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1.
Biochim Biophys Acta Gen Subj ; 1868(5): 130583, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38360076

RESUMO

Antimicrobial peptides (AMP) represent an alternative in the treatment of fungal infections associated with countless deaths. Here, we report a new AMP, named KWI-19, which was designed based on a peptide encrypted in the sequence of an Inga laurina Kunitz-type inhibitor (ILTI). KWI-19 inhibited the growth of Candida species and acted as a fungicidal agent from 2.5 to 20 µmol L-1, also showing synergistic activity with amphotericin B. Kinetic assays showed that KWI-19 killed Candida tropicalis cells within 60 min. We also report the membrane-associated mechanisms of action of KWI-19 and its interaction with ergosterol. KWI-19 was also characterized as a potent antibiofilm peptide, with activity against C. tropicalis. Finally, non-toxicity was reported against Galleria mellonella larvae, thus strengthening the interest in all the bioactivities mentioned above. This study extends our knowledge on how AMPs can be engineered from peptides encrypted in larger proteins and their potential as candicidal agents.


Assuntos
Antifúngicos , Candida , Animais , Antifúngicos/farmacologia , Anfotericina B/farmacologia , Peptídeos/farmacologia , Candida tropicalis , Inibidores de Proteases , Peptídeo Hidrolases
2.
Arch Biochem Biophys ; 753: 109884, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38218361

RESUMO

The spread of fungi resistant to conventional drugs has become a threatening problem. In this context, antimicrobial peptides (AMPs) have been considered as one of the main alternatives for controlling fungal infections. Here, we report the antifungal and antibiofilm activity and some clues about peptide RQ18's mechanism of action against Candida and Cryptococcus. This peptide inhibited yeast growth from 2.5 µM and killed all Candida tropicalis cells within 2 h incubation. Moreover, it showed a synergistic effect with antifungal agent the amphotericin b. RQ18 reduced biofilm formation and promoted C. tropicalis mature biofilms eradication. RQ18's mechanism of action involves fungal cell membrane damage, which was confirmed by the results of RQ18 in the presence of free ergosterol in the medium and fluorescence microscopy by Sytox green. No toxic effects were observed in murine macrophage cell lines and Galleria mellonella larvae, suggesting fungal target selectivity. Therefore, peptide RQ18 represents a promising strategy as a dual antifungal and antibiofilm agent that contributes to infection control without damaging mammalian cells.


Assuntos
Anfotericina B , Antifúngicos , Animais , Camundongos , Antifúngicos/farmacologia , Anfotericina B/farmacologia , Peptídeos/farmacologia , Candida tropicalis , Biofilmes , Testes de Sensibilidade Microbiana , Mamíferos
3.
Phys Chem Chem Phys ; 25(35): 23885-23893, 2023 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-37642522

RESUMO

Amyloids are cytotoxic protein aggregates that deposit in human tissues, leading to several health disorders. Their aggregates can also exhibit catalytic properties, and they have been used as candidates for the development of functional biomaterials. Despite being polymorphic, amyloids often assemble as cross-ß fibrils formed by in-register ß sheet layers. Recent studies of some amyloidogenic protein segments revealed that they crystallize as antiparallel out-of-register ß sheets. Such arrangement has been proposed to be responsible for the cytotoxicity in amyloid diseases, however, there is still no consensus on the molecular mechanism. Interestingly, two amyloidogenic peptide segments, NFGAILS and FGAILSS, arrange into out-of-register and in-register ß sheets, respectively, even though they solely differ by one aminoacid residue at both termini. In this work, we used density functional theory (DFT) to address how the strand register contributes into the packing and molecular properties of the NFGAILS and FGAILSS crystals. Our results show that the out-of-register structure is substantially more stable, at 0 K, than the in-register one due to stronger inter-strand contacts. Based on an analysis of the electrostatic potential of the crystal slabs, it is suggested that the out-of-register may potentially interact with negatively charged groups, like those found in cell membranes. Moreover, calculated reactivity descriptors indicate a similar outcome, where only the out-of-register peptide exhibits intrinsic reactive surface sites at the exposed amine and carboxylic groups. It is therefore suggested that the out-of-register arrangement may indeed be crucial for amyloid cytotoxicity. The findings presented here could help to further our understanding of amyloid aggregation, function, and toxicity.


