A scalable method for supporting multiple patient cohort discovery projects using i2b2.

Although i2b2, a popular platform for patient cohort discovery using electronic health record (EHR) data, can support multiple projects specific to individual disease areas or research interests, the standard approach for doing so duplicates data across projects, requiring additional disk space and processing time, which limits scalability. To address this deficiency, we developed a novel approach that stored data in a single i2b2 fact table and used structured query language (SQL) views to access data for specific projects. Compared to the standard approach, the view-based approach reduced required disk space by 59% and extract-transfer-load (ETL) time by 46%, without substantially impacting query performance. The view-based approach has enabled scalability of multiple i2b2 projects and generalized to another data model at our institution. Other institutions may benefit from this approach, code of which is available on GitHub (https://github.com/wcmc-research-informatics/super-i2b2).

Optimization of TRPV6 Calcium Channel Inhibitors Using a 3D Ligand-Based Virtual Screening Method.

Herein, we report the discovery of the first potent and selective inhibitor of TRPV6, a calcium channel overexpressed in breast and prostate cancer, and its use to test the effect of blocking TRPV6-mediated Ca(2+)-influx on cell growth. The inhibitor was discovered through a computational method, xLOS, a 3D-shape and pharmacophore similarity algorithm, a type of ligand-based virtual screening (LBVS) method described briefly here. Starting with a single weakly active seed molecule, two successive rounds of LBVS followed by optimization by chemical synthesis led to a selective molecule with 0.3 µM inhibition of TRPV6. The ability of xLOS to identify different scaffolds early in LBVS was essential to success. The xLOS method may be generally useful to develop tool compounds for poorly characterized targets.

SMIfp (SMILES fingerprint) chemical space for virtual screening and visualization of large databases of organic molecules.

SMIfp (SMILES fingerprint) is defined here as a scalar fingerprint describing organic molecules by counting the occurrences of 34 different symbols in their SMILES strings, which creates a 34-dimensional chemical space. Ligand-based virtual screening using the city-block distance CBD(SMIfp) as similarity measure provides good AUC values and enrichment factors for recovering series of actives from the directory of useful decoys (DUD-E) and from ZINC. DrugBank, ChEMBL, ZINC, PubChem, GDB-11, GDB-13, and GDB-17 can be searched by CBD(SMIfp) using an online SMIfp-browser at www.gdb.unibe.ch. Visualization of the SMIfp chemical space was performed by principal component analysis and color-coded maps of the (PC1, PC2)-planes, with interactive access to the molecules enabled by the Java application SMIfp-MAPPLET available from www.gdb.unibe.ch. These maps spread molecules according to their fraction of aromatic atoms, size and polarity. SMIfp provides a new and relevant entry to explore the small molecule chemical space.

A new calcium score to predict paravalvular leak in transcatheter aortic valve implantation.

OBJECTIVES: The present study sought to develop a reliable calcium score (Ca-score) to predict paravalvular leak (PVL) in patients undergoing transcatheter aortic valve (AV) implantation. METHODS: A total of 965 patients were prospectively included from 2012 to 2019. Preprocedural contrast-media-enhanced computed tomography scans were analysed regarding the amount of AV cusp calcification and the presence of upper and lower left ventricular outflow tract calcification. The calcium volume threshold of each AV cusp [non-coronary cusp (NCC); left coronary cusp (LCC); right coronary cusp (RCC)] with optimal PVL prediction was defined using the Youden index value derived from receiver operating characteristic analysis. The final score was developed based on the multivariable regression analysis, while individual variables were weighted based on their corresponding odds ratio. RESULTS: The AV calcium volume threshold with optimal PVL prediction was 733.6, 296.0 and 131.2 mm3 for the NCC, RCC and LCC respectively. Overall, calcification of the upper left ventricular outflow tract was present in 233 (23%), 111 (12%) and 304 (32%) of patients below the NCC, RCC and LCC respectively, while 260 (27%), 44 (5%) and 217 (23%) patients suffered from calcification under the NCC, RCC and LCC, respectively. A total Ca-score of ≥4 was present in 356 (37%) of patients and was independently associated with ≥ mild PVL [odds ratio 3.662; 95% confidence interval (2.740-4.911); P < 0.001]. The area under the curve of the Ca-score was 0.713 [95% confidence interval (0.678-0.748); P < 0.001]. CONCLUSION: The provided Ca-score independently correlates with the development of PVL and improves risk stratification in patients undergoing transcatheter AV implantation.

Interpreting experimental data by using molecular simulation instead of model building.

