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R Venkataraghavan

Publications and source records attributed to R Venkataraghavan.

15 recordsLinked to original sources
PubMed1992

A systematic search for protein signature sequences.

Signature sequences are contiguous patterns of amino acids 10-50 residues long that are associated with a particular structure or function in proteins. These may be of three types (by our nomenclature): superfamily signatures, remnant homologies, and motifs. We have performed a systematic search through a database of protein sequences to automatically and preferentially find remnant homologies and motifs. This was accomplished in three steps: 1. We generated a nonredundant sequence database. 2. We used BLAST3 (Altschul and Lipman, Proc. Natl. Acad. Sci. U.S.A. 87:5509-5513, 1990) to generate local pairwise and triplet sequence alignments for every protein in the database vs. every other. 3. We selected "interesting" alignments and grouped them into clusters. We find that most of the clusters contain segments from proteins which share a common structure or function. Many of them correspond to signatures previously noted in the literature. We discuss three previously recognized motifs in detail (FAD/NAD-binding, ATP/GTP-binding, and cytochrome b5-like domains) to demonstrate how the alignments generated by our procedure are consistent with previous work and make structural and functional sense. We also discuss two signatures (for N-acetyltransferases and glycerol-phosphate binding) which to our knowledge have not been previously recognized.

Amino Acid Sequence↗
PubMed1991

A method for automatic generation of novel chemical structures and its potential applications to drug discovery.

A novel method for generation of chemical structures of potential pharmaceutical interest is presented. Structures are generated by random combination of known fragments and selected by statistical topological techniques. The power of the method lies in the great profusion of candidates generated together with the extremely high selectivity imposed by the techniques of selection.

Chemistry, Pharmaceutical↗
PubMed1990

Role of lysine-54 in determining cofactor specificity and binding in human dihydrofolate reductase.

Lysine-54 of human dihydrofolate reductase (hDHFR) appears to be involved in the interaction with the 2'-phosphate of NADPH and is conserved as a basic residue in other species. Studies have suggested that in Lactobacillus casei dihydrofolate reductase Arg-43, the homologous residue at this position, plays an important role in the binding of NADPH and in the differentiation of Km values for NADPH and NADH. A Lys-54 to Gln-54 mutant (K54Q) of hDHFR has been constructed by oligodeoxynucleotide-directed mutagenesis in order to study the role of Lys-54 in differentiating Km and Kcat values for NADPH and NADH as well as in other functions of hDHFR. The purpose of this paper is to delineate in quantitative terms the magnitude of the effect of the Lys-54 to Gln-54 replacement on the various kinetic parameters of hDHFR. Such quantitative effects cannot be predicted solely on the basis of X-ray structures. The Km for NADPH for the K54Q mutant enzyme is 58-fold higher, while the Km for NADH for K54Q is only 3.9-fold higher than that of the wild type, indicating that the substitution of Lys-54 with Gln-54 decreases the apparent affinity of the enzyme for NADPH dramatically, but has a lesser effect on the apparent affinity for NADH.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1989

Probing the role of two hydrophobic active site residues in the human dihydrofolate reductase by site-directed mutagenesis.

In the x-ray structure of the human dihydrofolate reductase, phenylalanine 31 and phenylalanine 34 have been shown to be involved in hydrophobic interactions with bound substrates and inhibitors. Using oligonucleotide-directed mutagenesis and a bacterial expression system producing the wild-type and mutant human dihydrofolate reductases at levels of 10% of the bacterial protein, we have constructed, expressed, and purified a serine 31 (S31) mutant and a serine 34 (S34) mutant. Fluorescence titration experiments indicated that S31 bound the substrate H2folate 10-fold tighter and the coenzyme NADPH 2-fold tighter than the wild-type human dihydrofolate reductase. The serine 31 mutation had little effect on the steady-state kinetic properties of the enzyme but produced a 100-fold increase in the dissociation constant (Kd) for the inhibitor methotrexate. The serine 34 mutant had much greater alterations in its properties than S31; specifically, S34 had a 3-fold reduction in the Km for NADPH, a 24-fold increase in the Km for H2folate, a 3-fold reduction in the overall reaction rate kcat, and an 80,000-fold increase in the Kd for methotrexate. In addition, the pH dependence of the steady-state kinetic parameters of S34 were different from that of the wild-type enzyme. These results suggest that phenylalanine 31 and phenylalanine 34 make very different contributions to ligand binding and catalysis in the human dihydrofolate reductase.