Assuntos
Amiloide , Peptídeos , Humanos , Proteínas Amiloidogênicas , Aminas , Aminoácidos
4.
Artigo em Espanhol | LILACS, CUMED | ID: biblio-1449915

RESUMO

La telemedicina, a través del uso de plataformas de videoconferencias por Internet, se encuentra cada vez más extendida en Chile, debido a la pandemia de COVID-19 y las restricciones para controlar el virus. El nutricionista no es ajeno a esta situación y ha tenido que modificar las consultas para dar respuesta a esta nueva realidad. Sin embargo, no existe suficiente información respecto al nivel de satisfacción de los usuarios de la telemedicina, que emplea este profesional. El objetivo de la investigación fue describir la percepción de la satisfacción usuaria relacionada con las consultas nutricionales mediante la telemedicina, realizadas durante la pandemia. Se realizó un estudio observacional, descriptivo y transversal. Se reclutaron 62 pacientes de Santiago de Chile, quienes fueron atendidos en una consulta nutricional por videoconferencia. Se diseñó un cuestionario online constituido por seis ítems para determinar la aceptabilidad de la consulta nutricional por telemedicina. El rol del nutricionista en la consulta nutricional por videoconferencia tuvo un grado de satisfacción superior al 70 por cientoEl 62,9 por ciento de los encuestados prefiere que la consulta nutricional sea combinada. Solo el 50 por ciento señala que la plataforma de videoconferencia zoom favorece la relación nutricionista-paciente. La consulta nutricional por telemedicina permite controlar el estado nutricional del paciente sin necesidad de asistir de manera presencial, lo que mejora el acceso a la atención. Existe un nivel elevado de aceptación por parte de los pacientes que han recibido atención nutricional por telemedicina(AU)


Telemedicine, through the use of Internet videoconferencing platforms, is increasingly widespread in Chile, as a consequence of the COVID-19 pandemic and the restrictions to control the virus. The nutritionist is no stranger to this situation and has had to modify consultations to respond to this new reality. However, there is insufficient information regarding the level of satisfaction of telemedicine users employed by this professional. The objective of the research was to describe the perception of user satisfaction related to nutritional consultations through telemedicine, carried out during the pandemic. An observational, descriptive and cross-sectional study was developed. Sixty-two patients were recruited from Santiago, Chile, who were attended in a nutritional consultation by videoconference. An online questionnaire consisting of six items was designed to determine the acceptability of the nutritional consultation by telemedicine. The role of the nutritionist in the nutritional consultation by videoconference had a degree of satisfaction higher than 70percen. 62.9percentof the respondents prefer the nutritional consultation to be combined. Only 50percent indicated that the zoom videoconferencing platform favors the nutritionist-patient relationship. The telemedicine nutritional consultation makes it possible to monitor the patient's nutritional status without the need to attend in person, which improves access to care. There is a high level of acceptance by patients who have received nutritional care via telemedicine(AU)


Assuntos
Humanos , Masculino , Feminino , Satisfação do Paciente , Telemedicina/métodos , Consulta Remota/métodos , Comunicação por Videoconferência , Nutricionistas
5.
Eur J Pediatr Surg ; 32(3): 258-262, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33378778

RESUMO

INTRODUCTION: Hepatobiliary scintigraphy (HS) is a noninvasive imaging technique whose use in the follow-up of liver transplantation has not been duly documented. The main objective of this study is to describe the experience of using this technique to detect biliary complications in pediatric patients following liver transplantation. MATERIALS AND METHODS: A retrospective, observational, and descriptive study involving 86 pediatric patients who had undergone liver transplantation between 2013 and 2018. Of the 86, 31 had undergone at least one HS during their postoperative period. RESULTS: A total of 45 studies were performed on 31 patients (36% of the patients undergoing transplantation during that time period). Patient ages ranged from 5 to 204 months (mean = 50 months). A total of 22 transplants (71%) were from living donors and 9 (29%) were from cadaveric donors. Of the 45 studies, 22 were positive for biliary complications, and all of them had an impact on clinical decision-making. The remaining 23 studies were negative. Of these 23, 19 continued under medical treatment and the other four underwent an additional intervention with positive surgical outcomes in all cases. All scintigraphy studies revealed hepatocellular dysfunction and cholestasis. CONCLUSION: The HS is a useful, noninvasive, and diagnostic procedure for the early diagnosis of biliary complications that may impact the evolution of disease in liver transplant patients. It allows the treating physician to make a more informed decision regarding expectant management, surgical management, or a less invasive course of action for transplantation complications.


