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1.
Mol Microbiol ; 119(4): 439-455, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36708073

RESUMO

The histone-like protein HU plays a diverse role in bacterial physiology from the maintenance of chromosome structure to the regulation of gene transcription. HU binds DNA in a sequence-non-specific manner via two distinct binding modes: (i) random binding to any DNA through ionic bonds between surface-exposed lysine residues (K3, K18, and K83) and phosphate backbone (non-specific); (ii) preferential binding to contorted DNA of given structures containing a pair of kinks (structure-specific) through conserved proline residues (P63) that induce and/or stabilize the kinks. First, we show here that the P63-mediated structure-specific binding also requires the three lysine residues, which are needed for a non-specific binding. Second, we demonstrate that substituting P63 to alanine in HU had no impact on non-specific binding but caused differential transcription of diverse genes previously shown to be regulated by HU, such as those associated with the organonitrogen compound biosynthetic process, galactose metabolism, ribosome biogenesis, and cell adhesion. The structure-specific binding also helps create DNA supercoiling, which, in turn, may influence directly or indirectly the transcription of other genes. Our previous and current studies show that non-specific and structure-specific HU binding appear to have separate functions- nucleoid architecture and transcription regulation- which may be true in other DNA-binding proteins.


Assuntos
Proteínas de Bactérias , Histonas , Histonas/metabolismo , Proteínas de Bactérias/metabolismo , Lisina , Proteínas de Ligação a DNA/metabolismo , DNA/metabolismo , DNA Bacteriano/metabolismo
2.
Int J Mol Sci ; 25(4)2024 Feb 08.
Artigo em Inglês | MEDLINE | ID: mdl-38396756

RESUMO

Immunoassays (IAs) with fluorescence-based detection are already well-established commercialized biosensing methods, such as enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay (LFIA). Immunoassays with surface-enhanced Raman spectroscopy (SERS) detection have received significant attention from the research community for at least two decades, but so far they still lack a wide clinical commercial application. This review, unlike any other review that we have seen, performs a three-dimensional performance comparison of SERS IAs vs. fluorescence IAs. First, we compared the limit of detection (LOD) as a key performance parameter for 30 fluorescence and 30 SERS-based immunoassays reported in the literature. We also compared the clinical performances of a smaller number of available reports for SERS vs. fluorescence immunoassays (FIAs). We found that the median and geometric average LODs are about 1.5-2 orders of magnitude lower for SERS-based immunoassays in comparison to fluorescence-based immunoassays. For instance, the median LOD for SERS IA is 4.3 × 10-13 M, whereas for FIA, it is 1.5 × 10-11 M. However, there is no significant difference in average relative standard deviation (RSD)-both are about 5-6%. The analysis of sensitivity, selectivity, and accuracy reported for a limited number of the published clinical studies with SERS IA and FIA demonstrates an advantage of SERS IA over FIA, at least in terms of the median value for all three of those parameters. We discussed common and specific challenges to the performances of both SERS IA and FIA, while proposing some solutions to mitigate those challenges for both techniques. These challenges include non-specific protein binding, non-specific interactions in the immunoassays, sometimes insufficient reproducibility, relatively long assay times, photobleaching, etc. Overall, this review may be useful for a large number of researchers who would like to use immunoassays, but particularly for those who would like to make improvements and move forward in both SERS-based IAs and fluorescence-based IAs.


Assuntos
Nanopartículas Metálicas , Análise Espectral Raman , Reprodutibilidade dos Testes , Análise Espectral Raman/métodos , Imunoensaio/métodos , Corantes , Ensaio de Imunoadsorção Enzimática , Ouro/química , Nanopartículas Metálicas/química
3.
Proteins ; 91(6): 807-821, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-36629323

