Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 49
Filtrar
Más filtros

Banco de datos
País/Región como asunto
Tipo del documento
Intervalo de año de publicación
1.
Scand J Clin Lab Invest ; 83(8): 533-539, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-38145316

RESUMEN

Vitamin B12 deficiency and insufficiency can lead to both hematological and neurological impairments. This review examines nondisease causes and risk factors associated with dietary availability, such as eating habits, food processing, cooking techniques, and bioavailability, as well as increased physiological needs and iatrogenic factors linked to medication use or surgical procedures. As a result of these nondisease influences, groups at higher risk include vegans, vegetarians, older adults, individuals with limited diets, breastfed and preterm infants, and those who primarily consume foods prepared or cooked in ways that reduce vitamin B12 content, as well as individuals on certain medications or who have undergone specific surgeries. Recognizing these diverse risk factors helps develop strategies for prevention and intervention to minimize the adverse health effects related to B12 deficiency and insufficiency.


Asunto(s)
Deficiencia de Vitamina B 12 , Vitamina B 12 , Recién Nacido , Lactante , Humanos , Anciano , Dieta Vegetariana/efectos adversos , Recien Nacido Prematuro , Deficiencia de Vitamina B 12/tratamiento farmacológico , Deficiencia de Vitamina B 12/etiología , Factores de Riesgo
2.
J Comput Aided Mol Des ; 36(1): 39-62, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-35059939

RESUMEN

Activity cliffs (ACs) are defined as closely analogous compounds of significant affinity discrepancies against certain biotarget. In this paper we propose to use AC pair(s) for extracting valid binding pharmacophores through exposing corresponding protein complexes to stochastic deformation/relaxation followed by applying genetic algorithm/machine learning (GA-ML) for selecting optimal pharmacophore(s) that best classify a long list of inhibitors. We compared the performances of ligand-based and structure-based pharmacophores with counterparts generated by this newly introduced technique. Sphingosine kinase 1 (SPHK-1) was used as case study. SPHK-1 is a lipid kinase that plays pivotal role in the regulation of a variety of biological processes including, cell growth, apoptosis, and inflammation. The new approach proved to yield pharmacophore and ML models of comparable accuracies to established ligand-based and structure-based pharmacophores. The resulting pharmacophores and ML models were used to capture hits from the national cancer institute list of compounds and predict their bioactivity categories. Two hits of novel chemotypes showed selective and low micromolar inhibitory IC50 values against SPHK-1.


Asunto(s)
Fosfotransferasas (Aceptor de Grupo Alcohol) , Relación Estructura-Actividad Cuantitativa , Ligandos , Simulación del Acoplamiento Molecular , Inhibidores de Proteínas Quinasas/química , Inhibidores de Proteínas Quinasas/farmacología
3.
Int J Clin Pract ; 75(5): e14036, 2021 May.
Artículo en Inglés | MEDLINE | ID: mdl-33512081

RESUMEN

BACKGROUND: Human soluble epoxide hydrolase plays a major role in cardiovascular homoeostasis. Genetic variants in the EPHX2 gene among different ethnic groups are associated with cardiovascular complications, such as hypertension. However, no reports regarding the association of EPHX2 genotype with hypertension among type II diabetic (T2D) patients of Middle Eastern Jordanian origin exist. OBJECTIVE: The current study aimed to elucidate the association of the EPHX2 allele, genotype and haplotype with T2D, hypertension and parameters of lipid profile parameters among Jordanian T2D patients. METHODS: Ninety-three genomic DNA samples of non-diabetic controls and 97 samples from T2D patients were genotyped for EPHX2 rs4149243, rs2234914 and rs751142 genetic variants. The DNA samples were amplified using polymerase chain reaction (PCR) and then sequenced using Applied Biosystems Model (ABI3730x1). The functionality of intronic EPHX2 variants was predicted using the in silico Berkely Drosophila Genome Project software. RESULTS: We found no significant (P >.05) association between the EPHX2 rs4149243, rs2234914 and rs751142 allele, genotype and haplotype and the incidence of T2D and hypertension. Additionally, no association (P >.05) between these EPHX2 genetic variants with the baseline total cholesterol, low- and high-density lipoproteins and triglycerides among both non-diabetic and diabetic volunteers was found. However, we found an inter-ethnic variation (χ2 -test, P value Ë‚ .05) in the allele frequency of the EPHX2 rs4149243 and rs2234914 variants between Jordanians and other ethnic populations. Also, the in silico Berkely Drosophila Genome Project software predicted that the intronic EPHX2 rs4149243 could alter the splicing of intron 7. CONCLUSIONS: It can be concluded from this study that EPHX2 rs4149243, rs2234914 and rs751142 genetic variants do not play a role in the development of T2D and hypertension among Jordanian T2D patients. Further genetic studies with larger sample sizes are needed to find out the association of other functional EPHX2 variants with cardiovascular diseases among T2D patients in Jordan.