Assuntos
Sistema Biliar , Transplante de Fígado , Sistema Biliar/diagnóstico por imagem , Criança , Humanos , Transplante de Fígado/efeitos adversos , Doadores Vivos , Complicações Pós-Operatórias/diagnóstico por imagem , Complicações Pós-Operatórias/etiologia , Cintilografia , Estudos Retrospectivos
6.
J Cell Physiol ; 237(2): 1547-1560, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-34779505

RESUMO

Large-pore channels, including those formed by connexin, pannexin, innexin proteins, are part of a broad family of plasma membrane channels found in vertebrates and invertebrates, which share topology features. Despite their relevance in parasitic diseases such as Chagas and malaria, it was unknown whether these large-pore channels are present in unicellular organisms. We identified 14 putative proteins in Trypanosomatidae parasites as presumptive homologs of innexin proteins. All proteins possess the canonical motif of the innexin family, a pentapeptide YYQWV, and 10 of them share a classical membrane topology of large-pore channels. A sequence similarity network analysis confirmed their closeness to innexin proteins. A bioinformatic model showed that a homolog of Trypanosoma cruzi (T. cruzi) could presumptively form a stable octamer channel with a highly positive electrostatic potential in the internal cavities and extracellular entrance due to the notable predominance of residues such as Arg or Lys. In vitro dye uptake assays showed that divalent cations-free solution increases YO-PRO-1 uptake and hyperosmotic stress increases DAPI uptake in epimastigotes of T. cruzi. Those effects were sensitive to probenecid. Furthermore, probenecid reduced the proliferation and transformation of T. cruzi. Moreover, probenecid or carbenoxolone increased the parasite sensitivity to antiparasitic drugs commonly used in therapy against Chagas. Our study suggests the existence of innexin homologs in unicellular organisms, which could be protein subunits of new large-pore channels in unicellular organisms.


Assuntos
Parasitos , Trypanosoma cruzi , Trypanosomatina , Animais , Conexinas/metabolismo , Parasitos/metabolismo , Probenecid/farmacologia , Trypanosoma cruzi/genética , Trypanosoma cruzi/metabolismo , Trypanosomatina/metabolismo
7.
Front Cell Dev Biol ; 10: 1094362, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36699007

RESUMO

Plasma membrane ionic channels selectively permeate potassium, sodium, calcium, and chloride ions. However, large-pore channels are permeable to ions and small molecules such as ATP and glutamate, among others. Large-pore channels are structures formed by several protein families with little or no evolutionary linkages including connexins (Cxs), pannexins (Panxs), innexin (Inxs), unnexins (Unxs), calcium homeostasis modulator (CALHMs), and Leucine-rich repeat-containing 8 (LRRC8) proteins. Large-pore channels are key players in inflammatory cell response, guiding the activation of inflammasomes, the release of pro-inflammatory cytokines such as interleukin-1 beta (IL-1ß), and the release of adenosine-5'-triphosphate (ATP), which is considered a danger signal. This review summarizes our current understanding of large-pore channels and their contribution to inflammation induced by microorganisms, virulence factors or their toxins.

8.
Int J Psychol Res (Medellin) ; 15(2): 10-21, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-37274514

RESUMO

Given the complete lack of instruments in Chile to measure the phenomenon of the sexual double standard (SDS), this study aimed to evaluate the psychometric properties of the sexual double standard scale (DSS). The sample contained 1036 university students from central and southern Chile. 61.1% (n = 633) were women, the average age was 20.4 years, and 31.7% (n = 259) identified as atheist or agnostic. The DSS demonstrated a unidimensional structure, excellent reliability, and evidence of convergent and discriminant validity: the higher the score in SDS, the greater the stereotypical attitudes about gender and the lower the transcendent attitudes. The religious participants obtained higher mean scores on the DSS and men obtained significantly higher SDS scores than women. In addition, the group of participants with extreme stereotypical attitudes obtained significantly higher scores on the DSS than the extreme transcendent attitudes group, in both men and women samples. Based on the evidence that links the SDS with sexual functioning and satisfaction, risky sexual practices, sexual aggression and victimization, and intimate partner violence, the DSS stands out as a contribution to the development of sex-affective education programs and the identification of individuals and groups at risk.