A proper description of the conformational equilibrium of polypeptides or proteins is essential for a correct description of their function. The conformational ensembles from 16 molecular dynamic simulations of two beta- heptapeptides were used to interpret the primary NMR data, which were also compared to a set of NMR model structures (see graphic).One of the most used spectroscopic techniques for resolving the structure of a biomolecule, such as a protein or peptide, is NMR spectroscopy. Because only NMR signal intensities and frequencies are measured in the experiment, a conformational interpretation of the primary data, that is, measured data, is not straightforward, especially for flexible molecules. It is hampered by the occurrence of conformational and/or time-averaging, by insufficient number of experimental data and by insufficient accuracy of experimental data. All three problematic aspects of structure refinement based on NMR nuclear Overhauser effect (NOE) intensities and (3)J coupling data are illustrated by using two beta-heptapeptides in methanol as an example. We have performed 16 molecular dynamics (MD) simulations between 20 to 100 ns in length of unrestrained and NOE distance-restrained cases (instantaneous and time-averaged) of two beta-heptapeptides with a central beta-HAla(alpha-OH) amino acid in methanol at two different temperatures using two different GROMOS force-field parameter sets, 45 A3 and 53 A6. The created conformational ensembles were used to interpret the primary NMR data on these molecules. They also were compared to a set of NMR model structures derived by single-structure refinement in vacuo by using standard techniques. It is shown that the conformational interpretation of measured experimental data can be significantly improved by using unrestrained, instantaneous and time-averaged restrained MD simulations of the peptides by using a thermodynamically calibrated force field and by explicitly including solvent degrees of freedom.

Directed assembly of nanodiamond nitrogen-vacancy centers on a chemically modified patterned surface.

Nitrogen-vacancy (NV) centers in nanodiamond (ND) particles are an attractive material for photonic, quantum information, and biological sensing technologies due to their optical properties-bright single photon emission and long spin coherence time. To harness these features in practical devices, it is essential to realize efficient methods to assemble and pattern NDs at the micro-/nanoscale. In this work, we report the large scale patterned assembly of NDs on a Au surface by creating hydrophobic and hydrophilic regions using self-assembled monolayer (SAM). Hydrophobic regions are created using a methyl (-CH3) terminated SAM of octadecanethiol molecules. Evaporating a water droplet suspension of NDs on the SAM patterned surface assembles the NDs in the bare Au, hydrophilic regions. Using this procedure, we successfully produced a ND structures in the shape of dots, lines, and rectangles. Subsequent photoluminescence imaging of the patterned NDs confirmed the presence of optically active NV centers. Experimental evidence in conjunction with computational analysis indicates that the surface wettability of the SAM modified Au surface plays a dominant role in the assembly of NDs as compared to van der Waals and other substrate-ND interactions.

CH-π "T-shape" interaction with histidine explains binding of aromatic galactosides to Pseudomonas aeruginosa lectin LecA.

The galactose specific lectin LecA mediates biofilm formation in the opportunistic pathogen P. aeruginosa . The interaction between LecA and aromatic ß-galactoside biofilm inhibitors involves an intermolecular CH-π T-shape interaction between C(ε1)-H of residue His50 in LecA and the aromatic ring of the galactoside aglycone. The generality of this interaction was tested in a diverse family of ß-galactosides. LecA binding to aromatic ß-galactosides (KD ∼ 8 µM) was consistently stronger than to aliphatic ß-galactosides (KD ∼ 36 µM). The CH-π interaction was observed in the X-ray crystal structures of six different LecA complexes, with shorter than the van der Waals distances indicating productive binding. Related XH/cation/π-π interactions involving other residues were identified in complexes of aromatic glycosides with a variety of carbohydrate binding proteins such as concanavalin A. Exploiting such interactions might be generally useful in drug design against these targets.

Synthesis and nicotinic receptor activity of chemical space analogues of N-(3R)-1-azabicyclo[2.2.2]oct-3-yl-4-chlorobenzamide (PNU-282,987) and 1,4-diazabicyclo[3.2.2]nonane-4-carboxylic acid 4-bromophenyl ester (SSR180711).

The Chemical Universe Generated Databases up to 11 atoms of CNOF (GDB-11) and up to 13 atoms of CNOClS (GDB-13) were used to enumerate analogues of the diamine part of two known α7 nicotinic receptor agonists and construct libraries of virtual analogues of these drugs. The libraries were scored using structure-based (docking to the nicotine binding site of the acetylcholine binding protein 1uw6.pdb) or ligand-based (similarity to the parent drugs) methods, and the top-scoring virtual ligands were inspected for easily accessible synthetic targets. In total, 21 diamines were prepared and acylated with aromatic carboxylic or oxycarbonic acids to produce 85 analogues of the parent drugs. The compounds were profiled by electrophysiology in Xenopus oocytes expressing human nicotinic acetylcholine receptor (nAChR) subtypes α7, α3ß2, α4ß2, α3ß4, or α4ß4. Characterization of selected compounds revealed eight inhibitors of the α7 nicotinic receptor and three positive allosteric modulators of the α3ß2 nAChR.

Expanding the accessible chemical space by solid phase synthesis of bicyclic homodetic peptides.

Norbornapeptides (bicyclo[2.2.1]heptapeptides) and related bicyclic homodetic peptides were prepared by solid-phase peptide synthesis using an orthogonal protection scheme. These conformationally rigid peptides cover an almost pristine area of peptide topological space and adopt globular shapes similar to those of short α-helical peptides.