Asunto(s)
Diabetes Mellitus Tipo 2 , Epóxido Hidrolasas , Diabetes Mellitus Tipo 2/genética , Epóxido Hidrolasas/genética , Predisposición Genética a la Enfermedad , Genotipo , Haplotipos , Humanos , Jordania , Polimorfismo de Nucleótido Simple/genética
4.
Molecules ; 25(21)2020 Oct 29.
Artículo en Inglés | MEDLINE | ID: mdl-33138197

RESUMEN

The new coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has recently put the world under stress, resulting in a global pandemic. Currently, there are no approved treatments or vaccines, and this severe respiratory illness has cost many lives. Despite the established antimicrobial and immune-boosting potency described for honey, to date there is still a lack of evidence about its potential role amid COVID-19 outbreak. Based on the previously explored antiviral effects and phytochemical components of honey, we review here evidence for its role as a potentially effective natural product against COVID-19. Although some bioactive compounds in honey have shown potential antiviral effects (i.e., methylglyoxal, chrysin, caffeic acid, galangin and hesperidinin) or enhancing antiviral immune responses (i.e., levan and ascorbic acid), the mechanisms of action for these compounds are still ambiguous. To the best of our knowledge, this is the first work exclusively summarizing all these bioactive compounds with their probable mechanisms of action as antiviral agents, specifically against SARS-CoV-2.


Asunto(s)
Antivirales/uso terapéutico , Betacoronavirus/efectos de los fármacos , Infecciones por Coronavirus/tratamiento farmacológico , Miel/análisis , Fitoquímicos/farmacología , Neumonía Viral/tratamiento farmacológico , Animales , COVID-19 , Predicción , Humanos , Factores Inmunológicos/uso terapéutico , Pandemias , Fitoquímicos/aislamiento & purificación , SARS-CoV-2 , Tratamiento Farmacológico de COVID-19
5.
Int J Mol Sci ; 20(15)2019 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-31357721

RESUMEN

Combinatorial therapeutic strategies using siRNA and small molecules to eradicate tumors are emerging. Targeting multiple signaling pathways decreases the chances of cancer cells switching and adapting new signaling processes that may occur when using a single therapeutic modality. Aberrant functioning of Notch-1, Wnt/ß-catenin, and STAT3 proteins and their crosstalk signaling pathways have been found to be involved in tumor survival, drug resistance, and relapse. In the current study, we describe a therapeutic potential of single and combinations of siRNA designed for silencing Notch-1, Wnt/ß-catenin, and STAT3 in MCF7_DoxS (wild type) and MCF7_DoxR (doxorubicin resistant) breast cancer cells. The MCF7_DoxR cells were developed through treatment with a gradual increase in doxorubicin concentration, the expression of targeted genes was investigated, and the expression profiling of CD44/CD24 of the MCF7_DoxS and MCF7_DoxR cells were detected by flow cytometry. Both MCF7_DoxS and MCF7_DoxR breast cancer cells were treated with single and combinations of siRNA to investigate synergism and were analyzed for their effect on cell proliferation with and without doxorubicin treatment. The finding of this study showed the overexpression of targeted genes and the enrichment of the CD44-/CD24+ phenotype in MCF7_DoxR cells when compared to MCF7_DoxS cells. In both cell lines, the gene silencing efficacy showed a synergistic effect when combining STAT3/Notch-1 and STAT3/Notch-1/ß-catenin siRNA. Interestingly, the chemosensitivity of MCF7_DoxS and MCF7_DoxR cells to doxorubicin was increased when combined with siRNA treatment. Our study shows the possibility of using single and combinations of siRNA to enhance the chemosensitivity of cancer cells to conventional antitumor chemotherapy.