Amino Acid Sequence↗
PubMed1989

Searching for pharmacophores in large coordinate data bases and its use in drug design.

Pharmacophores, three-dimensional arrangements of chemical groups essential for biological activity, are being proposed in increasing numbers. We have developed a system to search data bases of three-dimensional coordinates for compounds that contain a particular pharmacophore. The coordinates can be derived from experiment (e.g., Cambridge Crystal Database) or be generated from data bases of connection tables (e.g., Cyanamid Laboratories proprietary compounds) via the program CONCORD. We discuss the results of searches for three sample pharmacophores. Two have been proposed by others based on the conformational analysis of active compounds, and one is inferred from the crystal structure of a protein-ligand complex. These examples show that such searches can identify classes of compounds that are structurally different from the compounds from which the pharmacophore was derived but are known to have the appropriate biological activity. Occasionally, the searches find bond "frameworks" in which the important groups are rigidly held in the proper geometry. These may suggest new structural classes for synthesis.

Antidepressive Agents↗
PubMed1988

Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure.

Finding novel leads from which to design drug molecules has traditionally been a matter of screening and serendipity. We present a method for finding a wide assortment of chemical structures that are complementary to the shape of a macromoleculer receptor site whose X-ray crystallographic structure is known. Each of a set of small molecules from the Cambridge Crystallographic Database (Allen; et al. J. Chem. Doc. 1973, 13, 119) is individually docked to the receptor in a number of geometrically permissible orientations with use of the docking algorithm developed by Kuntz et al. (J. Mol. Biol. 1982, 161, 269). The orientations are evaluated for goodness-of-fit, and the best are kept for further examination using the molecular mechanics program AMBER (Weiner; Kollman J. Comput. Chem. 1981, 106, 765). The shape-search algorithm finds known ligands as well as novel molecules that fit the binding site being studied. The highest scoring orientations of known ligands resemble binding modes generated by interactive modeling or determined crystallographically. We describe the application of this procedure to the binding sites of papain and carbonic anhydrase. While the compounds recovered from the Cambridge Crystallographic Database are not, themselves, likely to be inhibitors or substrates of these enzymes, we expect that the structures from such searches will be useful in the design of active compounds.

Algorithms↗
PubMed1987

Designing novel nicotinic agonists by searching a database of molecular shapes.

We introduce an approach by which novel ligands can be designed for a receptor if a pharmacophore geometry has been established and the receptor-bound conformations of other ligands are known. We use the shape-matching method of Kuntz et al. [J. Mol. Biol., 161 (1982) 269-288] to search a database of molecular shapes for those molecules which can fit inside the combined volume of the known ligands and which have interatomic distances compatible with the pharmacophore geometry. Some of these molecules are then modified by interactive modeling techniques to better match the chemical properties of the known ligands. Our shape database (about 5000 candidate molecules) is derived from a subset of the Cambridge Crystallographic Database [Allen et al., Acta Crystallogr., Sect. B,35 (1979) 2331-2339]. We show, as an example, how several novel designs for nicotinic agonists can be derived by this approach, given a pharmacophore model derived from known agonists [Sheridan et al., J. Med. Chem., 29 (1986) 889-906]. This report complements our previous report [DesJarlais et al., J. Med. Chem., in press], which introduced a similar method for designing ligands when the structure of the receptor is known.

Algorithms↗
PubMed1986

The ensemble approach to distance geometry: application to the nicotinic pharmacophore.