RESUMO

Degradation of solid polyethylene terephthalate (PET) by leaf branch compost cutinase (LCC) produces various PET-derived degradation intermediates (DIs), in addition to terephthalic acid (TPA), which is the recyclable terminal product of all PET degradation. Although DIs can also be converted into TPA, in solution, by LCC, the TPA that is obtained through enzymatic degradation of PET, in practice, is always contaminated by DIs. Here, we demonstrate that the primary reason for non-degradation of DIs into TPA in solution is the efficient binding of LCC onto the surface of solid PET. Although such binding enhances the degradation of solid PET, it depletes the surrounding solution of enzyme that could otherwise have converted DIs into TPA. To retain a subpopulation of enzyme in solution that would mainly degrade DIs, we introduced mutations to reduce the hydrophobicity of areas surrounding LCC's active site, with the express intention of reducing LCC's binding to solid PET. Despite the consequent reduction in invasion and degradation of solid PET, overall levels of production of TPA were ~3.6-fold higher, due to the partitioning of enzyme between solid PET and the surrounding solution, and the consequent heightened production of TPA from DIs. Further, synergy between such mutated LCC (F125L/F243I LCC) and wild-type LCC resulted in even higher yields, and TPA of nearly ~100% purity.


Assuntos
Plásticos , Polietilenotereftalatos , Polietilenotereftalatos/metabolismo , Hidrolases/metabolismo
4.
Pharm Res ; 40(1): 215-230, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36473984

RESUMO

OBJECTIVE: There is increasing interest in simultaneous endovascular delivery of more than one drug from a drug-loaded stent into a diseased artery. There may be an opportunity to obtain a therapeutically desirable uptake profile of the two drugs over time by appropriate design of the initial drug distribution in the stent. Due to the non-linear, coupled nature of diffusion and reversible specific/non-specific binding of both drugs as well as competition between the drugs for a fixed binding site density, a comprehensive numerical investigation of this problem is critically needed. METHODS: This paper presents numerical computation of dual drug delivery in a stent-artery system, accounting for diffusion as well as specific and non-specific reversible binding. The governing differential equations are discretized in space, followed by integration over time using a stiff numerical solver. Three different cases of initial dual drug distribution are considered. RESULTS: For the particular case of sirolimus and paclitaxel, results show that competition for a limited non-specific binding site density and the significant difference in the forward/backward reaction coefficients play a key role in determining the nature of drug uptake. The nature of initial distribution of the two drugs in the stent is also found to influence the binding process, which can potentially be used to engineer a desirable dual drug uptake profile. CONCLUSIONS: These results help improve the fundamental understanding of endovascular dual drug delivery. In addition, the numerical technique and results presented here may be helpful for designing and optimizing other drug delivery problems as well.


Assuntos
Stents Farmacológicos , Preparações Farmacêuticas , Stents , Sirolimo , Paclitaxel
5.
Xenobiotica ; 52(8): 943-956, 2022 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-36222269

RESUMO

Non-specific binding in in vitro metabolism systems leads to an underestimation of the true intrinsic metabolic clearance of compounds being studied. Therefore in vitro binding needs to be accounted for when extrapolating in vitro data to predict the in vivo metabolic clearance of a compound. While techniques exist for experimentally determining the fraction of a compound unbound in in vitro metabolism systems, early in drug discovery programmes computational approaches are often used to estimate the binding in the in vitro system.Experimental fraction unbound data (n = 60) were generated in liver microsomes (fumic) from five commonly used pre-clinical species (rat, mouse, dog, minipig, monkey) and humans. Unbound fraction in incubations with mouse, rat or human hepatocytes was determined for the same 60 compounds. These data were analysed to determine the relationship between experimentally determined binding in the different matrices and across different species. In hepatocytes there was a good correlation between fraction unbound in human and rat (r2=0.86) or mouse (r2=0.82) hepatocytes. Similar correlations were observed between binding in human liver microsomes and microsomes from rat, mouse, dog, Göttingen minipig or monkey liver microsomes (r2 of >0.89, n = 51 - 52 measurements in different species). Physicochemical parameters (logP, pKa and logD) were predicted for all evaluated compounds. In addition, logP and/or logD were measured for a subset of compounds.Binding to human hepatocytes predicted using 5 different methods was compared to the measured data for a set of 59 compounds. The best methods evaluated used measured microsomal binding in human liver microsomes to predict hepatocyte binding. The collated physicochemical data were used to predict the human fumic using four different in silico models for a set of 53-60 compounds. The correlation (r2) and root mean square error between predicted and observed microsomal binding was 0.69 & 0.20, 0.47 & 0.23, 0.56 & 0.21 and 0.54 & 0.26 for the Turner-Simcyp, Austin, Hallifax-Houston and Poulin models, respectively. These analyses were extended to include measured literature values for binding in human liver microsomes for a larger set of compounds (n=697). For the larger dataset of compounds, microsomal binding was well predicted for neutral compounds (r2=0.67 - 0.70) using the Poulin, Austin, or Turner-Simcyp methods but not for acidic or basic compounds (r2<0.5) using any of the models. While the lipophilicity-based models can be used, the in vitro binding should be measured for compounds where more certainty is needed, using appropriately calibrated assays and possibly established weak, moderate, and strong binders as reference compounds to allow comparison across databases.