Asunto(s)
Neoplasias de la Mama/tratamiento farmacológico , Receptor Notch1/genética , Factor de Transcripción STAT3/genética , beta Catenina/genética , Apoptosis/efectos de los fármacos , Neoplasias de la Mama/genética , Neoplasias de la Mama/patología , Antígeno CD24/genética , Proliferación Celular/efectos de los fármacos , Doxorrubicina/efectos adversos , Doxorrubicina/farmacología , Resistencia a Antineoplásicos/genética , Femenino , Silenciador del Gen/efectos de los fármacos , Humanos , Receptores de Hialuranos/genética , Células MCF-7 , Recurrencia Local de Neoplasia/tratamiento farmacológico , Recurrencia Local de Neoplasia/genética , Recurrencia Local de Neoplasia/patología , ARN Interferente Pequeño/antagonistas & inhibidores , ARN Interferente Pequeño/genética , ARN Interferente Pequeño/farmacología , Factor de Transcripción STAT3/antagonistas & inhibidores , beta Catenina/antagonistas & inhibidores
6.
Medicina (Kaunas) ; 55(9)2019 Aug 26.
Artículo en Inglés | MEDLINE | ID: mdl-31454983

RESUMEN

Background and Objectives: This study aimed to investigate the possible association between exclusive breastfeeding duration during early infancy and susceptibility to allergy and influenza in adulthood. Furthermore, we also investigated the association of breastfeeding duration with DNA methylation at two sites in the promoter of the toll-like receptor-1 (TLR1) gene, as well as the association between DNA methylation of the toll-like receptor-1 (TLR1) gene and susceptibility to different diseases. Materials and Methods: Blood samples were collected from 100 adults and classified into two groups according to breastfeeding duration (<6 months and ≥6 months) during infancy. Subjects were asked to complete a questionnaire on their susceptibilities to different diseases and sign a consent form separately. Fifty-three samples underwent DNA extraction, and the DNA samples were divided into two aliquots, one of which was treated with bisulfite reagent. The promoter region of the TLR1 gene was then amplified by polymerase chain reaction (PCR) and sequenced. Results: We found a significant association between increased breastfeeding duration and a reduction in susceptibility to influenza and allergy, as well asa significant reduction in DNA methylation within the promoter of the TLR1 gene. No association was found between DNA methylation and susceptibility to different diseases. Conclusions: The findings demonstrate the significance of increased breastfeeding duration for improved health outcomes at the gene level.


Asunto(s)
Lactancia Materna/psicología , Susceptibilidad a Enfermedades/psicología , Hipersensibilidad/psicología , Gripe Humana/psicología , Receptor Toll-Like 1/análisis , Adolescente , Adulto , Lactancia Materna/métodos , Lactancia Materna/estadística & datos numéricos , Distribución de Chi-Cuadrado , Estudios Transversales , Metilación de ADN/fisiología , Susceptibilidad a Enfermedades/epidemiología , Femenino , Predisposición Genética a la Enfermedad , Humanos , Hipersensibilidad/epidemiología , Gripe Humana/epidemiología , Masculino , Proyectos Piloto , Reacción en Cadena de la Polimerasa/métodos , Factores de Tiempo , Receptor Toll-Like 1/sangre
7.
J Chem Inf Model ; 58(4): 879-893, 2018 04 23.
Artículo en Inglés | MEDLINE | ID: mdl-29529367

RESUMEN

We previously combined molecular dynamics (classical or simulated annealing) with ligand-receptor contacts analysis as a means to extract valid pharmacophore model(s) from single ligand-receptor complexes. However, molecular dynamics methods are computationally expensive and time-consuming. Here we describe a novel method for extracting valid pharmacophore model(s) from a single crystallographic structure within a reasonable time scale. The new method is based on ligand-receptor contacts analysis following energy relaxation of a predetermined set of randomly deformed complexes generated from the targeted crystallographic structure. Ligand-receptor contacts maintained across many deformed/relaxed structures are assumed to be critical and used to guide pharmacophore development. This methodology was implemented to develop valid pharmacophore models for PI3K-γ, RENIN, and JAK1. The resulting pharmacophore models were validated by receiver operating characteristic (ROC) analysis against inhibitors extracted from the CHEMBL database. Additionally, we implemented pharmacophores extracted from PI3K-γ to search for new inhibitors from the National Cancer Institute list of compounds. The process culminated in new PI3K-γ/mTOR inhibitory leads of low micromolar IC50s.


