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In earlier work from our laboratory, we have described the use of the ring system and ring scaffold as descriptors. We showed that these descriptors could be used for fast compound clustering, novelty determination, compound acquisition, and combinatorial library design. Here we extend the concept to a whole family of structural descriptors with the ring system as the centerpiece. We show how this simple idea can be used to build powerful search tools for mining chemical databases in useful ways. We have also built recursive partition trees using these fragments as descriptors. We will discuss how these trees can help in analyzing complex structure-activity data.

We address the problem of designing a general-purpose combinatorial library to screen for pharmaceutical leads. Conventional approaches focus on diversity as the primary factor in designing such libraries. We suggest making screening libraries out of a set of pharmaceutically relevant scaffolds, with multiple analogs per scaffold. The rationale for this rests on the fact that even though the hit-rate in active series is much higher than in the database as a whole, often a large fraction of the compounds in active series are inactive. This is especially true when the series has not been optimized for the target under study. We introduce the concept of hit-rate within a series and use historic screening data to arrive at a crude estimate for it. We then use simple probability arguments to show that 50-100 compounds are required in each series in order to be nearly certain of finding at least one active compound in each true active series for any given target.

A protocol is described for rapidly screening small organic molecules for their ability to bind a target protein while obtaining structure-related information as part of a structure-based drug discovery and design program. The methodology takes advantage of and combines the inherent strengths of size exclusion gel chromatography, mass spectrometry, and NMR to identify bound complexes in a relatively universal high-throughput screening approach. Size exclusion gel chromatography in the spin column format provides the high-speed separation of a protein-ligand complex from free ligands. The spin column eluent is then analyzed under denaturing conditions by electrospray ionization mass spectrometry (MS) for the presence of small molecular weight compounds formerly bound to the protein. Hits identified by MS are then individually assayed by chemical shift perturbations in a 2D 1H-15N HSQC NMR spectrum to verify specific interactions of the compound with the protein and identification of the binding site on the protein. The utility of the MS/NMR assay is demonstrated with the use of the catalytic fragment of human fibroblast collagenase (MMP-1) as a target protein and the screening of a library consisting of approximately 32 000 compounds for the identification of molecules that exhibit specific binding to the RGS4 protein.

We present some new ideas for characterizing and comparing large chemical databases. The comparison of the contents of large databases is not trivial since it implies pairwise comparison of hundreds of thousands of compounds. We have developed methods for categorizing compounds into groups or series based on their ring-system content, using precalculated structure-based hashcodes. Two large databases can then be compared by simply comparing their hashcode tables. Furthermore, the number of distinct ring-system combinations can be used as an indicator of database diversity. We also present an independent technique for diversity assessment called the saturation diversity approach. This method is based on picking as many mutually dissimilar compounds as possible from a database or a subset thereof. We show that both methods yield similar results. Since the two methods measure very different properties, this probably says more about the properties of the databases studied than about the methods.

1. Clam-foot paramyosin strongly inhibited superprecipitation of clam-foot actomyosin whereas it did not at all affect its ATPase reaction. On the other hand, superprecipitation of rabbit actomyosin and its ATPase reaction were both inhibited by clam foot paramyosin. 2. Clam-foot paramyosin did not at all affect the Mg-ATPase activity of clam-foot myosin alone (with no actin) but inhibited that of rabbit skeletal myosin alone. 3. Clam-foot paramyosin did not affect the ATPase reaction of rabbit acto-clam myosin but inhibited its superprecipitation. In other words, the effect of paramyosin on the ATPase reaction of actomyosin was simply dependent on the myosin source. 4. Clam-foot tropomyosin slightly enhanced superprecipitation of clam-foot actomyosin and scarcely affected its ATPase reaction, but it inhibited the reactions both of skeletal actomyosin and of rabbit acto-clam myosin. 5. Rabbit skeletal light-meromyosin (LMM) inhibited the ATPase and superprecipitation reactions of rabbit skeletal actomyosin, but it scarcely affected the ATPase reaction of rabbit acto-clam myosin while inhibiting its superprecipitation. In other words, rabbit LMM behaved the same way as clam paramyosin did. 6. Speculating on these findings and our previous findings, we suggest that the formation of a certain filamentous structure is the essential link between the ATPase reaction and contraction in molluscan muscles.