Assuntos
Hepatócitos , Microssomos Hepáticos , Animais , Cães , Humanos , Camundongos , Ratos , Haplorrinos , Hepatócitos/metabolismo , Taxa de Depuração Metabólica , Microssomos Hepáticos/metabolismo , Modelos Biológicos , Suínos , Porco Miniatura , Reprodutibilidade dos Testes
6.
Sensors (Basel) ; 22(11)2022 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-35684716

RESUMO

Label-free biosensors are plagued by the issue of non-specific protein binding which negatively affects sensing parameters such as sensitivity, selectivity, and limit-of-detection. In the current work, we explore the possibility of using the Rayleigh waves in ST-Quartz devices to efficiently remove non-specifically bound proteins via acoustic streaming. A coupled-field finite element (FE) fluid structure interaction (FSI) model of a surface acoustic wave (SAW) device based on ST-Quartz substrate in contact with a liquid loading was first used to predict trends in forces related to SAW-induced acoustic streaming. Based on model predictions, it is found that the computed SAW body force is sufficient to overcome adhesive forces between particles and a surface while lift and drag forces prevent reattachment for a range of SAW frequencies. We further performed experiments to validate the model predictions and observe that the excitation of Rayleigh SAWs removed non-specifically bound (NSB) antigens and antibodies from sensing and non-sensing regions, while rinsing and blocking agents were ineffective. An amplified RF signal applied to the device input disrupted the specific interactions between antigens and their capture antibody as well. ST-quartz allows propagation of Rayleigh and leaky SH-SAW waves in orthogonal directions. Thus, the results reported here could allow integration of three important biosensor functions on a single chip, i.e., removal of non-specific binding, mixing, and sensing in the liquid phase.


Assuntos
Técnicas Biossensoriais , Quartzo , Acústica , Anticorpos , Técnicas Biossensoriais/métodos , Ligação Proteica , Proteínas
7.
Sensors (Basel) ; 22(15)2022 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-35957486

RESUMO

Non-specific binding (NSB) is one of the important issues in biosensing performance. Herein, we designed a strategy for removing non-specific binding including anti-mouse IgG antibody and bovine serum albumin (BSA) by utilizing anisotropic cadmium selenide tetrapods (CdSe TPs) in a vortex flow. The shear force on the tetrapod nanoparticles was increased by controlling the rotation rate of the vortex flow from 0 rpm to 1000 rpm. As a result, photoluminescence (PL) signals of fluorescein (FITC)-conjugated protein, anti-mouse IgG antibody-FITC and bovine serum albumin (BSA)-FITC, were reduced by 35% and 45%, respectively, indicating that NSB can be removed under vortex flow. In particular, simultaneous NSB removal and protein capture can be achieved even with mixture solutions of target antibodies and anti-mouse IgG antibodies by applying cyclic mode vortex flow on anisotropic CdSe TPs. These results demonstrate successfully that NSB can be diminished by rotating CdSe TPs to generate shear force under vortex flow. This study opens up new research protocols for utilization of anisotropic nanoparticles under vortex flow, which increases the feasibility of protein capture and non-specific proteins removal for biosensors.