Asunto(s)
Descubrimiento de Drogas/métodos , Simulación de Dinámica Molecular , Proteínas/metabolismo , Ligandos , Conformación Proteica , Proteínas/química , Transducción de Señal/efectos de los fármacos , Procesos Estocásticos
8.
J Dairy Sci ; 101(5): 3771-3777, 2018 May.
Artículo en Inglés | MEDLINE | ID: mdl-29501341

RESUMEN

Cancer is a major health problem in many parts of the world. Conventional anticancer treatments are painful, expensive, and unsafe. Therefore, demand is increasing for cancer treatments preferentially in the form of functional foods or nutritional supplements. Kefir, a traditional fermented milk dairy product, has significant antimutagenic and antitumor properties. This research addresses the hypothesis that kefir's anticancer properties are affected by fermentation conditions. Initially, kefir extracts prepared under standard conditions were screened against 7 cancer cell lines using the tetrazolium dye 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide colorimetric assay. Colon cancer and chronic myelogenous leukemia cells were found to be most susceptible to kefir extracts. Subsequently, a factorial design was implemented to assess the effects of 3 fermentation times (24, 48, and 72 h), 3 kefir-to-milk ratios (2, 5, and 10% wt/vol), and 3 fermentation temperatures (4, 25, and 40°C) on kefir's anticancer properties. Remarkably, exploration of the fermentation conditions allowed the anticancer properties of kefir to be enhanced by 5- to 8-fold against susceptible cell lines. Overall, these results demonstrate the possibility of optimizing the anticancer properties of kefir as a functional food in cancer therapy.


Asunto(s)
Antineoplásicos/química , Kéfir/análisis , Leche/química , Animales , Antineoplásicos/farmacología , Bovinos , Línea Celular Tumoral , Supervivencia Celular/efectos de los fármacos , Fermentación , Humanos
9.
J Comput Aided Mol Des ; 30(12): 1149-1163, 2016 12.
Artículo en Inglés | MEDLINE | ID: mdl-27722817

RESUMEN

Ligand-based pharmacophore modeling require relatively long lists of active compounds, while a pharmacophore based on a single ligand-receptor crystallographic structure is often promiscuous. These problems prompted us to combine molecular dynamics (MD) simulation with ligand-receptor contacts analysis as means to develop valid pharmacophore model(s). The particular ligand-receptor complex is allowed to perturb over a few nano-seconds using MD simulation. Subsequently, ligand-receptor contact points (≤2.5 Å) are identified. Ligand-receptor contacts maintained above certain threshold during molecular dynamics simulation are considered critical and used to guide pharmacophore development. We termed this method as Molecular-Dynamics Based Ligand-Receptor Contact Analysis. We implemented this new methodology to develop valid pharmacophore models for check point kinase 1 (Chk1) and beta-secretase 1 (BACE1) inhibitors as case studies. The resulting pharmacophore models were validated by receiver operating characteristic curved analysis against inhibitors obtained from CHEMBL database.


Asunto(s)
Secretasas de la Proteína Precursora del Amiloide/química , Quinasa 1 Reguladora del Ciclo Celular (Checkpoint 1)/química , Secretasas de la Proteína Precursora del Amiloide/antagonistas & inhibidores , Quinasa 1 Reguladora del Ciclo Celular (Checkpoint 1)/antagonistas & inhibidores , Diseño de Fármacos , Humanos , Enlace de Hidrógeno , Ligandos , Simulación de Dinámica Molecular , Unión Proteica , Conformación Proteica , Relación Estructura-Actividad Cuantitativa , Curva ROC , Bibliotecas de Moléculas Pequeñas/química
10.
Parasitol Res ; 115(9): 3345-55, 2016 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-27160331

RESUMEN

Phlebotomine sand flies are the known vectors of Leishmania parasites. New approaches in vaccination against Leishmania have investigated the possibility of integrating Phlebotomus papatasi salivary proteins to enhance the immune response and protect against the transmission of the infection. The aim of the present study was to screen human immune responses to wild sand fly saliva and evaluate immunogenic salivary proteins. Blood samples were collected from donors in control and sand fly infested areas. Antibodies specific for sand fly antigens in donor plasma were probed using immunoblotting. In addition, recall proliferation capability of peripheral blood mononuclear cells (PBMC) was tested after sand fly salivary homogenates stimulation. The significant immunogenic salivary proteins (SPs) identified by immunoblotting were SP28, SP32, and SP36. A specific proliferative response of PBMC after stimulation with sand fly salivary homogenates was evident in donors that have antibody responses against sand fly salivary proteins. Individuals with antibody recognition to a higher number of salivary proteins (i.e., 3 or more SP bands) showed lower PBMC proliferative responses after in vitro stimulation with salivary gland homogenates (SGH) only in the sand fly infested, leishmaniasis free area. Interestingly, the presence of a humoral immune response to many SP antigens inversely correlates with a strong cell-mediated immune response (CMI). It was also noticed that some other heavily expressed antigens, in sand fly salivary homogenate, lack or have weak humoral immune reactivity in exposed individuals. Therefore, considering these antigens alone as CMI activators, without including the immunodominant humoral immune response proteins, needs future investigation.


