function relationship in proteins, but represents a methodological challenge. The Mustguseal web-server can build large structure-guided sequence alignments of thousands of homologs that cover all currently available sequence variants within a common structural fold. The input to the method is a PDB code of the query protein, which represents the protein superfamily of interest. The collection and subsequent alignment of protein sequences and structures is fully automated and driven by the particular choice of parameters. Four integrated sister web-methods-the Zebra, pocketZebra, visualCMAT, and Yosshi-are available to further analyze the resulting superimposition and identify conserved, subfamily-specific, and co-evolving residues, as well as to classify and study disulfide bonds in protein superfamilies. The integration of these web-based bioinformatic tools provides an out-of-the-box easy-to-use solution, first of its kind, to study protein function and regulation and design improved enzyme variants for practical applications and selective ligands to modulate their functional properties. In this chapter, we provide a step-by-step protocol for a comprehensive bioinformatic analysis of a protein superfamily using a web-browser as the main tool and notes on selecting the appropriate values for the key algorithm parameters depending on your research objective. The web-servers are freely available to all users at https://biokinet.belozersky.msu.ru/m-platform with no login requirement.


Asunto(s)
Biología Computacional/métodos , Proteínas/química , Alineación de Secuencia/métodos , Programas Informáticos , Algoritmos , Secuencia de Aminoácidos , Biología Computacional/instrumentación , Disulfuros/química , Internet , Ligandos , Estructura Terciaria de Proteína , Alineación de Secuencia/instrumentación
17.
J Ethnopharmacol ; 264: 113380, 2021 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-32918994

RESUMEN

ETHNOPHARMACOLOGICAL RELEVANCE: Sea buckthorn is popularly used as a herbal medicine and food additive in the world. Sea buckthorn flavonoids (SF) is reported to have an ameliorative effect on obesity and hyperlipidemia (HLP). AIM: To identify the major bioactive compounds and the lipid-lowering mechanism of SF. METHODS: We used network pharmacology analysis and in vitro experiments to identify the major bioactive compounds and the lipid-lowering mechanism of SF. RESULTS: A total of 12 bioactive compounds, 60 targets related to SF and HLP were identified, and a component-target-disease network was constructed. The KEGG analysis revealed that SF regulated cholesterol metabolism, fat digestion and absorption, and PPAR signaling pathways in HLP. The experimental validation indicated that sea buckthorn flavonoids extract (SFE) and 4 bioactive compounds reduced lipid droplet accumulation, up-regulated the mRNA expression of PPAR-γ, PPAR-α, ABCA1 and CPT1A, etc, down-regulated SREBP-2 and its target gene LDLR, which are closely related to cholesterol conversion into bile acids, de novo synthesis and fatty acids oxidation. The major bioactive flavonoid isorhamnetin (ISOR) also increased the protein expression of PPAR-γ, LXRα and CYP7A1. CONCLUSION: SF might promote cholesterol transformation into bile acids and cholesterol efflux, inhibit cholesterol de novo synthesis and accelerate fatty acids oxidation for ameliorating HLP.


Asunto(s)
Flavonoides/farmacología , Hippophae , Extractos Vegetales/farmacología , Mapas de Interacción de Proteínas/efectos de los fármacos , Línea Celular , Supervivencia Celular/efectos de los fármacos , Supervivencia Celular/fisiología , Relación Dosis-Respuesta a Droga , Flavonoides/aislamiento & purificación , Flavonoides/uso terapéutico , Humanos , Hiperlipidemias/tratamiento farmacológico , Hiperlipidemias/metabolismo , Extractos Vegetales/aislamiento & purificación , Extractos Vegetales/uso terapéutico , Mapas de Interacción de Proteínas/fisiología , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Reproducibilidad de los Resultados
18.
Angew Chem Int Ed Engl ; 60(9): 4689-4697, 2021 02 23.
Artículo en Inglés | MEDLINE | ID: mdl-33320993

RESUMEN

Fatty acid ß-oxidation (FAO) and oxidative phosphorylation (OXPHOS) are mitochondrial redox processes that generate ATP. The biogenesis of the respiratory Complex I, a 1 MDa multiprotein complex that is responsible for initiating OXPHOS, is mediated by assembly factors including the mitochondrial complex I assembly (MCIA) complex. However, the organisation and the role of the MCIA complex are still unclear. Here we show that ECSIT functions as the bridging node of the MCIA core complex. Furthermore, cryo-electron microscopy together with biochemical and biophysical experiments reveal that the C-terminal domain of ECSIT directly binds to the vestigial dehydrogenase domain of the FAO enzyme ACAD9 and induces its deflavination, switching ACAD9 from its role in FAO to an MCIA factor. These findings provide the structural basis for the MCIA complex architecture and suggest a unique molecular mechanism for coordinating the regulation of the FAO and OXPHOS pathways to ensure an efficient energy production.


