Squaramide Formation for DNA-Encoded Library Synthesis.

DNA-encoded libraries (DELs) can be considered as one of the most powerful tools for the discovery of small molecules of biological interest. However, the ability to access large DELs is contingent upon having chemical transformations that work in aqueous phase and generate minimal DNA alterations and the availability of building blocks compatible with on-DNA chemistry. In addition, accessing scaffolds of interest to medicinal chemists can be challenging in a DEL setting because of inherent limitations of DNA-supported chemistry. In this context, a squaramide formation reaction was developed by using a two-step process. The mild and high-yielding reaction tolerates a wide array of functional groups and was shown to be safe for DNA, thereby making this methodology ideal for DELs.

Synthesis and evaluation of NS5A inhibitors containing diverse heteroaromatic cores.

Inhibitors of the HCV NS5A nonstructural protein are showing promising clinical potential in the treatment of hepatitis C when used in combination with other direct-acting antiviral agents. Current NS5A clinical candidates such as daclatasvir, ledipasvir, and ombitasvir share a common pharmacophore that features a pair of (S)-methoxycarbonylvaline capped pyrrolidines linked to various cores by amides, imidazoles and/or benzimidazoles. In this Letter, we describe the evaluation of NS5A inhibitors which contain alternative heteroaromatic replacements for these amide mimetics. The SAR knowledge gleaned in the optimization of scaffolds containing benzoxazoles was parlayed toward the identification of potent NS5A inhibitors containing other heteroaromatic replacements such as indoles and imidazopyridines.

Benzimidazole-containing HCV NS5A inhibitors: effect of 4-substituted pyrrolidines in balancing genotype 1a and 1b potency.

The treatment of HCV with highly efficacious, well-tolerated, interferon-free regimens is a compelling clinical goal. Trials employing combinations of direct-acting antivirals that include NS5A inhibitors have shown significant promise in meeting this challenge. Herein, we describe our efforts to identify inhibitors of NS5A and report on the discovery of benzimidazole-containing analogs with subnanomolar potency against genotype 1a and 1b replicons. Our SAR exploration of 4-substituted pyrrolidines revealed that the subtle inclusion of a 4-methyl group could profoundly increase genotype 1a potency in multiple scaffold classes.

Beneficial 'unintended effects' of a cereal cystatin in transgenic lines of potato, Solanum tuberosum.

BACKGROUND: Studies reported unintended pleiotropic effects for a number of pesticidal proteins ectopically expressed in transgenic crops, but the nature and significance of such effects in planta remain poorly understood. Here we assessed the effects of corn cystatin II (CCII), a potent inhibitor of C1A cysteine (Cys) proteases considered for insect and pathogen control, on the leaf proteome and pathogen resistance status of potato lines constitutively expressing this protein. RESULTS: The leaf proteome of lines accumulating CCII at different levels was resolved by 2-dimensional gel electrophoresis and compared with the leaf proteome of a control (parental) line. Out of ca. 700 proteins monitored on 2-D gels, 23 were significantly up- or downregulated in CCII-expressing leaves, including 14 proteins detected de novo or up-regulated by more than five-fold compared to the control. Most up-regulated proteins were abiotic or biotic stress-responsive proteins, including different secretory peroxidases, wound inducible protease inhibitors and pathogenesis-related proteins. Accordingly, infection of leaf tissues by the fungal necrotroph Botryris cinerea was prevented in CCII-expressing plants, despite a null impact of CCII on growth of this pathogen and the absence of extracellular Cys protease targets for the inhibitor. CONCLUSIONS: These data point to the onset of pleiotropic effects altering the leaf proteome in transgenic plants expressing recombinant protease inhibitors. They also show the potential of these proteins as ectopic modulators of stress responses in planta, useful to engineer biotic or abiotic stress tolerance in crop plants of economic significance.

A SELDI-TOF MS procedure for the detection, quantitation, and preliminary characterization of low-molecular-weight recombinant proteins expressed in transgenic plants.

We describe a SELDI-TOF MS procedure for the rapid detection and quantitation of low-molecular-weight recombinant proteins expressed in plants. Transgenic lines of potato (Solanum tuberosum L.) expressing the clinically useful protein bovine aprotinin or the cysteine protease inhibitor corn cystatin II were generated by Agrobacterium tumefaciens-mediated transformation, and then used as test material for the analyses. Real-time RT-PCR amplifications and detection of the recombinant proteins by immunoblotting were first conducted for transformed potato lines accumulating the proteins in different cell compartments. Both proteins were found at varying levels in leaves, depending on their final cellular destination and transgene expression rate. These conclusions drawn from standard immunodetection assays were easily confirmed by SELDI-TOF MS comparative profiling, after immobilizing the leaf proteins of control and transformed lines on protein biochips for weak cationic exchange. This procedure, carried out in less than 2 h, allows for the rapid comparison of recombinant protein levels in transgenic plant lines. The molecular weight of immobilized proteins can also be determined directly from the MS spectra, thus providing a simple way to assess the structural integrity and homogeneity of recombinant proteins in planta, and to identify the most suitable cellular compartments for their heterologous production.