Asunto(s)
Formación de Anticuerpos , Proteínas de Insectos/inmunología , Leishmaniasis/inmunología , Phlebotomus/inmunología , Proteínas y Péptidos Salivales/inmunología , Adulto , Animales , Femenino , Humanos , Proteínas de Insectos/genética , Leishmania/inmunología , Leishmaniasis/parasitología , Leishmaniasis/prevención & control , Leishmaniasis/transmisión , Leucocitos Mononucleares/inmunología , Masculino , Phlebotomus/genética , Phlebotomus/parasitología , Proteínas y Péptidos Salivales/genética , Vacunas/genética , Vacunas/inmunología , Adulto Joven
11.
Life (Basel) ; 14(2)2024 Jan 28.
Artículo en Inglés | MEDLINE | ID: mdl-38398699

RESUMEN

Human viruses and viruses from animals can cause illnesses in humans after the consumption of contaminated food or water. Contamination may occur during preparation by infected food handlers, during food production because of unsuitably controlled working conditions, or following the consumption of animal-based foods contaminated by a zoonotic virus. This review discussed the recent information available on the general and clinical characteristics of viruses, viral foodborne outbreaks and control strategies to prevent the viral contamination of food products and water. Viruses are responsible for the greatest number of illnesses from outbreaks caused by food, and risk assessment experts regard them as a high food safety priority. This concern is well founded, since a significant increase in viral foodborne outbreaks has occurred over the past 20 years. Norovirus, hepatitis A and E viruses, rotavirus, astrovirus, adenovirus, and sapovirus are the major common viruses associated with water or foodborne illness outbreaks. It is also suspected that many human viruses including Aichi virus, Nipah virus, tick-borne encephalitis virus, H5N1 avian influenza viruses, and coronaviruses (SARS-CoV-1, SARS-CoV-2 and MERS-CoV) also have the potential to be transmitted via food products. It is evident that the adoption of strict hygienic food processing measures from farm to table is required to prevent viruses from contaminating our food.

12.
Pathophysiology ; 30(1): 63-82, 2023 Mar 14.
Artículo en Inglés | MEDLINE | ID: mdl-36976734

RESUMEN

Cells employ a well-preserved physiological stress response mechanism, termed the heat shock response, to activate a certain type of molecular chaperone called heat shock proteins (HSPs). HSPs are activated by transcriptional activators of heat shock genes known as heat shock factors (HSFs). These molecular chaperones are categorized as the HSP70 superfamily, which includes HSPA (HSP70) and HSPH (HSP110) families; the DNAJ (HSP40) family; the HSPB family (small heat shock proteins (sHSPs)); chaperonins and chaperonin-like proteins; and other heat-inducible protein families. HSPs play a critical role in sustaining proteostasis and protecting cells against stressful stimuli. HSPs participate in folding newly synthesized proteins, holding folded proteins in their native conformation, preventing protein misfolding and accumulation, and degrading denatured proteins. Ferroptosis is a recently identified type of oxidative iron-dependent cell demise. It was coined recently in 2012 by Stockwell Lab members, who described a special kind of cell death induced by erastin or RSL3. Ferroptosis is characterized by alterations in oxidative status resulting from iron accumulation, increased oxidative stress, and lipid peroxidation, which are mediated by enzymatic and non-enzymatic pathways. The process of ferroptotic cell death is regulated at multiple, and it is involved in several pathophysiological conditions. Much research has emerged in recent years demonstrating the involvement of HSPs and their regulator heat shock factor 1 (HSF1) in ferroptosis regulation. Understanding the machinery controlling HSF1 and HSPs in ferroptosis can be employed in developing therapeutic interventions for ferroptosis occurrence in a number of pathological conditions. Therefore, this review comprehensively summarized the basic characteristics of ferroptosis and the regulatory functions of HSF1 and HSPs in ferroptosis.