Ante la ausencia de instrumentos en Chile para medir el fenómeno del Doble Estándar Sexual (SDS), el presente estudio tuvo como objetivo evaluar las propiedades psicométricas de la Escala de Doble Estándar Sexual (DSS). La muestra se compuso de 1036 personas universitarias del centro y sur de Chile. El 61.1% (n = 633) fueron mujeres, la edad promedio fue de 20.4 años y un 31.7% (n = 259) se identificó como ateo o agnóstico. Mediante análisis factorial confirmatorio, la DSS obtuvo una estructura unidimensional en la muestra de estudio, un α Ordinal = .918, y evidencias de validez convergente y discriminante: a mayor puntuación en SDS, mayores actitudes estereotipadas sobre el género y menores actitudes trascendentes. Los participantes religiosos obtuvieron puntuaciones medias más altas en la DSS y los hombres obtuvieron puntajes de SDS significativamente mayores que los de las mujeres. Además, tanto en el caso de los hombres como en el de las mujeres, el grupo de participantes con actitudes estereotipadas extremas obtuvo puntuaciones significativamente más elevadas en DSS que el grupo participante con actitudes trascendentes extremas. Con base en la evidencia que asocia el SDS con el funcionamiento y satisfacción sexual, prácticas sexuales de riesgo, la agresión y victimización sexual, y la violencia en relaciones de pareja, la DSS se distingue como un aporte para el desarrollo de programas educativos sexoafectivos y la identificación de individuos y grupos de riesgo.

9.
Biochim Biophys Acta Mol Basis Dis ; 1867(10): 166188, 2021 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-34102257

RESUMO

The proteins connexins, innexins, and pannexins are the subunits of non-selective channels present in the cell membrane in vertebrates (connexins and pannexins) and invertebrates (innexins). These channels allow the transfer of ions and molecules across the cell membrane or, and in many cases, between the cytoplasm of neighboring cells. These channels participate in various physiological processes, particularly under pathophysiological conditions, such as bacterial, viral, and parasitic infections. Interestingly, some anti-parasitic drugs also block connexin- or pannexin-formed channels. Their effects on host channels permeable to molecules that favor parasitic infection can further explain the anti-parasitic effects of some of these compounds. In this review, the effects of drugs with known anti-parasitic activity that modulate non-selective channels formed by connexins or pannexins are discussed. Previous studies that have reported the presence of these proteins in worms, ectoparasites, and protozoa that cause parasitic infections have also been reviewed.


Assuntos
Antiparasitários/farmacologia , Conexinas/metabolismo , Parasitos/efeitos dos fármacos , Animais , Junções Comunicantes/efeitos dos fármacos , Junções Comunicantes/metabolismo , Humanos , Parasitos/metabolismo
10.
Braz J Infect Dis ; 23(3): 203-206, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31228460

RESUMO

Global dissemination of mcr-like genes represents a serious threat to public health since it jeopardizes the effectiveness of colistin, an antibiotic used as a last-resort treatment against highly antibiotic-resistant bacteria. In 2017, a mcr-1-positive isolate of Escherichia coli was found in Chile for the first time. Herein we report the genetic features of this strain (UCO-457) by whole-genome sequencing (WGS) and conjugation experiments. The UCO-457 strain belonged to ST4204 and carried a 285 kb IncI2-type plasmid containing the mcr-1 gene. Moreover, this plasmid was transferred by conjugation to an E. coli J53 strain at high frequency. The isolate harbored the cma, iroN, and iss virulence genes and did carry resistance genes to trimethoprim/sulfamethoxazole and fluoroquinolones. Other antibiotic resistance determinants such as ß-lactamases-encoding genes were not detected, making the isolate highly susceptible to these antibiotics. Our results revealed that such susceptible isolates could be acting as platforms to disseminate plasmid-mediated colistin resistance. Based on this evidence, we consider that mcr-like prevalence deserves urgent attention and should be examined not only in highly resistant bacteria but also in susceptible isolates.


Assuntos
Infecções por Escherichia coli/microbiologia , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Antibacterianos/farmacologia , Chile , Testes de Sensibilidade a Antimicrobianos por Disco-Difusão , Escherichia coli/efeitos dos fármacos , Humanos , Pacientes Ambulatoriais
11.
Braz. j. infect. dis ; 23(3): 203-206, May-June 2019. graf
Artigo em Inglês | LILACS | ID: biblio-1039226

RESUMO

ABSTRACT Global dissemination of mcr-like genes represents a serious threat to public health since it jeopardizes the effectiveness of colistin, an antibiotic used as a last-resort treatment against highly antibiotic-resistant bacteria. In 2017, a mcr-1-positive isolate of Escherichia coli was found in Chile for the first time. Herein we report the genetic features of this strain (UCO-457) by whole-genome sequencing (WGS) and conjugation experiments. The UCO-457 strain belonged to ST4204 and carried a 285 kb IncI2-type plasmid containing the mcr-1 gene. Moreover, this plasmid was transferred by conjugation to an E. coli J53 strain at high frequency. The isolate harbored the cma, iroN, and iss virulence genes and did carry resistance genes to trimethoprim/sulfamethoxazole and fluoroquinolones. Other antibiotic resistance determinants such as β-lactamases-encoding genes were not detected, making the isolate highly susceptible to these antibiotics. Our results revealed that such susceptible isolates could be acting as platforms to disseminate plasmid-mediated colistin resistance. Based on this evidence, we consider that mcr-like prevalence deserves urgent attention and should be examined not only in highly resistant bacteria but also in susceptible isolates.


Assuntos
Humanos , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Infecções por Escherichia coli/microbiologia , Pacientes Ambulatoriais , Chile , Escherichia coli/efeitos dos fármacos , Testes de Sensibilidade a Antimicrobianos por Disco-Difusão , Antibacterianos/farmacologia
12.
Folia Parasitol (Praha) ; 652018 Sep 14.
Artigo em Inglês | MEDLINE | ID: mdl-30275346

RESUMO

Knowledge of blood parasites in Brazilian chelonians is limited, since they have been recorded in only six species. Mesoclemmys vanderhaegei (Bour) is a freshwater turtle with a wide geographic distribution in Brazil, but there is little information about its natural history. This paper reports on a study of the prevalence and infection intensity of a haemogregarine in two subpopulations of M. vanderhaegei. The study was conducted in two areas of Cerrado in the Upper Paraguay River basin in the state of Mato Grosso, Brazil, between November 2010 and August 2013. Ninety-five (53%) of the 179 turtles captured were positive for haemogregarine parasites. The parasitic forms observed were two morphotypes of intraerythrocytic gametocytes. The prevalence differed between size classes, increasing significantly according to the animals' body size. There was no significant difference between prevalence and sex, or between sampling periods. The mean parasite intensity was 9 parasites/2,000 erythrocytes (0.45%) and the parasite population presented an aggregated distribution, with an aggregation index of 19 and discrepancy of 0.772. This is the first record of a hemoparasite in the freshwater turtle M. vanderhaegei.


Assuntos
Coccidiose/veterinária , Eucoccidiida/fisiologia , Tartarugas , Animais , Brasil/epidemiologia , Coccidiose/epidemiologia , Coccidiose/parasitologia , Feminino , Pradaria , Masculino , Prevalência
13.
PLoS One ; 12(12): e0189213, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-29216268

RESUMO

PDE3s belong to the phosphodiesterases family, where the PDE3A isoform is the major subtype in platelets involved in the cAMP regulation pathway of platelet aggregation. PDE3A inhibitors have been designed as potential antiplatelet agents. In this work, a homology model of PDE3A was developed and used to obtain the binding modes of bicyclic heteroaromatic pyridazinones and pyrazolones. Most of the studied compounds adopted similar orientations within the PDE3A active site, establishing hydrogen bonds with catalytic amino acids. Besides, the structure-activity relationship of the studied inhibitors was described by using a field-based 3D-QSAR method. Different structure alignment strategies were employed, including template-based and docking-based alignments. Adequate correlation models were obtained according to internal and external validations. In general, QSAR models revealed that steric and hydrophobic fields describe the different inhibitory activities of the compounds, where the hydrogen bond donor and acceptor fields have minor contributions. It should be stressed that structural elements of PDE3A inhibitors are reported here, through descriptions of their binding interactions and their differential affinities. In this sense, the present results could be useful in the future design of more specific and potent PDE3A inhibitors that may be used for the treatment of cardiovascular diseases.