We develop an extension of conventional distance geometry techniques that treats two or more molecules as a single "ensemble". This extension can be used to find a common pharmacophore, i.e., the spatial arrangement of essential groups, from a small set of biologically active molecules. The approach can generate, in one step, coordinates for the set of molecules in their "active" conformations such that their essential groups are superimposed. As an example, we show how the nicotinic pharmacophore can be deduced from a set of four nicotinic agonists: nicotine, cytisine, ferruginine methiodide, and muscarone. Three essential groups in each agonist are chosen: the cationic center (A), an electronegative atom (B), and an atom (C) that forms a dipole with B. There is only one pharmacophore possible for the superposition of these essential groups: a triangle with sides 4.8 A (A-B), 4.0 A (A-C), and 1.2 A (B-C). The pharmacophore triangle, which is consistent with previous models in the literature, can also be achieved by the agonist trans-3,3'-bis[(trimethylammonio)methyl]azobenzene and the antagonists strychnine, trimethaphan, and dihydro-beta-erythroidine. An examination of the common volumes of agonists suggests a specific disposition of molecular volume relative to the pharmacophore triangle. We discuss the relative strengths and drawbacks of the ensemble approach vs. other conformational search methods.

Alkaloids↗
PubMed1986

Docking flexible ligands to macromolecular receptors by molecular shape.

We present a method to explore the interaction of flexible ligands with receptors of known geometry on the basis of molecular shape. This method is an extension of that described by Kuntz et al. (J. Mol. Biol. 1982, 161, 269). The shape of a binding site on a macromolecular receptor is represented as a set of overlapping spheres. Each ligand is divided into a small set of large rigid fragments that are docked separately into the binding site and then rejoined later in the calculation. The division of ligands into separate fragments allows a degree of flexibility at the position that joins them. The rejoined fragments are then energy minimized in the receptor site. We illustrate the method with two test cases: dihydrofolate reductase/methotrexate and prealbumin/thyroxine. For each test case, the method finds binding geometries for the ligand near that observed crystallographically as well as others that provide good steric fit with the receptor.

Binding Sites↗
PubMed1985

Design of anticancer drugs using modeling techniques.

Flexibility of intercalation site geometries within a B-DNA helix was investigated in the twist-shift plane using energy minimization methods. The parameters optimized included sugar conformation, the glycosidic angles and phosphodiester torsion angles. Our calculations show several regions of energetically favorable intercalation geometries in the twist-shift plane. Modeling studies using interactive computer graphics and electrostatic potential surface compatibility provided initial hypotheses for the structures of the drug-DNA complexes. These hypotheses were supported and extended by energy minimizations of these complexes. Binding positions, conformational features and relative minimum binding energies of two anticancer drugs, mitoxantrone and bisantrene, were computed for intercalation complexes with DNA in the theoretically defined intercalation sites. Mitoxantrone intercalates DNA from the minor groove and the side chain OH or NH groups are involved in hydrogen bonds with the main chain phosphate groups of DNA, thereby cross-linking the complementary strands. The hydroxyl groups of mitoxantrone can also participate in hydrogen bonding with phosphate oxygens of another chain, thereby cross-linking DNA helices. Bisantrene intercalates DNA favorably from the major groove and the NH group of the dihydroimidazole ring can participate in hydrogen bonding with the phosphate oxygens of the backbone. These models are consistent with the physicochemical and electron microscopic studies of the interaction of mitoxantrone and bisantrene with DNA. Our results are now being used to guide the design of novel anticancer drugs that should interact with DNA in a manner similar to that proposed for our representative drugs.

Anthracenes↗
PubMedDate not supplied

New method for rapid characterization of molecular shapes: applications in drug design.

We present a method for the rapid quantitative shape match between two molecules or a molecule and a template, using atom triplets as descriptors. This technique can be used either as a rapid screen preceding the computationally expensive shape-based docking method developed by Kuntz and co-workers or as a stand-alone method to rank compounds in a large database for their fit to a shape template. The merits and limitations of this method are discussed in detail with examples.

Binding Sites↗