13.
J Biomol Struct Dyn ; 41(8): 3222-3233, 2023 05.
Artículo en Inglés | MEDLINE | ID: mdl-35261335

RESUMEN

Many missense mutations/SNPs of the TCN2 gene (which yield Transcobalamin (TC)) were reported in the literature but no study is available about their effect on binding to vitamin B12(B12) at the structural level experimentally nor computationally. Predict the effect of TC missense mutations/SNPs on binding affinity to B12 and characterize their contacts to B12 at the structural level. TC-B12 binding energy difference from the wildtype (ΔΔGmut) was calculated for 378 alanine scanning mutations and 76 ClinVar missense mutations, repeated on two distinct X-ray structures of holoTC namely 2BB5 and 4ZRP. Destabilizing mutations then went through 100 ns molecular dynamics simulation to study their effect on TC-B12 binding at the structural level employing 2BB5 structure. Out of the studied 454 mutations (378 alanine mutations + 76 ClinVar mutations), 19 were destabilizing representing 17 amino acid locations. Mutation energy results show a neutral effect on B12 binding of several missense SNPs reported in the literature including I23V, G94S, R215W, P259R, S348F, L376S, and R399Q. Compared to the wildtype, all the destabilizing mutations have higher average RMSD-Ligand in the last 25% of the MD simulation trajectories and lower average hydrogen bond count while the other parameters vary. Previously reported TCN2 SNPs with an unknown effect on TC-B12 binding were found to have a neutral effect in the current study based on mutation energy calculations. Also, we reported 17 possible amino acids that destabilize TC-B12 binding upon mutation (four listed in ClinVar) and studied their structural effect computationally.


Asunto(s)
Polimorfismo de Nucleótido Simple , Transcobalaminas , Humanos , Transcobalaminas/genética , Transcobalaminas/metabolismo , Mutación Missense , Alanina/genética , Vitamina B 12/química , Vitamina B 12/metabolismo , Aminoácidos/genética
14.
Mol Inform ; 42(6): e2300022, 2023 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-37222400

RESUMEN

Dual specificity protein kinase threonine/Tyrosine kinase (TTK) is one of the mitotic kinases. High levels of TTK are detected in several types of cancer. Hence, TTK inhibition is considered a promising therapeutic anti-cancer strategy. In this work, we used multiple docked poses of TTK inhibitors to augment training data for machine learning QSAR modeling. Ligand-Receptor Contacts Fingerprints and docking scoring values were used as descriptor variables. Escalating docking-scoring consensus levels were scanned against orthogonal machine learners, and the best learners (Random Forests and XGBoost) were coupled with genetic algorithm and Shapley additive explanations (SHAP) to determine critical descriptors for predicting anti-TTK bioactivity and for pharmacophore generation. Three successful pharmacophores were deduced and subsequently used for in silico screening against the NCI database. A total of 14 hits were evaluated in vitro for their anti-TTK bioactivities. One hit of novel chemotype showed reasonable dose-response curve with experimental IC50 of 1.0 µM. The presented work indicates the validity of data augmentation using multiple docked poses for building successful machine learning models and pharmacophore hypotheses.


Asunto(s)
Neoplasias , Farmacóforo , Humanos , Ligandos , Aprendizaje Automático
15.
J Taibah Univ Med Sci ; 18(3): 600-638, 2023 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-36570799

RESUMEN

Unlike pandemics in the past, the outbreak of coronavirus disease 2019 (COVID-19), which rapidly spread worldwide, was met with a different approach to control and measures implemented across affected countries. The lack of understanding of the fundamental nature of the outbreak continues to make COVID-19 challenging to manage for both healthcare practitioners and the scientific community. Challenges to vaccine development and evaluation, current therapeutic options, convalescent plasma therapy, herd immunity, and the emergence of reinfection and new variants remain the major obstacles to combating COVID-19. This review discusses these challenges in the management of COVID-19 at length and highlights the mechanisms needed to provide better understanding of this pandemic.

