Encoding method for OBOC small molecule libraries using a biphasic approach for ladder-synthesis of coding tags

In the "one-bead one-compound" (OBOC) combinatorial library method, each compound bead displays only one compound entity. Hundreds of thousands to millions of compound beads can be synthesized rapidly and screened simultaneously. Positive compound beads are then isolated for structural analysis. To fully exploit the power of OBOC combinatorial small molecule libraries, a robust and high throughput encoding method is needed to decode the positive compound beads. In this paper, we report on the development of a novel encoding strategy that combines the concepts of ladder-synthesis and chemical encoding on bilayer beads. In these encoded libraries, small molecule compounds are displayed on the bead surface, and cleavable coding tags consisting of a series of truncated molecules reside in the bead interior. Such a library can be easily constructed using the biphasic approach (J. Am. Chem. Soc.2002, 124, 7678) to topologically segregate the functionalities of the beads during library synthesis. The ladder members and coding tags are then released for MALDI-TOF-MS analysis. To simplify the interpretation of the mass spectra, we purposely add bromine into the cleavable linker so that the cleavage products generate a characteristic isotope fingerprint. The chemical structure of library compounds can be determined by analyzing the mass differences between adjacent peaks on the mass spectra. This encoding strategy also provides valuable information on the quality of the testing compound on the surface of the bead. To validate this methodology, a model OBOC small molecule library with 12,288 members was synthesized on TentaGel beads and screened against streptavidin. The chemical structures of the compound on each positive bead were unambiguously identified.     

Vibrational spectroscopy of 3,4-difluorocyclobutenes: cis-d0, trans-d0 and trans-d4 species

Infrared and Raman spectra were recorded for cis-3,4-difluorocyclobutene (cDFCB) and trans-3,4-difluorocyclobutene-d4. Unscaled density functional theory (DFT) calculations of frequencies and intensities at the B3LYP/6-311++G(d,p) level supported the complete assignment of the vibrational fundamentals. The previous assignment of fundamentals of trans-3,4-difluorocyclobutene was revised. An unusual blue shift occurs for the methylenic CH-stretching frequencies of cis-3,4-difluorocyclobutene in going from the gas phase to the liquid phase. This hydrogen bond effect is related to similar observations recently reported and interpreted. The blue shift does not occur for the vinylic CH bonds of the cis isomer and does not occur for either type of CH bond in the trans isomer.     

Crystal engineering of urea alpha-network via I...O2N synthon and design of SHG active crystal N-4-iodophenyl-N'-4'-nitrophenylurea

Crystalline nitrodiphenyl ureas adopt the N-H...O tape alpha-network only when stabilization accrues from the I...O(2)N or C[triple bond]C-H...O(2)N synthon, otherwise the ureanitro motif is preferred; soft, weak interactions can direct polar self-assembly in strong N-HO hydrogen-bonded crystals.     

Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery

We here outline the importance of open-source, accessible tools for computer-aided drug discovery (CADD). We begin with a discussion of drug discovery in general to provide context for a subsequent discussion of structure-based CADD applied to small-molecule ligand discovery. Next, we identify usability challenges common to many open-source CADD tools. To address these challenges, we propose a browser-based approach to CADD tool deployment in which CADD calculations run in modern web browsers on users’ local computers. The browser app approach eliminates the need for user-initiated download and installation, ensures broad operating system compatibility, enables easy updates, and provides a user-friendly graphical user interface. Unlike server apps—which run calculations “in the cloud” rather than on users’ local computers—browser apps do not require users to upload proprietary information to a third-party (remote) server. They also eliminate the need for the difficult-to-maintain computer infrastructure required to run user-initiated calculations remotely. We conclude by describing some CADD browser apps developed in our lab, which illustrate the utility of this approach. Aside from introducing readers to these specific tools, we are hopeful that this review highlights the need for additional browser-compatible, user-friendly CADD software.     

Toward the computer-aided discovery of FabH inhibitors. Do predictive QSAR models ensure high quality virtual screening performance?

Antibiotic resistance has increased over the past two decades. New approaches for the discovery of novel antibacterials are required and innovative strategies will be necessary to identify novel and effective candidates. Related to this problem, the exploration of bacterial targets that remain unexploited by the current antibiotics in clinical use is required. One of such targets is the \(\beta \) -ketoacyl-acyl carrier protein synthase III (FabH). Here, we report a ligand-based modeling methodology for the virtual-screening of large collections of chemical compounds in the search of potential FabH inhibitors. QSAR models are developed for a diverse dataset of 296 FabH inhibitors using an in-house modeling framework. All models showed high fitting, robustness, and generalization capabilities. We further investigated the performance of the developed models in a virtual screening scenario. To carry out this investigation, we implemented a desirability-based algorithm for decoys selection that was shown effective in the selection of high quality decoys sets. Once the QSAR models were validated in the context of a virtual screening experiment their limitations arise. For this reason, we explored the potential of ensemble modeling to overcome the limitations associated to the use of single classifiers. Through a detailed evaluation of the virtual screening performance of ensemble models it was evidenced, for the first time to our knowledge, the benefits of this approach in a virtual screening scenario. From all the obtained results, we could arrive to a significant main conclusion: at least for FabH inhibitors, virtual screening performance is not guaranteed by predictive QSAR models.     

Barium ferrite (BaFe12O19) thin films prepared by pulsed laser deposition on MgO buffered Si substrates

Barium ferrite (BaFe₁₂O₁₉) thin films have been deposited by pulsed laser deposition (PLD) on Si substrates with MgO underlayers. The films were deposited in oxygen atmosphere by excimer laser (=248 nm, pulse duration=23 ns) in the temperature range 750–900 °C. The experiments showed that the substrate temperature has remarkable effect on the films magnetic and structural properties. The BaFe₁₂O₁₉ films deposited at 900 °C in 200 mTorr oxygen showed some perpendicular orientation, with a perpendicular squareness of 0.5 and an in-plane squareness of 0.3. Such thin BaFe₁₂O₁₉ films have platelet grains with a size of about 300 nm. The perpendicular saturation magnetization and coercivity are 185 emu/cm³ and 1.4 kOe, respectively. PACS 81.15.Fg.; 75.70.Ak; 75.50.Pp; 68.55.j     

Peripatetic Highlights in Bern

This tour of significant scientific sites in Bern uses the local legacy of its most illustrious scientists, Albert Einstein (1879–1955) and Fritz Houtermans (1903–1966), as its guiding thread through the old town and the university district.Ann M.Hentschel is translator of the correspondence volumes of The Collected Papers of Albert Einstein and is currently employed by the Institute for the History and Philosophy of Science at the University of Bern to write the guide for a city tour of Einsteins old haunts in Bern for the coming jubilee of special relativity in 2005. For the historical companion guidebook, see Hentschel and Grasshoff, Albert Einstein (ref. 4) and the website <.