Molecular diversity management strategies for building and enhancement of diverse and focused lead discovery compound screening collections

This publication describes processes for the selection of chemical compounds for the building of a high-throughput screening (HTS) collection for drug discovery, using the currently implemented process in the Discovery Technologies Unit of the Novartis Institute for Biomedical Research, Basel Switzerland as reference. More generally, the currently existing compound acquisition models and practices are discussed. Our informatics, chemistry and biology-driven compound selection consists of two steps: 1) The individual compounds are filtered and grouped into three priority classes on the basis of their individual structural properties. Substructure filters are used to eliminate or penalize compounds based on unwanted structural properties. The similarity of the structures to reference ligands of the main proven druggable target families is computed, and drug-similar compounds are prioritized for the following diversity analysis. 2) The compounds are compared to the archive compounds and a diversity analysis is performed. This is done separately for the prioritized, regular and penalized compounds with increasingly stringent dissimilarity criterion. The process includes collecting vendor catalogues and monitoring the availability of samples together with the selection and purchase decision points. The development of a corporate vendor catalogue database is described. In addition to the selection methods on a per single molecule basis, selection criteria for scaffold and combinatorial chemistry projects in collaboration with compound vendors are discussed.     

Sequential superparamagnetic clustering for unbiased classification of high-dimensional chemical data

For the clustering of chemical structures that are described by the Similog, ISIS count, and ISIS binary fingerprints, we propose a sequential superparamagnetic clustering approach. To appropriately handle nonbinary feature keys, we introduce an extension of the binary Tanimoto similarity measure. In our applications, data sets composed of structures from seven chemically distinct compound classes are evaluated and correctly clustered. The comparison, with results from leading methods, indicates the superiority of our sequential superparamagnetic clustering approach.     

Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures

Fingerprint-based similarity searching is widely used for virtual screening when only a single bioactive reference structure is available. This paper reviews three distinct ways of carrying out such searches when multiple bioactive reference structures are available: merging the individual fingerprints into a single combined fingerprint; applying data fusion to the similarity rankings resulting from individual similarity searches; and approximations to substructural analysis. Extended searches on the MDL Drug Data Report database suggest that fusing similarity scores is the most effective general approach, with the best individual results coming from the binary kernel discrimination technique.     

Ion cloud manipulation using the radiofrequency-only-mode as an improvement for high mass detection in fourier transform mass spectrometry

It has been difficult to achieve the expected high resolving power for high-mass biomolecule ions in Fourier transform mass spectrometry. Our hypothesis is that ion clouds produced by laser desorption or injection are diffuse and produce poor signals. To test the hypothesis, clouds of benzene molecular ions produced by electron ionization were purposefully expanded via magnetron mode excitation and characterized by a new experimental sequence for cloud sectional analysis. The expanded cloud was then successfully focused to the trap center by using a high-pressure dynamic event (radiofrequency-only mode). The expanded cloud in a conventional cubic trap produces no detectable signal, whereas the focused cloud in a compensated trap yields a high-resolution signal with good signal-to-noise ratio.     

Beam lifetimes of low-charged ions in storage rings

The beam lifetimes and the charge-changing cross-sections for fast low-charged ions are calculated for the energy range of 1–100 MeV/u and compared with experimental data for Mg¹⁺ and U¹⁰⁺ ions recently measured at SIS GSI, Darmstadt. A moderate agreement of calculations with experiment was obtained. The results show that the heavy components of the residual gas (N₂ and Ar) play a key role for projectile charge-changing processes in the energy range considered. This revised version was published online in July 2006 with corrections to the Cover Date.     

A comparison of intermolecular vibrations and tautomerism in benzimidazole, benzotriazole and their binary water clusters

Resonance-enhanced two-photon ionization spectra of benzotriazole, benzimidazole and their water clusters have been taken in a molecular beam. The tautomerism of the benzotriazole and benzimidazole monomers is studied. In order to obtain an assignment of the vibronic bands of the benzotriazole- and benzimidazole-water clusters, ab initio calculations have been performed, which allow the assignment of the intermolecular vibrations and the determination of the most stable cluster structures. In the case of benzotriazole the cyclic cluster of the 2H-tautomer has been found to be the most stable one, whereas for benzimidazole the most stable cluster could be shown to have a linear arrangement, with the benzimidazole moiety acting as proton donor. Received: 2 March 2000 / Revised version: 31 May 2000 / Published online: 5 October 2000     

Search for sub-eV mass solar axions by the CERN Axion Solar Telescope with 3He buffer gas

The CERN Axion Solar Telescope (CAST) has extended its search for solar axions by using (3)He as a buffer gas. At T=1.8 K this allows for larger pressure settings and hence sensitivity to higher axion masses than our previous measurements with (4)He. With about 1 h of data taking at each of 252 different pressure settings we have scanned the axion mass range 0.39 eV?m(a)?0.64 eV. From the absence of excess x rays when the magnet was pointing to the Sun we set a typical upper limit on the axion-photon coupling of g(aγ)?2.3×10(-10) GeV(-1) at 95% C.L., the exact value depending on the pressure setting. Kim-Shifman-Vainshtein-Zakharov axions are excluded at the upper end of our mass range, the first time ever for any solar axion search. In the future we will extend our search to m(a)?1.15 eV, comfortably overlapping with cosmological hot dark matter bounds.     

Ligand-specific scoring functions: improved ranking of docking solutions

Molecular docking is a powerful computational method that has been widely used in many biomolecular studies to predict geometry of a protein-ligand complex. However, while its conformational search algorithms are usually able to generate correct conformation of a ligand in the binding site, the scoring methods often fail to discriminate it among many false variants. We propose to treat this problem by applying more precise ligand-specific scoring filters to re-rank docking solutions. In this way specific features of interactions between protein and different types of compounds can be implicitly taken into account. New scoring functions were constructed including hydrogen bonds, hydrophobic and hydrophilic complementarity terms. These scoring functions also discriminate ligands by the size of the molecule, the total hydrophobicity, and the number of peptide bonds for peptide ligands. Weighting coefficients of the scoring functions were adjusted using a training set of 60 protein-ligand complexes. The proposed method was then tested on the results of docking obtained for an additional 70 complexes. In both cases the success rate was 5-8% better compared to the standard functions implemented in popular docking software.     

Shaping of intense ion beams into hollow cylindrical form

A specifically tailored plasma lens could shape a high-energy, heavy-ion beam into the form of a hollow cylinder without loss of beam intensity. It has been experimentally confirmed that both a positive as well as a negative radial gradient of the current density in the active plasma lens can be the underlying principle. Calculations were performed that yield the ideal current density distribution for both cases. A numerical simulation of an experiment with an intense ion beam highlights that the shaping of the beam increases the achievable compression in a lead sample.     

New methods for ligand-based virtual screening: use of data fusion and machine learning to enhance the effectiveness of similarity searching

Similarity searching using a single bioactive reference structure is a well-established technique for accessing chemical structure databases. This paper describes two extensions of the basic approach. First, we discuss the use of group fusion to combine the results of similarity searches when multiple reference structures are available. We demonstrate that this technique is notably more effective than conventional similarity searching in scaffold-hopping searches for structurally diverse sets of active molecules; conversely, the technique will do little to improve the search performance if the actives are structurally homogeneous. Second, we make the assumption that the nearest neighbors resulting from a similarity search, using a single bioactive reference structure, are also active and use this assumption to implement approximate forms of group fusion, substructural analysis, and binary kernel discrimination. This approach, called turbo similarity searching, is notably more effective than conventional similarity searching.