On-chip detection of low-molecular-weight recombinant proteins in plant crude extracts by SELDI-TOF MS.

This chapter presents a general procedure for the on-chip detection and quantitation of low-molecular-weight recombinant proteins in transgenic plant crude extracts by surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF MS). A protocol is first described to detect the protein of interest in crude protein extracts of transgenic plant lines, by differential protein mapping against similar extracts from a control, nontransgenic line. A complementary protocol is then presented to generate a standard curve with the SELDI system, allowing the protein to be quantified in different transgenic lines. Overall, this procedure may be carried out within a few hours, without the need for prior purification or enrichment of the recombinant protein.

Exposing Small-Molecule Nanoentities by a Nuclear Magnetic Resonance Relaxation Assay.

Small molecules can self-assemble in aqueous solution into a wide range of nanoentity types and sizes (dimers, n-mers, micelles, colloids, etc.), each having their own unique properties. This has important consequences in the context of drug discovery including issues related to nonspecific binding, off-target effects, and false positives and negatives. Here, we demonstrate the use of the spin-spin relaxation Carr-Purcell-Meiboom-Gill NMR experiment, which is sensitive to molecular tumbling rates and can expose larger aggregate species that have slower rotational correlations. The strategy easily distinguishes lone-tumbling molecules versus nanoentities of various sizes. The technique is highly sensitive to chemical exchange between single-molecule and aggregate states and can therefore be used as a reporter when direct measurement of aggregates is not possible by NMR. Interestingly, we found differences in solution behavior for compounds within structurally related series, demonstrating structure-nanoentity relationships. This practical experiment is a valuable tool to support drug discovery efforts.

Pyrimidine as an Aryl C-H Activating Group.

The Pd-catalyzed regioselective C-H activation/arylation, /iodination, and/acetoxylation reactions of 4-arylpyrimidines using aryl iodides, N-iodosuccinimide, and (diacetoxyiodo)benzene respectively as coupling partners are described. Suzuki-Miyaura coupling and Sonogashira reactions of the resulting aryl iodides are demonstrated. The scalability of the C-H activation/functionalization starting with readily accessible 4-aryl pyrimidines is also reported.

Outcomes of bilateral sequential implantation of the Boston keratoprosthesis type 1.

OBJECTIVE: To evaluate the risks and benefits of sequential bilateral Boston type 1 keratoprosthesis (KPro) implantation for bilateral corneal blindness. DESIGN: Comparative retrospective study. PARTICIPANTS: Patients who underwent a sequential bilateral KPro surgery. METHODS: All 11 patients who underwent sequential bilateral KPro surgery at the Centre Hospitalier de l'Université de Montréal between October 2008 and October 2011 were recruited. Data from the 22 patient eyes in our study were separated in 2 groups based on the first (group 1) or second eye (group 2) implanted with the Kpro. Both groups were then compared for the best corrected visual acuity (BCVA) and complications. Bilateral BCVA following both surgeries and the overall number of complications that affected each patient after both interventions were also analyzed. RESULTS: At 24 months, BCVA was 20/150 in group 1 and 20/200 in group 2 (p = 0.67). Throughout the study, there was no significant difference in BCVA between the 2 groups (p > 0.05), and bilateral BCVA was similar. The complication rate was comparable in the 2 groups. Patients had a mean of 2.45 complications following the first surgery and a mean of 5.27 in both eyes combined after the second intervention (p = 0.03). CONCLUSIONS: Because visual gain observed following the second surgery was the same as that with the first and multiple surgeries increased the number of complications for each patient, we recommend saving bilateral KPro implantation for cases in which the first eye with KPro develops a disease limiting its visual potential.

Corneal Densitometry as a Tool to Measure Epithelial Ingrowth After Laser In Situ Keratomileusis.

PURPOSE: This study evaluates the correlation between corneal densitometry and epithelial ingrowth (EI) after laser in situ keratomileusis (LASIK). METHODS: Corneal densitometry of 3 patients who developed EI after LASIK was measured with the Oculus Pentacam. Corneal densitometry readings of each patient were obtained preoperatively and postoperatively after ingrowth was discovered. Densitometry was recorded at the central nest of opacity and at the leading edges of EI. RESULTS: For all patients, the most severe stages of EI observed on slit-lamp photographs correlated with the highest densitometry readings, with peak densitometry ranging from 73.3 to 95.1. These values were much higher than preoperative densitometry readings, which ranged from 21.8 to 27.2. In 2 cases, the Pentacam densitometry map revealed progression of EI toward the visual axis that was only faintly detectable or not detectable at all on the corresponding slit-lamp photographs. CONCLUSIONS: Corneal densitometry seems to be an objective measure of the severity and progression of EI after LASIK.

