The principle of bioisosterismsimilarly shaped molecules are more likely to share biological properties than are other moleculeshas long helped to guide drug discovery. An algorithmic ...implementation of this principle, based on shape comparisons of a single rule-generated “topomer” conformation per molecule, had been found to be the descriptor most consistently predictive of similar biological properties, in retrospective studies, and also to be well-suited for searching large (>1012) “virtual libraries” of potential reaction products. Therefore a prospective trial of this shape similarity searching method was carried out, with synthesis of 425 compounds and testing of them for inhibition of binding of angiotensin II (A-II). The 63 compounds that were identified by shape searching as most similar to any of four query structures included all of the seven compounds found to be highly active, with none of the other 362 structures being highly active (p < 0.001). Additional consistent relations (p < 0.05) were found, among all 425 compounds, between the degree of shape similarity to the nearest query structure and the frequency of various levels of observed activity. Known “SAR” (rules specifying structural features required for A-II antagonism) were also regenerated within the biological data for the 63 shape similar structures.
One of the early and effective approaches to G-coupled protein receptor target family library design was the analysis of a set of ligands for frequently occurring chemical moieties or substructures. ...Various methods ranging from frameworks analysis to pharmacophores have been employed to find these so-called target-family-privileged substructures. Although the use of these substructures is common practice in combinatorial library design and has produced leads, the methods used for finding them rarely verified their selectivity for the particular target family from which they were derived. The frequency of occurrence among ligands associated with a target receptor family is not a sufficient criterion for those substructures to receive the label of target-family-privileged substructure. This study explores the question of selectivity of ClassPharmer generated fragments for a series of target families: GPCRs, nuclear hormone receptors, serine proteases, protein kinases, and ligand-gated ion channels. In addition, a GPCR focused library and a random set of 10k compounds are examined in terms of their target-family-privileged-substructure composition. The results challenge the combinatorial chemistry concept of target-family-privileged substructures and suggest that many of these fragments may simply be drug-like or attractive for various receptors in accordance with the original definition of privileged substructures. ,
Diversity assessment Mason, Jonathan S; Hermsmeier, Mark A
Current opinion in chemical biology,
06/1999, Volume:
3, Issue:
3
Journal Article
Peer reviewed
Several themes have been highlighted recently in both conferences and publications: the availability of productfocused and pharmacophore-based methods for the analysis and design of combinatorial ...libraries; the power of cell-based methods for molecular similarity, diversity and library design applications; methods for ‘rational’ diverse subset selection (with applicability to library design); the need for specialized optimization programs for the design of combinatorial libraries that maximize the use of common reagents; and the concept of ‘drug-likeness’ and its importance in the design of combinatorial libraries.
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A novel Genetic Algorithm guided Selection method, GAS, has been described. The method utilizes a simple encoding scheme which can represent both compounds and variables used to construct a QSAR/QSPR ...model. A genetic algorithm is then utilized to simultaneously optimize the encoded variables that include both descriptors and compound subsets. The GAS method generates multiple models each applying to a subset of the compounds. Typically the subsets represent clusters with different chemotypes. Also a procedure based on molecular similarity is presented to determine which model should be applied to a given test set compound. The variable selection method implemented in GAS has been tested and compared using the Selwood data set (n = 31 compounds; v = 53 descriptors). The results showed that the method is comparable to other published methods. The subset selection method implemented in GAS has been first tested using an artificial data set (n = 100 points; v = 1 descriptor) to examine its ability to subset data points and second applied to analyze the XLOGP data set (n = 1831 compounds; v = 126 descriptors). The method is able to correctly identify artificial data points belonging to various subsets. The analysis of the XLOGP data set shows that the subset selection method can be useful in improving a QSAR/QSPR model when the variable selection method fails.
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The dynamic nature and comparatively young age of computational chemistry is such that novel algorithms continue to be developed at a rapid pace. Such efforts are often wrought at the expense of ...extensive experimental validations of said techniques, preventing a deeper understanding of their potential utility and limitations. Here we address this issue for ligand-based virtual screening descriptors through design of validation experiments that better reflect the aims of real world application. Applying the newly defined chemotype enrichment approach, a variety of two- and three-dimensional (2D/3D) similarity descriptors have been compared extensively across data sets from four diverse target types. The inhibitors within said data sets contain molecules exhibiting a wide array of substructure functionality, size and flexibility, permitting descriptor comparison in myriad settings. Relative descriptor performance under these conditions is examined, including results obtained using more typical virtual screening validation experiments. Guidelines for optimal application of said descriptors are also discussed in the context of the results obtained, as is the potential utility of fingerprint filtering.
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DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Circularly polarized soft x-rays have been used with an imaging photoelectron microscope to record images of magnetic domains at a spatial resolution of 1 micrometer. The magnetic contrast, which can ...be remarkably large, arises from the fact that the x-ray absorption cross section at inner-shell absorption edges of aligned magnetic atoms depends on the relative orientation of the photon spin and the local magnetization direction. The technique is element-specific, and, because of the long mean free paths of the x-rays and secondary electrons, it can record images of buried magnetic layers.
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A series of novel aminodiol inhibitors of HIV protease based on the lead compound 1 with structural modifications at P1‘ were synthesized in order to reduce the cytotoxicity of 1. We have observed a ...high degree of correlation between the lipophilicity and the cytotoxicity of this series of inhibitors. It was found that appropriate substitution at the para position of the P1‘ phenyl group of 1 resulted in the identification of equipotent (both against the enzyme and in cell culture) compounds (10l, 10m, 10n, and 15c) which possess significantly decreased cytotoxicity.
Magnetic circular x-ray dichroism measurements at the Co {ital L}{sub 3} and {ital L}{sub 2} edges in Co/Pd multilayers give first experimental evidence for a greatly enhanced orbital moment compared ...to that in bulk Co, confirming recent theoretical predictions. Our results also show that, in general, there is no simple relationship between the dichroism signal and either the spin moment or the total moment. This is verified by a simple model calculation.
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A series of HIV protease inhibitors containing a novel C2 symmetrical "aminodiol" core structure were prepared from amino acid starting materials. The ability of the aminodiols to inhibit HIV ...replication in cell culture is comparable to their ability to inhibit the isolated enzyme, a result compatible with good cell membrane penetration by this class of compounds. Optimization of the structure-activity in this series led to aminodiol 9a (Ki = 100 nM; ED50 (HIV-1) = 80 nM) containing P1/P1 benzyl and P2/P2 Boc substituents. Compound 9a is a selective inhibitor of HIV protease versus other aspartyl proteases such as human renin, human cathepsin D, and porcine pepsin. In addition, 9a is equipotent against HIV-1 and HIV-2 in cell culture and demonstrates similar activity in infected T-lymphocytes and PBMCs. After i.v. and oral administration in rats, 9a displayed significant oral bioavailability (ca. 40%) and a promising plasma elimination half-life (4 h).