16.
J Am Chem Soc ; 134(5): 2644-52, 2012 Feb 08.
Artículo en Inglés | MEDLINE | ID: mdl-22229766

RESUMEN

The condensation of bacteriophage phi29 genomic DNA into its preformed procapsid requires the DNA packaging motor, which is the strongest known biological motor. The packaging motor is an intricate ring-shaped protein/RNA complex, and its function requires an RNA component called packaging RNA (pRNA). Current structural information on pRNA is limited, which hinders studies of motor function. Here, we used site-directed spin labeling to map the conformation of a pRNA three-way junction that bridges binding sites for the motor ATPase and the procapsid. The studies were carried out on a pRNA dimer, which is the simplest ring-shaped pRNA complex and serves as a functional intermediate during motor assembly. Using a nucleotide-independent labeling scheme, stable nitroxide radicals were attached to eight specific pRNA sites without perturbing RNA folding and dimer formation, and a total of 17 internitroxide distances spanning the three-way junction were measured using Double Electron-Electron Resonance spectroscopy. The measured distances, together with steric chemical constraints, were used to select 3662 viable three-way junction models from a pool of 65 billion. The results reveal a similar conformation among the viable models, with two of the helices (H(T) and H(L)) adopting an acute bend. This is in contrast to a recently reported pRNA tetramer crystal structure, in which H(T) and H(L) stack onto each other linearly. The studies establish a new method for mapping global structures of complex RNA molecules, and provide information on pRNA conformation that aids investigations of phi29 packaging motor and developments of pRNA-based nanomedicine and nanomaterial.


Asunto(s)
ARN Viral/química , Marcadores de Spin , Bacteriófagos/química , Dimerización , Modelos Moleculares , Conformación de Ácido Nucleico
17.
J Chem Inf Model ; 52(11): 2983-91, 2012 Nov 26.
Artículo en Inglés | MEDLINE | ID: mdl-23116372

RESUMEN

Fibrils formed by assembly of human islet amyloid polypeptide (hIAPP) are found in most patients with type II diabetes. Structurally, these fibrils are composed of multiple protofilaments and are characterized by extended beta sheets, variable helical twists, and different morphologies. We have previously derived models for the hIAPP protofilament using simulations constrained by data from EPR spectroscopy. In the current work, these models were used as a basis for generating idealized hIAPP protofilaments with symmetrical geometrical properties using a new algorithm, MFIBRIL. We show good agreement of the idealized protofilaments with experimental data for amino acid side chain orientations and geometrical features including the inter-ß sheet distance and the protofilament radius. These idealized protofilaments can be used in MFIBRIL to generate fibril models that may be experimentally testable at the molecular level. MFIBRIL can also be used for building structures of any repetitive molecular assembly starting with a single building block obtained from any source.


Asunto(s)
Algoritmos , Aminoácidos/química , Polipéptido Amiloide de los Islotes Pancreáticos/química , Modelos Moleculares , Simulación por Computador , Diabetes Mellitus Tipo 2/metabolismo , Diabetes Mellitus Tipo 2/patología , Humanos , Pliegue de Proteína , Estructura Secundaria de Proteína
18.
RSC Adv ; 12(17): 10686-10700, 2022 Mar 31.
Artículo en Inglés | MEDLINE | ID: mdl-35424985

RESUMEN

Cdc2-like kinase 4 (CLK4) inhibitors are of potential therapeutic value in many diseases particularly cancer. In this study, we combined extensive ligand-based pharmacophore exploration, ligand-receptor contact fingerprints generated by flexible docking, physicochemical descriptors and machine learning-quantitative structure-activity relationship (ML-QSAR) analysis to investigate the pharmacophoric/binding requirements for potent CLK4 antagonists. Several ML methods were attempted to tie these properties with anti-CLK4 bioactivities including multiple linear regression (MLR), random forests (RF), extreme gradient boosting (XGBoost), probabilistic neural network (PNN), and support vector regression (SVR). A genetic function algorithm (GFA) was combined with each method for feature selection. Eventually, GFA-SVR was found to produce the best self-consistent and predictive model. The model selected three pharmacophores, three ligand-receptor contacts and two physicochemical descriptors. The GFA-SVR model and associated pharmacophore models were used to screen the National Cancer Institute (NCI) structural database for novel CLK4 antagonists. Three potent hits were identified with the best one showing an anti-CLK4 IC50 value of 57 nM.