Assuntos
Compostos Bicíclicos com Pontes/química , Compostos Bicíclicos com Pontes/farmacologia , Nucleotídeo Cíclico Fosfodiesterase do Tipo 3/efeitos dos fármacos , Inibidores da Fosfodiesterase 3/farmacologia , Pirazolonas/química , Pirazolonas/farmacologia , Piridonas/química , Piridonas/farmacologia , Simulação de Acoplamento Molecular , Relação Quantitativa Estrutura-Atividade
14.
Life Sci ; 186: 59-65, 2017 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-28757415

RESUMO

Peroxisome proliferator-activated receptor γ (PPARγ) is a ligand-activated transcription factor with an important role in lipid metabolism, inflammation and cardiovascular diseases. PPARγ ligands have inhibitory effects on platelet aggregation via the cAMP pathway, which may confer them a protective cardioprotective role. Edaglitazone and Ciglitazone are two chemically-similar thiazolidinedione (TZD) drugs that have been described as potent PPARγ agonists; however, Edaglitazone is over 100 times more potent than Ciglitazone. Here, we report a computational study to describe the ligand binding and the experimental antiplatelet profiles of Edaglitazone and Ciglitazone. Both ligands presented similar orientations within the PPARγ binding site. Their polar heads exhibit complex hydrogen bond networks with the residues at arm I pocket, while their hydrophobic tails are oriented inside arm II or the entrance pocket. The bulkier and longer tail of Edaglitazone exhibited additional hydrophobic interactions, explaining its stronger binding to PPARγ supported by binding affinity calculations. On the other hand, both Edaglitazone and Ciglitazone displayed an antiplatelet activity, but only Edaglitazone retained such effect at low concentrations. Furthermore, we evidenced that Edaglitazone increases intraplatelet cAMP levels and prevents PPARγ secretion, explaining its greater antiplatelet activity. Altogether, the more potent PPARγ agonist Edaglitazone seems to be a potent antiplatelet agent.


Assuntos
Oxazóis/química , PPAR gama/química , Inibidores da Agregação Plaquetária/química , Tiazóis/química , Tiazolidinedionas/química , Sítios de Ligação , Plaquetas/efeitos dos fármacos , Plaquetas/metabolismo , Células Cultivadas , AMP Cíclico/metabolismo , Relação Dose-Resposta a Droga , Voluntários Saudáveis , Humanos , Ligantes , Simulação de Acoplamento Molecular , Estrutura Molecular , Oxazóis/farmacologia , PPAR gama/agonistas , Agregação Plaquetária/efeitos dos fármacos , Inibidores da Agregação Plaquetária/farmacologia , Ligação Proteica , Tiazóis/farmacologia , Tiazolidinedionas/farmacologia
15.
J Comput Aided Mol Des ; 30(9): 707-730, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27565797

RESUMO

We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.


Assuntos
Proteínas de Choque Térmico HSP90/química , Simulação de Acoplamento Molecular , Sítios de Ligação , Entropia , Humanos , Cinética , Ligantes , Ligação Proteica , Conformação Proteica , Solventes/química , Termodinâmica , Água/química
16.
Phys Chem Chem Phys ; 16(27): 14047-58, 2014 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-24901037

RESUMO

A conformational selection method, based on hydrogen bond (Hbond) network analysis, has been designed in order to rationalize the configurations sampled using molecular dynamics (MD), which are commonly used in the estimation of the relative binding free energy of ligands to macromolecules through the MM/GBSA or MM/PBSA method. This approach makes use of protein-ligand complexes obtained from X-ray crystallographic data, as well as from molecular docking calculations. The combination of several computational approaches, like long MD simulations on protein-ligand complexes, Hbond network-based selection by scripting techniques and finally MM/GBSA, provides better statistical correlations against experimental binding data than previous similar reported studies. This approach has been successfully applied in the ranking of several protein kinase inhibitors (CDK2, Aurora A and p38), which present both diverse and related chemical structures.


Assuntos
Algoritmos , Hidrogênio/química , Modelos Químicos , Simulação de Acoplamento Molecular/métodos , Inibidores de Proteínas Quinases/química , Proteínas Quinases/química , Sítios de Ligação , Simulação por Computador , Ligação de Hidrogênio , Ligação Proteica
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