The Boston Keratoprosthesis type 1 as primary penetrating corneal procedure.

BACKGROUND/AIMS: Penetrating keratoplasty (PK) has a poor prognosis in certain corneal eye diseases. The safety and efficacy of Boston type 1 Keratoprosthesis (KPro) surgery as a primary penetrating corneal surgery were evaluated for patients with corneal blindness and poor prognosis for PK. METHODS: In this retrospective interventional comparative study, all patients who underwent KPro implantation by a single surgeon between October 2008 and March 2011 at the Centre Hospitalier de l'Université de Montréal were divided into two groups. Thirty patients with KPro as a primary procedure (group 1) were compared with 40 patients who had PK prior to KPro (group 2). A chart review examining preoperative and postoperative best-corrected visual acuity (BCVA), intraoperative and postoperative complications and KPro retention rate over the first postoperative year was performed. RESULTS: Preoperative BCVA was 20/200 or better in 10% of eyes in group 1 (range 20/150 light perception (LP)), and in 5% of eyes in group 2 (range 20/100 LP; p=0.42). BCVA was significantly better in group 1 throughout the follow-up (p<0.05). At 12 months, 87% and 63% of eyes achieved a BCVA better than 20/200 in groups 1 and 2, respectively (p<0.05). The complication rates and retention rate were similar in the two groups. CONCLUSIONS: This study demonstrates that the Boston KPro implantation may be successful as a primary procedure in patients at high risk of failure with traditional PK. Further, there appears to be a visual benefit to primary KPro surgery.

Tailoring the specificity of a plant cystatin toward herbivorous insect digestive cysteine proteases by single mutations at positively selected amino acid sites.

Plant cystatins, similar to other defense proteins, include hypervariable, positively selected amino acid sites presumably impacting their biological activity. Using 29 single mutants of the eighth domain of tomato (Solanum lycopersicum) multicystatin, SlCYS8, we assessed here the potential of site-directed mutagenesis at positively selected amino acid sites to generate cystatin variants with improved inhibitory potency and specificity toward herbivorous insect digestive cysteine (Cys) proteases. Compared to SlCYS8, several mutants (22 out of 29) exhibited either improved or lowered potency against different model Cys proteases, strongly suggesting the potential of positively selected amino acids as target sites to modulate the inhibitory specificity of the cystatin toward Cys proteases of agronomic significance. Accordingly, mutations at positively selected sites strongly influenced the inhibitory potency of SlCYS8 against digestive Cys proteases of the insect herbivore Colorado potato beetle (Leptinotarsa decemlineata). In particular, several variants exhibited improved potency against both cystatin-sensitive and cystatin-insensitive digestive Cys proteases of this insect. Of these, some variants also showed weaker activity against leaf Cys proteases of the host plant (potato [Solanum tuberosum]) and against a major digestive Cys protease of the two-spotted stinkbug Perillus bioculatus, an insect predator of Colorado potato beetle showing potential for biological control. Overall, these observations suggest the usefulness of site-directed mutagenesis at positively selected amino acid sites for the engineering of recombinant cystatins with both improved inhibitory potency toward the digestive proteases of target herbivores and weaker potency against nontarget Cys proteases in the host plant or the environment.

Discovery of 4-aryl-4H-chromenes as a new series of apoptosis inducers using a cell- and caspase-based high-throughput screening assay. 2. Structure-activity relationships of the 7- and 5-, 6-, 8-positions.

As a continuation of our efforts to discover and develop the apoptosis inducing 4-aryl-4H-chromenes as novel anticancer agents, we explored the SAR of 4-aryl-4H-chromenes with modifications at the 7- and 5-, 6-, 8-positions. It was found that a small hydrophobic group, such as NMe2, NH2, NHEt, and OMe, is preferred at the 7-position. Di-substitution at either the 5,7-positions or the 6,7-positions generally led to a large decrease in potency. Di-substitution at the 7,8-positions, in general, was found to result in potent compounds. 7-NMe2, 7-NHEt, 7-OMe, and 7,8-di-NH2 analogs were found to have similar SAR for the 4-aryl group, and several 7-substituted and 7,8-di-substituted analogs were found to have similar potencies as the lead compound MX58151 (2a) both as caspase activators and inhibitors of cell proliferation.