19.
Mol Med Rep ; 25(6)2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35514310

RESUMEN

Variants in T­box transcription factor 5 (TBX5) can result in a wide phenotypic spectrum, specifically in the heart and the limbs. TBX5 has been implicated in causing non­syndromic cardiac defects and Holt­Oram syndrome (HOS). The present study investigated the underlying molecular etiology of a family with heterogeneous heart defects. The proband had mixed­type total anomalous pulmonary venous return (mixed­type TAPVR), whereas her mother had an atrial septal defect. Genetic testing through trio­based whole­exome sequencing was used to reveal the molecular etiology. A nonsense variant was identified in TBX5 (c.577G>T; p.Gly193*) initially showing co­segregation with a presumably non­syndromic presentation of congenital heart disease. Subsequent genetic investigations and more complete phenotyping led to the correct diagnosis of HOS, documenting the novel association of mixed­type TAPVR with HOS. Finally, protein modeling of the mutant TBX5 protein that harbored this pathogenic nonsense variant (p.Gly193*) revealed a substantial drop in the quantity of non­covalent bonds. The decrease in the number of non­covalent bonds suggested that the resultant mutant dimer was less stable compared with the wild­type protein, consequently affecting the protein's ability to bind DNA. The present findings extended the phenotypic cardiac defects associated with HOS; to the best of our knowledge, this is the first association of mixed­type TAPVR with TBX5. Prior to the current analysis, the molecular association of TAPVR with HOS had never been documented; hence, this is the first genetic investigation to report the association between TAPVR and HOS. Furthermore, it was demonstrated that the null­variants reported in the T­box domain of TBX5 were associated with a wide range of cardiac and/or skeletal anomalies on both the inter­and intrafamilial levels. In conclusion, genetic testing was highlighted as a potentially powerful approach in the prognostication of the proper diagnosis.


Asunto(s)
Cardiopatías Congénitas , Defectos del Tabique Interatrial , Síndrome de Cimitarra , Proteínas de Dominio T Box , Anomalías Múltiples , Femenino , Cardiopatías Congénitas/diagnóstico , Cardiopatías Congénitas/genética , Cardiopatías Congénitas/patología , Defectos del Tabique Interatrial/diagnóstico , Defectos del Tabique Interatrial/genética , Humanos , Deformidades Congénitas de las Extremidades Inferiores , Fenotipo , Síndrome de Cimitarra/genética , Proteínas de Dominio T Box/genética , Deformidades Congénitas de las Extremidades Superiores
20.
Front Mol Biosci ; 9: 865833, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35480890

RESUMEN

Since the ancient times, bee products (i.e., honey, propolis, pollen, bee venom, bee bread, and royal jelly) have been considered as natural remedies with therapeutic effects against a number of diseases. The therapeutic pleiotropy of bee products is due to their diverse composition and chemical properties, which is independent on the bee species. This has encouraged researchers to extensively study the therapeutic potentials of these products, especially honey. On the other hand, amid the unprecedented growth in nanotechnology research and applications, nanomaterials with various characteristics have been utilized to improve the therapeutic efficiency of these products. Towards keeping the bee products as natural and non-toxic therapeutics, the green synthesis of nanocarriers loaded with these products or their extracts has received a special attention. Alginate is a naturally produced biopolymer derived from brown algae, the desirable properties of which include biodegradability, biocompatibility, non-toxicity and non-immunogenicity. This review presents an overview of alginates, including their properties, nanoformulations, and pharmaceutical applications, placing a particular emphasis on their applications for the enhancement of the therapeutic effects of bee products. Despite the paucity of studies on fabrication of alginate-based nanomaterials loaded with bee products or their extracts, recent advances in the area of utilizing alginate-based nanomaterials and other types of materials to enhance the therapeutic potentials of bee products are summarized in this work. As the most widespread and well-studied bee products, honey and propolis have garnered a special interest; combining them with alginate-based nanomaterials has led to promising findings, especially for wound healing and skin tissue engineering. Furthermore, future directions are proposed and discussed to encourage researchers to develop alginate-based stingless bee product nanomedicines, and to help in selecting suitable methods for devising nanoformulations based on multi-criteria decision making models. Also, the commercialization prospects of nanocomposites based on alginates and bee products are discussed. In conclusion, preserving original characteristics of the bee products is a critical challenge in developing nano-carrier systems. Alginate-based nanomaterials are well suited for this task because they can be fabricated without the use of harsh conditions, such as shear force and freeze-drying, which are often used for other nano-carriers. Further, conjunction of alginates with natural polymers such as honey does not only combine the medicinal properties of alginates and honey, but it could also enhance the mechanical properties and cell adhesion capacity of alginates.

SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA