Classification of Membrane Permeability of Drug Candidates: A Methodological Investigation

Evaluation of freeze-dried phenolic extract from cashew apple by-product: Physical properties, in vitro gastric digestion and chemometric analysis of the powders

The aim of this study was to produce powders from the phenolic extract of the cashew by-product using maltodextrin and gum arabic as encapsulating agents to preserve these bioactive compounds and their antioxidative activity. Extraction was assisted by an ultrasound bath to increase the release of the bioactive compounds, resulting in the hydroalcoholic extract from cashew bagasse. The powders were physically and morphologically characterized, and their total phenolics, antioxidant activity and bioaccessibility were evaluated. All parameters were analyzed by chemometrics. In addition, UPLC-HRMS analysis was used to evaluate the phenolic profile of the extracts, revealing that the powders were able to protect some of the original compounds of the extract, such as catechin, the myricetin fraction and quercetin. The powders showed high total phenolic retention capacity, especially maltodextrin (2893.34 ± 20.18 mg GAE/100 g (DW)), which was the encapsulant that preserved the highest content of polyphenols and antioxidant activity after bioaccessibility in comparison to the unencapsulated extract. The powders showed low water activity (<0.2), low moisture (<8%), high solubility (>60 %) and low hygroscopicity (<4%). The SEM analysis showed that lyophilized extract samples resembled broken glass, which is characteristic of the lyophilization process, and in addition to a predominantly amorphous structure as demonstrated by the X-ray diffraction. The extraction and encapsulation of phenolic compounds from the cashew by-product through lyophilization and using maltodextrin and gum arabic as encapsulants enabled their preservation and potential use of these compounds by the nutraceutical or food industry, and can be used as food additive in order to enrich the content of compounds and the antioxidant activity of numerous products.

Development of a bioorthogonal fluorescence-based assay for assessing drug uptake and delivery in bacteria

Bioorthogonal chemistry can facilitate the development of fluorescent probes that can be used to sensitively and specifically detect the presence of biological targets. In this study, such an assay was developed to evaluate the uptake and delivery of antimicrobials into Escherichia coli, building on and extending previous work which utilised more resource intensive LCMS detection. The bacteria were genetically engineered to express streptavidin in the periplasmic or cytoplasmic compartments, which was used to localise a bioorthogonal probe (BCN-biotin). Azido-compounds which are delivered to these compartments react with the localised BCN-biotin–streptavidin in a concentration-dependent manner via a strain-promoted alkyne–azide cycloaddition. The amount of azido-compound taken up by bacteria was determined by quantifying unreacted BCN-biotin–streptavidin via an inverse electron demand Diels–Alder reaction between remaining BCN-biotin and a tetrazine-containing fluorescent dye. Following optimisation and validation, the assay was used to assess uptake of liposome-formulated azide-functionalised luciferin and cefoxitin. The results demonstrated that formulation into cationic liposomes improved the uptake of azide-functionalised compounds into the periplasm of E. coli, providing insight on the uptake mechanism of liposomes in the bacteria. This newly developed bioorthogonal fluorescence plate-reader based assay provides a bioactivity-independent, medium-to-high throughput tool for screening compound uptake/delivery.

Bioorthogonal alkyne–azide and alkyne–tetrazine chemistries were used to assess drug uptake in bacteria. Azido-drug reacts with streptavidin bound alkyne-biotin within bacteria, the remaining unreacted alkyne is then quantified with a tetrazine-dye.

NIR and 1H qNMR methods coupled to chemometrics discriminate the chemotypes of the gastroprotective herb Egletes viscosa

Egletes viscosa is a Brazilian medicinal herb consumed as flower bud tea due to its gastroprotective properties. This plant possesses two essential oil-based chemical varieties: trans-pinocarveyl acetate-rich chemotype A and cis-isopinocarveyl acetate- rich chemotype B. Therefore, we developed two simple, fast and reliable methods for discrimination of E. viscosa chemotypes using NIR and ¹H qNMR spectroscopies combined with the chemometrics tools (iPLS and PLS-DA). Both methods showed high sensitivity, precision and specificity in the cross-validation tests. The NIR method has the advantages of being non-destructive and analyzable by portable devices, enabling its application for field and industrial evaluations. Meanwhile, the ¹H qNMR method allows the quantification of the bioactive components ternatin, tanabalin, and centipedic acid. These aforementioned compounds were found higher in the chemotype A. Accordingly, our methods showed to be complimentary approaches for authenticity and/or quality control of E. viscosa-derived raw materials and herbal products.

Discovery of novel selective inhibitors of Staphylococcus aureus β-ketoacyl acyl carrier protein synthase III

β-Ketoacyl-acyl carrier protein synthase III (KAS III) is a condensing enzyme in bacterial fatty acid synthesis and a potential target while designing novel antibiotics. In our previous report, we discovered the lead compound YKAs3003, which serves as an inhibitor of Escherichia coli KAS III (ecKAS III), and determined a reliable pharmacophore map from in silico screening. In this study, we determined two pharmacophore maps from receptor-oriented pharmacophore-based in silico screening of the x-ray structure of Staphylococcus aureus KAS III (saKAS III) to identify potent saKAS III inhibitors. We discovered a new potential inhibitor (6) with broad-spectrum antimicrobial activity and 0.8 nM binding affinity for saKAS III, proving the reliability of our pharmacophore map. Using optimization procedures, we identified three new antimicrobial saKAS III inhibitors: 6c (2,4-dichloro-benzoic acid (2,3,4-trihydroxy-benzylidene)-hydrazide), 6e (4-[(3-chloro-pyrazin-2-yl)-hydrazonomethyl]-benzene-1,3-diol), and 6 (4-[(5-trifluoromethyl-pyridin-2-yl)-hydrazonomethyl]-benzene-1,3-diol). All three inhibitors have a novel 4-hydrazonomethyl-benzene-1,3-diol core structure. These inhibitors exhibited high binding affinity to saKAS III and highly selective antimicrobial activities against S. aureus and methicillin-resistant S. aureus, with minimal inhibitory concentration values of 1-2 μg/mL.

Antimicrobial natural products as beta-ketoacyl-acyl carrier protein synthase III inhibitors

Beta-ketoacyl-acyl carrier protein synthase III (KAS III) initiates bacterial fatty acid biosynthesis, making it one of the most promising condensing enzymes. In a previous study, we developed three pharmacophore maps from receptor-oriented pharmacophore-based in silico screening and proposed a potent antimicrobial inhibitor for KAS III. Using these pharmacophore maps, we examined a natural product database and chose 4 natural compounds as possible KAS III inhibitors. Here, we propose that YKAF01 (3,6-dihydroxyflavone) and YKAF04, 3-(4-hydroxyphenyl)-1-(2,4,6-tri-hydroxyphenyl)propan-1-one (or 4,2',4',6'-tetra-hydroxychalcone, phloretin) are potent antimicrobial inhibitors of KAS III with high binding affinity. In particular, these compounds display an excellent antimicrobial effect against Staphylococcus aureus and MRSA in the range of 16-32 microM.

Novel E. coli beta-ketoacyl-acyl carrier protein synthase III inhibitors as targeted antibiotics

Beta-ketoacyl-acyl carrier protein synthase (KAS) III is a condensing enzyme that initiates fatty acid biosynthesis in most bacteria. We determined three pharmacophore maps from receptor-oriented pharmacophore-based in silico screening of the X-ray structure of Escherichia coli KAS III (ecKAS III) and choose 16 compounds as candidate ecKAS III inhibitors. Binding inhibitors were characterized using saturation-transfer difference NMR spectroscopy (STD-NMR), and binding constants were determined with fluorescence quenching experiments. Based on the results, we propose that the antimicrobial compound, 4-cyclohexyliminomethyl-benzene-1,3-diol (YKAs3003), is a potent inhibitor of pathogenic KAS III, displaying minimal inhibitory concentration (MIC) values in the range 128-256 microg/mL against various bacteria.

In Silico Prediction of Cytochrome P450 2D6 and 3A4 Inhibition Using Gaussian Kernel Weighted k-Nearest Neighbor and Extended Connectivity Fingerprints, Including Structural Fragment Analysis of Inhibitors versus Noninhibitors

Inhibition of cytochrome P450 (CYP) enzymes is unwanted because of the risk of severe side effects due to drug-drug interactions. We present two in silico Gaussian kernel weighted k-nearest neighbor models based on extended connectivity fingerprints that classify CYP2D6 and CYP3A4 inhibition. Data used for modeling consisted of diverse sets of 1153 and 1382 drug candidates tested for CYP2D6 and CYP3A4 inhibition in human liver microsomes. For CYP2D6, 82% of the classified test set compounds were predicted to the correct class. For CYP3A4, 88% of the classified compounds were correctly classified. CYP2D6 and CYP3A4 inhibition were additionally classified for an external test set on 14 drugs, and multidimensional scaling plots showed that the drugs in the external test set were in the periphery of the training sets. Furthermore, fragment analyses were performed and structural fragments frequent in CYP2D6 and CYP3A4 inhibitors and noninhibitors are presented.