Assuntos
Compostos de Cádmio , Compostos de Selênio , Fluoresceína-5-Isotiocianato , Imunoglobulina G , Soroalbumina Bovina/metabolismo
8.
Biochem Biophys Res Commun ; 528(3): 493-498, 2020 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-32505345

RESUMO

FLAG-tags are commonly used for protein abundance measurements and for identification of protein-protein interactions in living cells. We have observed that the cholera pathogen Vibrio cholerae encodes a FLAG-antibody-reactive protein and identified this protein as an outer membrane porin, Porin4, which contains a sequence very similar to the 3xFLAG epitope tag. We have demonstrated the binding affinity of the conserved peptide sequence (called Porin 4 tag) in Porin4 against monoclonal anti-FLAG M2 antibody. In addition, we created a porin4 deletion mutant, which can be used for background-less FLAG antibody detection experiments.


Assuntos
Anticorpos Monoclonais/metabolismo , Proteínas de Bactérias/metabolismo , Oligopeptídeos/imunologia , Vibrio cholerae/metabolismo , Marcadores de Afinidade/metabolismo , Sequência de Aminoácidos , Animais , Proteínas de Bactérias/genética , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Camundongos , Mutação , Porinas/genética , Porinas/metabolismo , Ligação Proteica , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Vibrio cholerae/genética , Vibrio cholerae/crescimento & desenvolvimento
9.
Int J Mol Sci ; 22(1)2020 Dec 29.
Artigo em Inglês | MEDLINE | ID: mdl-33383946

RESUMO

Ions play significant roles in biological processes-they may specifically bind to a protein site or bind non-specifically on its surface. Although the role of specifically bound ions ranges from actively providing structural compactness via coordination of charge-charge interactions to numerous enzymatic activities, non-specifically surface-bound ions are also crucial to maintaining a protein's stability, responding to pH and ion concentration changes, and contributing to other biological processes. However, the experimental determination of the positions of non-specifically bound ions is not trivial, since they may have a low residential time and experience significant thermal fluctuation of their positions. Here, we report a new release of a computational method, the BION-2 method, that predicts the positions of non-specifically surface-bound ions. The BION-2 utilizes the Gaussian-based treatment of ions within the framework of the modified Poisson-Boltzmann equation, which does not require a sharp boundary between the protein and water phase. Thus, the predictions are done by the balance of the energy of interaction between the protein charges and the corresponding ions and the de-solvation penalty of the ions as they approach the protein. The BION-2 is tested against experimentally determined ion's positions and it is demonstrated that it outperforms the old BION and other available tools.


Assuntos
Fenômenos Biofísicos , Íons/química , Modelos Teóricos , Proteínas/química , Eletricidade Estática , Algoritmos , Modelos Moleculares , Conformação Proteica , Relação Estrutura-Atividade
10.
Int J Mol Sci ; 21(20)2020 Oct 12.
Artigo em Inglês | MEDLINE | ID: mdl-33053650

RESUMO

The success of antibody therapeutics is strongly influenced by their multifunctional nature that couples antigen recognition mediated by their variable regions with effector functions and half-life extension mediated by a subset of their constant regions. Nevertheless, the monospecific IgG format is not optimal for many therapeutic applications, and this has led to the design of a vast number of unique multispecific antibody formats that enable targeting of multiple antigens or multiple epitopes on the same antigen. Despite the diversity of these formats, a common challenge in generating multispecific antibodies is that they display suboptimal physical and chemical properties relative to conventional IgGs and are more difficult to develop into therapeutics. Here we review advances in the design and engineering of multispecific antibodies with drug-like properties, including favorable stability, solubility, viscosity, specificity and pharmacokinetic properties. We also highlight emerging experimental and computational methods for improving the next generation of multispecific antibodies, as well as their constituent antibody fragments, with natural IgG-like properties. Finally, we identify several outstanding challenges that need to be addressed to increase the success of multispecific antibodies in the clinic.


Assuntos
Anticorpos Biespecíficos/química , Anticorpos Biespecíficos/farmacologia , Anticorpos Monoclonais/química , Anticorpos Monoclonais/farmacologia , Especificidade de Anticorpos , Desenho de Fármacos , Engenharia de Proteínas , Animais , Anticorpos Biespecíficos/genética , Anticorpos Biespecíficos/imunologia , Anticorpos Monoclonais/genética , Anticorpos Monoclonais/imunologia , Afinidade de Anticorpos/imunologia , Especificidade de Anticorpos/imunologia , Fenômenos Químicos , Desenvolvimento de Medicamentos , Estabilidade de Medicamentos , Humanos , Modelos Moleculares , Solubilidade , Relação Estrutura-Atividade
11.
Anal Biochem ; 587: 113446, 2019 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-31545947

RESUMO

The effect of sample containers made of different materials on the MS-based analysis of oligonucleotides remains unknown. Here, we evaluated five types of sample containers on the MS signal stability of oligonucleotide, and they were normal glass insert, silanized glass insert with three different silanization techniques, and polypropylene sample vial. Also, we attempted to tackle signal stability issue by varying modifiers in dissolution solvent. Our results showed that sample containers made of different materials can significantly influence the MS signal stability of oligonucleotide at low concentration. Triethylamine (TEA) evidently improved both the signal stability and intensity of oligonucleotide.


Assuntos
Etilaminas/química , Oligonucleotídeos/análise , Espectrometria de Massas
12.
Nanomedicine ; 20: 102024, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31176045

RESUMO

Therapeutic efficacy of nanoparticle-drug formulations for cancer applications is significantly impacted by the extent of intra-tumoral accumulation and tumor tissue penetration. We advanced the application of surface plasmon resonance to examine interfacial properties of various clinical and emerging nanoparticles related to tumor tissue penetration. We observed that amine-terminated or positively-charged dendrimers and liposomes bound strongly to tumor extracellular matrix (ECM) proteins, whereas hydroxyl/carboxyl-terminated dendrimers and PEGylated/neutrally-charged liposomes did not bind. In addition, poly(lactic-co-glycolic acid) (PLGA) nanoparticles formulated with cholic acid or F127 surfactants bound strongly to tumor ECM proteins, whereas nanoparticles formulated with poly(vinyl alcohol) did not bind. Unexpectedly, following blood serum incubation, this binding increased and particle transport in ex vivo tumor tissues reduced markedly. Finally, we characterized the protein corona on PLGA nanoparticles using quantitative proteomics. Through these studies, we identified valuable criteria for particle surface characteristics that are likely to mediate their tissue binding and tumor penetration.


Assuntos
Nanopartículas/química , Neoplasias/metabolismo , Ressonância de Plasmônio de Superfície , Animais , Transporte Biológico , Proteínas Sanguíneas/metabolismo , Linhagem Celular Tumoral , Dendrímeros/química , Proteínas da Matriz Extracelular/metabolismo , Feminino , Humanos , Lipossomos , Camundongos Nus , Nanopartículas/ultraestrutura , Copolímero de Ácido Poliláctico e Ácido Poliglicólico/química , Ligação Proteica , Coroa de Proteína/química , Propriedades de Superfície , Tensoativos/química
13.
Sensors (Basel) ; 19(18)2019 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-31500397

RESUMO

One challenge for current surface acoustic wave (SAW) biosensors is reducing nonspecific adsorption. A device propagating Rayleigh and shear horizontal surface acoustic waves in orthogonal directions fabricated in ST quartz has the capability of achieving simultaneous detection and nonspecific binding (NSB) protein removal. Current measurement methods for a SAW sensor system based on this device require large-size and expensive equipment such as a vector network analyzer (VNA), signal generator, and frequency counter, which are not suitable for portable, especially point-of-care, applications. In this work, a portable platform based on a direct digital synthesizer (DDS) is investigated for the orthogonal SAW sensor, integrating signal synthesis, gain control, phase/amplitude measurement, and data processing in a small, portable electronic system. This prototype was verified for both stability and repeatability, and the results matched very well with VNA measurements. Finally, system performance in real-time sensing and NSB removal was evaluated.


Assuntos
Técnicas Biossensoriais , Proteínas/isolamento & purificação , Som , Ligação Proteica , Proteínas/química , Propriedades de Superfície
14.
Bioorg Med Chem Lett ; 27(7): 1620-1623, 2017 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-28202328

RESUMO

The present study discovered four novel hyaluronan-degrading enzyme (hyaluronidase) inhibitors including chikusetsusaponins and catechins through the activity-guided separation of Panax japonicus and Prunus salicina, respectively. Although the discovery resulted in identification of usual frequent hitters, subsequent mechanistic characterizations under our DMSO-perturbed assay conditions and related protocols revealed that chikusetusaponin IV would serve as an aggregating and non-specific binding inhibitor, while (-)-epicatechin would interact specifically with enzyme at the catalytic site or more likely at a kind of catechin-binding site with a relatively week inhibitory activity. The latter description might provide a possible explanation for the well-known fact that a series of catechin have been described as frequent hitters in biological assays with a moderate activity. Thus, the present study demonstrated a practical and robust methodology to characterize initial screening hits mechanistically molecule-by-molecule in the early stage of natural product-based drug discovery.


Assuntos
Dimetil Sulfóxido/química , Inibidores Enzimáticos/química , Hialuronoglucosaminidase/antagonistas & inibidores , Panax/química , Prunus domestica/química , Saponinas/química , Animais , Sítios de Ligação , Catequina/química , Bovinos , Descoberta de Drogas , Ensaios Enzimáticos , Inibidores Enzimáticos/isolamento & purificação , Ácido Glicirrízico/química , Hialuronoglucosaminidase/química , Masculino , Octoxinol/química , Extratos Vegetais/farmacologia , Saponinas/isolamento & purificação
15.
Bioorg Med Chem Lett ; 26(13): 3153-3157, 2016 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-27165854

RESUMO

Hyaluronan-degrading enzyme (hyaluronidase) is involved in tumor growth and inflammation, and as such, hyaluronidase inhibitors have received recent attention as potential therapeutics. The previous studies have successfully discovered a wide range of inhibitors, but unfortunately most of them are dissimilar to original ligand hyaluronan and the mode of action is poorly understood. The present study mechanistically characterized these structurally unrelated inhibitors by interpreting the behavior of concentration-response curves under several in vitro assay conditions. Detergent-addition conditions definitely identified aggregation-based inhibitors. Subsequently, DMSO-perturbed conditions, though preliminary, highlighted the inhibitors that might bind to enzyme non-specifically. Here, an intriguing implication of the latter description is that DMSO-perturbed conditions would generate non-productive but not-denatured enzyme that is an assembly of effective species to capture non-specific binding molecules, and thereby would attenuate their inhibitory activities.


Assuntos
Dimetil Sulfóxido/química , Inibidores Enzimáticos/farmacologia , Hialuronoglucosaminidase/antagonistas & inibidores , Sulfatos de Condroitina/síntese química , Sulfatos de Condroitina/química , Sulfatos de Condroitina/farmacologia , Cromolina Sódica/síntese química , Cromolina Sódica/química , Cromolina Sódica/farmacologia , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Flavonoides/síntese química , Flavonoides/química , Flavonoides/farmacologia , Ácido Glicirrízico/síntese química , Ácido Glicirrízico/química , Ácido Glicirrízico/farmacologia , Hialuronoglucosaminidase/metabolismo , Estrutura Molecular , Relação Estrutura-Atividade
16.
Sensors (Basel) ; 16(10)2016 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-27754429

RESUMO

Bisphenol A (BPA) is an estrogen-mimicking chemical that can be selectively detected in water using a chemical sensor based on molecularly imprinted polymers (MIPs). However, the utility of BPA-MIPs in sensor applications is limited by the presence of non-specific binding sites. This study explored a dual approach to eliminating these sites: optimizing the molar ratio of the template (bisphenol A) to functional monomer (methacrylic acid) to cross-linker (ethylene glycol dimethacrylate), and esterifying the carboxylic acid residues outside of specific binding sites by treatment with diazomethane. The binding selectivity of treated MIPs and non-treated MIPs for BPA and several potential interferents was compared by capillary electrophoresis with ultraviolet detection. Baclofen, diclofenac and metformin were demonstrated to be good model interferents to test all MIPs for selective binding of BPA. Treated MIPs demonstrated a significant decrease in binding of the interferents while offering high selectivity toward BPA. These results demonstrate that conventional optimization of the molar ratio, together with advanced esterification of non-specific binding sites, effectively minimizes the residual binding of interferents with MIPs to facilitate BPA sensing.