Asunto(s)
Complejo I de Transporte de Electrón/química , Flavina-Adenina Dinucleótido/metabolismo , Mitocondrias/metabolismo , Acil-CoA Deshidrogenasas/genética , Acil-CoA Deshidrogenasas/metabolismo , Proteínas Adaptadoras Transductoras de Señales/química , Proteínas Adaptadoras Transductoras de Señales/metabolismo , Microscopía por Crioelectrón , Complejo I de Transporte de Electrón/metabolismo , Metabolismo Energético , Flavina-Adenina Dinucleótido/química , Humanos , Fosforilación Oxidativa , Dominios y Motivos de Interacción de Proteínas , Estructura Terciaria de Proteína , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/química , Proteínas Recombinantes/aislamiento & purificación
19.
Adv Drug Deliv Rev ; 169: 100-117, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33309815

RESUMEN

To address the COVID-19 pandemic, there has been an unprecedented global effort to advance potent neutralizing mAbs against SARS-CoV-2 as therapeutics. However, historical efforts to advance antiviral monoclonal antibodies (mAbs) for the treatment of other respiratory infections have been met with categorical failures in the clinic. By investigating the mechanism by which SARS-CoV-2 and similar viruses spread within the lung, along with available biodistribution data for systemically injected mAb, we highlight the challenges faced by current antiviral mAbs for COVID-19. We summarize some of the leading mAbs currently in development, and present the evidence supporting inhaled delivery of antiviral mAb as an early intervention against COVID-19 that could prevent important pulmonary morbidities associated with the infection.


Asunto(s)
Anticuerpos Monoclonales/uso terapéutico , Antivirales/uso terapéutico , Factores Inmunológicos/uso terapéutico , /efectos de los fármacos , /antagonistas & inhibidores , Animales , Anticuerpos Monoclonales/química , Anticuerpos Monoclonales/metabolismo , Antivirales/química , Antivirales/metabolismo , /metabolismo , Humanos , Inmunización Pasiva , Factores Inmunológicos/química , Factores Inmunológicos/metabolismo , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , /metabolismo , Esparcimiento de Virus/efectos de los fármacos , Esparcimiento de Virus/fisiología
20.
Mol Immunol ; 130: 148-153, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33358568

RESUMEN

MR1 is an MHC class I-like molecule with unique structural and biological features that make it an important member among the molecules involved in antigen presentation to T cells. Distinctive features include ubiquitous expression of the MR1 gene and its monomorphism. Another relevant property is that the MR1 protein appears at very low levels on the plasma membrane and its surface expression is regulated by antigen binding. Finally, the nature of presented antigens differs from those that bind other presenting molecules and includes small metabolites of microbial and self-origin, small drugs and tumor-associated antigens. This opinion paper describes in detail some of those features and discusses recent literature in the field.


Asunto(s)
Presentación de Antígeno , Antígenos de Histocompatibilidad Clase I/metabolismo , Antígenos de Histocompatibilidad Menor/metabolismo , Especificidad del Receptor de Antígeno de Linfocitos T , Linfocitos T/metabolismo , Presentación de Antígeno/genética , Presentación de Antígeno/inmunología , Antígenos Bacterianos/inmunología , Antígenos Bacterianos/metabolismo , Antígenos de Histocompatibilidad Clase I/química , Antígenos de Histocompatibilidad Clase I/genética , Antígenos de Histocompatibilidad Clase I/inmunología , Humanos , Ligandos , Activación de Linfocitos/genética , Activación de Linfocitos/inmunología , Antígenos de Histocompatibilidad Menor/química , Antígenos de Histocompatibilidad Menor/genética , Antígenos de Histocompatibilidad Menor/inmunología , Unión Proteica , Estructura Terciaria de Proteína , Especificidad del Receptor de Antígeno de Linfocitos T/genética , Especificidad del Receptor de Antígeno de Linfocitos T/inmunología , Linfocitos T/inmunología
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