Assuntos
Compostos Benzidrílicos/química , Impressão Molecular/métodos , Fenóis/química , Polímeros/química , Baclofeno/análise , Baclofeno/química , Compostos Benzidrílicos/análise , Diclofenaco/análise , Diclofenaco/química , Eletroforese Capilar , Metformina/análise , Metformina/química , Fenóis/análise , Poluentes Químicos da Água/análise , Poluentes Químicos da Água/química
17.
J Mol Recognit ; 27(12): 755-62, 2014 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-25319624

RESUMO

Diazomethane (CH(2)N(2)) was used to methylate the non-specific binding sites after molecularly imprinted polymer particles were prepared using methacrylic acid as the functional monomer, ethylene glycol dimethacrylate as the cross-linker and bisphenol A (BPA) as the template. After diazomethane treatment and subsequent removal of BPA by triethylamine, the treated molecularly imprinted polymer (TMIP) particles were tested for binding selectivity toward BPA and other organic compounds by capillary electrophoresis with ultraviolet detection. Even in the presence of compounds that were positively charged, neutral or negatively charged in the background electrolyte, BPA was selectively bound with the highest efficiency. A significant decrease in the affinity for metformin (MF, a positively charged compound), along with (13) C nuclear magnetic resonance spectra and electrophoretic mobility data, provided strong evidence for the elimination of non-specific -COOH binding sites in the TMIP particles. Only 8% of MF and 16% of diclofenac sodium salt (a negatively charged compound) remained as non-specific bindings because of hydrophobic interactions. Further comparison with poly(methyl methacrylate) revealed the true merits of the TMIP, which exhibited minimal non-specific bindings while preserving a high level of specific binding owing to molecular recognition.


Assuntos
Diazometano/química , Impressão Molecular/métodos , Polímeros/química , Compostos Benzidrílicos/química , Sítios de Ligação , Espectroscopia de Ressonância Magnética Nuclear de Carbono-13 , Ácidos Carboxílicos/química , Diclofenaco/química , Eletroforese Capilar , Esterificação , Metformina/química , Metilação , Fenóis/química , Polimetil Metacrilato/química
18.
Artigo em Inglês | MEDLINE | ID: mdl-38761468

RESUMO

In clinical practice, the determination of unbound drug concentration is very important for dose adjustment and toxicity prediction because only the unbound fraction can achieve a pharmacological effect. A fast, sensitive and accurate analytical method of centrifugal ultrafiltration coupled with high performance liquid chromatography-tandem mass spectrometry method was developed and applied to allow the quantification of unbound lenvatinib concentration. The application of linear regression analysis was used to examine the effects of centrifugal force, centrifugal time, and protein content on ultrafiltrate volume (Vu). The results indicated that the centrifugal force and centrifugal time have an influence on Vu that is significantly positive (P < 0.05). This developed method with good linearity (r2 = 0.9996), good accuracy (bias % ≤ 2.24 %), good precision (CV % ≤ 7.10 %), and good recovery (95.46 %-106.46 %) was suitable for routine clinical practice and studies. Particularly, the ultrafiltration membrane had no non-specific binding to lenvatinib. The unbound fractions can be separated in just 15 min. This method was applied to quantify clinical samples and to determine the plasma protein binding and unbound fraction of lenvatinib. This study provides a more effective and promising method for determination of unbound lenvatinib. It could be beneficial to measure the unbound concentration of lenvatinib in personalized medicine and therapeutic drug monitoring in routine clinical practice.


Assuntos
Compostos de Fenilureia , Quinolinas , Espectrometria de Massas em Tandem , Ultrafiltração , Humanos , Compostos de Fenilureia/sangue , Compostos de Fenilureia/farmacocinética , Compostos de Fenilureia/química , Compostos de Fenilureia/análise , Quinolinas/sangue , Quinolinas/química , Quinolinas/farmacocinética , Espectrometria de Massas em Tandem/métodos , Cromatografia Líquida de Alta Pressão/métodos , Ultrafiltração/métodos , Modelos Lineares , Reprodutibilidade dos Testes , Ligação Proteica , Limite de Detecção
19.
Cell Rep ; 43(10): 114801, 2024 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-39392756

RESUMO

Although antibody variable regions mediate antigen-specific binding, they can also mediate non-specific interactions with non-cognate antigens, impacting diverse immunological processes and the efficacy, safety, and half-life of antibody therapeutics. To understand the molecular basis of antibody non-specificity, we sorted two dissimilar human naïve antibody libraries against multiple reagents to enrich for variants with different levels of polyreactivity. Sequence analysis of >300,000 paired antibody variable regions revealed that the heavy chain primarily mediates human antibody polyreactivity, and this is due to the high positive charge, high hydrophobicity, and combinations thereof in the corresponding complementarity-determining regions, which can be predicted using a machine learning model developed in this work. Notably, a subset of the most important features governing antibody non-specific interactions, namely those that contain tyrosine, also govern specific antigen recognition. Our findings are broadly relevant for understanding fundamental aspects of antibody molecular recognition and the applied aspects of antibody-drug design.


Assuntos
Regiões Determinantes de Complementaridade , Cadeias Pesadas de Imunoglobulinas , Humanos , Regiões Determinantes de Complementaridade/imunologia , Cadeias Pesadas de Imunoglobulinas/imunologia , Cadeias Pesadas de Imunoglobulinas/química , Especificidade de Anticorpos , Anticorpos/imunologia , Sequência de Aminoácidos
20.
J Pharm Biomed Anal ; 228: 115306, 2023 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-36868028

RESUMO

Neuromedin U (NmU) and neuromedin S (NmS) are two closely related neuropeptides belonging to the neuromedin family. NmU usually occurs either as a truncated eight amino acid long peptide (NmU-8) or as an 25 amino acid long peptide, although other molecular forms exist depending on the species considered. NmS, on the other hand, is a 36 amino acid long peptide, sharing the same amidated C-terminal heptapeptide with NmU. Nowadays, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is the preferred analytical technique for peptide quantification, because of its excellent sensitivity and selectivity. However, reaching the required quantification limits for these compounds in biological samples remains an extremely challenging task, especially because of their nonspecific binding (NSB). This study highlights the difficulties that are faced when quantifying larger neuropeptides (23-36 amino acids) compared to smaller ones (< 15 amino acids). The first part of this work aims to solve the adsorption problem for NmU-8 and NmS, by investigating the different steps involved in the sample preparation, i.e. the different solvents applied and the pipetting protocol. The addition of 0.05% plasma as an adsorption competitor was found to be primordial to avoid peptide loss due to NSB. The second part of this work focusses on further improving the sensitivity of the LC-MS/MS method for NmU-8 and NmS, by evaluating some UHPLC-parameters, including the stationary phase, the column temperature and the trapping conditions. For both peptides of interest, the best results were achieved when combining a C18 trap column with a C18 iKey separation device containing a positively charged surface. Column temperatures of 35 and 45 °C for NmU-8 and NmS respectively, resulted in the highest peak areas and S/N ratios, while applying higher column temperatures substantially decreased sensitivity. Moreover, a gradient starting at 20% organic modifier instead of 5% significantly improved the peak shape of both peptides. Finally, some compound-specific MS parameters, i.e. the capillary and the cone voltages, were evaluated. The peak areas increased with a factor 2 and 7 for NmU-8 and NmS respectively and peptide detection in the low picomolar range is now feasible.


Assuntos
Neuropeptídeos , Espectrometria de Massas em Tandem , Adsorção , Cromatografia Líquida , Cromatografia Líquida de Alta Pressão , Neuropeptídeos/química
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