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Y S Babu

Publications and source records attributed to Y S Babu.

At least 37 records · Page 2Linked to original sources
PubMed1995

Calculation of relative binding affinities of purine nucleoside phosphorylase inhibitors.

The competitive binding of inhibitors to purine nucleoside phosphorylase (PNP) has been experimentally measured. Fast and reliable computational methods to estimate binding would allow assessment of any proposed inhibitor before its synthesis. Binding-energy calculations with a representative set of PNP inhibitors were compared to the empirical values. Relatively simple and fast calculations were executed with X-PLOR, DelPhi and SoftDock. The computational results are mixed.

Journal Article↗
PubMed1994

Structure-based design of inhibitors of purine nucleoside phosphorylase. 4. A study of phosphate mimics.

9-(3,3-Dimethyl-5-phosphonopentyl)guanine was synthesized and found to be a potent inhibitor of purine nucleoside phosphorylase (PNP) (IC50 = 44 nM). A number of other functional end groups were investigated as phosphate mimics attached to the 9-position of guanine by this same alkyl side chain, which provided a sensitive method for the detection of any interaction of these groups with the phosphate binding site of PNP. Both the sulfonic acid (compound 13) and the carboxylic acid (compound 15) end groups interact significantly with the phosphate binding site, but in different ways, as determined by X-ray crystallographic analysis of the complexes. The sulfonic acid of 13, which binds about one-fourth as tightly as the phosphonate 12, binds in the phosphate subsite much like the phosphonic acid. The carboxylic acid, the interaction of which is much weaker, turns away from the center of the phosphate binding site to form hydrogen bonds with Ser 200 and Met 219. Thus, the only phosphate mimics that bind like phosphate itself are themselves highly ionic, probably with limited ability to penetrate cell membranes.

Binding Sites↗
PubMed1993

Structure-based design of inhibitors of purine nucleoside phosphorylase. 3. 9-Arylmethyl derivatives of 9-deazaguanine substituted on the methylene group.

X-ray crystallography and computer-assisted molecular modeling (CAMM) studies aided in the design of a potent series of mammalian purine nucleoside phosphorylase (PNP) inhibitors. Enhanced potency was achieved by designing substituted 9-(arylmethyl)-9-deazaguanine analogs that interact favorably with all three of the binding subsites of the PNP active site, namely the purine binding site, the hydrophobic pocket, and the phosphate binding site. The most potent PNP inhibitor prepared during our investigation, (S)-9-[1-(3-chlorophenyl)-2-carboxyethyl]-9-deazaguanine (18b), was shown to have an IC50 of 6 nM, whereas the corresponding (R)-isomer was 30-fold less potent.

Binding Sites↗
PubMed1993

Three-dimensional structure of influenza A N9 neuraminidase and its complex with the inhibitor 2-deoxy 2,3-dehydro-N-acetyl neuraminic acid.

We present here the three-dimensional structure of neuraminidase (E.C. 3.2.1.18) from influenza virus A/Tern/Australia/G70c/75 (N9), determined by the method of multiple isomorphous replacement, and the structure of the neuraminidase complexed with an inhibitor, 2-deoxy-2,3-dehydro-N-acetyl neuraminic acid (DANA). Native and inhibitor complex crystals are isomorphous and belong to space group I432 with unit cell dimensions of 183.78 A. The native enzyme structure and the inhibitor complex structure have been refined at 2.5 A and 2.8 A resolution, respectively, with crystallographic R-factor values of 0.193 for the native enzyme, and 0.179 for the inhibitor complex. The current enzyme model includes 387 amino acid residues which comprise the asymmetric unit. The root-mean-square deviation from ideal values is 0.013 A for bond lengths and 1.6 degree for bond angles. The neuraminidase (NA), as proteolytically cleaved from the virus, retains full enzymatic and antigenic activity, and is a box-shaped tetramer with edge lengths of 90 A and a maximal depth of 60 A. The NA tetramers are composed of crystallographically equivalent monomers related by circular 4-fold symmetry. Each monomer folds into six antiparallel beta-sheets of four strands. The secondary structure composition is 50% beta-sheet. The remaining 50% of the residues form 24 strand-connecting loops or turns. One of the loops contains a small alpha-helix. The structure of the complex of NA with DANA, a transition state analog, has enabled us to identify and characterize the site of enzyme catalysis. The center of mass of bound inhibitor is 32 A from the 4-fold axis of the tetramer, lodged at the end of a shallow crater of diameter 16 A with a depth of 8 to 10 A. There are 12 amino acid residues that directly bind DANA, with a further six conserved amino acids lining the active site pocket. The neuraminidase inhibitor complex provides a three-dimensional model which will be used to further the understanding of enzymatic hydrolysis and aid the design of specific, antineuraminidase antiviral compounds.

Binding Sites↗
PubMed1993

Structure-based design of inhibitors of purine nucleoside phosphorylase. 2. 9-Alicyclic and 9-heteroalicyclic derivatives of 9-deazaguanine.

Alicyclic and heteroalicyclic derivatives of 9-deazaguanine (2-amino-1,5-dihydro-4H-pyrrolo[3,2-d] [pyrimidin-4-one) are, with one exception, potent inhibitors of purine nucleoside phosphorylase (PNP) equaling the corresponding 9-arylmethyl derivatives previously investigated. The mode of binding of these compounds to PNP was determined by X-ray crystallography.

Binding Sites↗
PubMed1993

Structure-based design of inhibitors of purine nucleoside phosphorylase. 1. 9-(arylmethyl) derivatives of 9-deazaguanine.

Purine nucleoside phosphorylase (PNP, EC 2.4.2.1) is a salvage enzyme important to the T-cell-mediated part of the immune system and as such is an important therapeutic target. This paper describes the design, synthesis, and enzymatic evaluation of potent, competitive inhibitors of PNP. Potential inhibitors were designed using the three-dimensional structure of the enzyme in an iterative process that involved interactive computer graphics to model the native enzyme and complexes of it with the inhibitors, Monte Carlo-based conformational searching, and energy minimization. Studies of the enzyme/inhibitor complexes were used to determine priorities of the synthetic efforts. The resulting compounds were then evaluated by determination of their IC50 values and by X-ray diffraction analysis using difference Fourier maps. In this manner, we have developed a series of 9-(arylmethyl)-9-deazapurines (2-amino-7-(arylmethyl)-4H-pyrrolo[3,2-d]-pyrimidin-4-ones) that are potent, membrane-permeable inhibitors of the enzyme. The IC50 values of these compounds range from 17 to 270 nM (in 1 mM phosphate), with 9-(3,4-dichlorobenzyl)-9-deazaguanine being the most potent inhibitor. X-ray analysis explained the role of the aryl groups and revealed the rearrangement of hydrogen bonds in the binding of the 9-deazaguanines in the active site of PNP relative to the binding of the 8-aminoguanines that results in more potent inhibition of the enzyme.

Animals↗
PubMed1991

Application of crystallographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors.

Competitive inhibitors of the salvage pathway enzyme purine-nucleoside phosphorylase (purine-nucleoside:orthophosphate ribosyltransferase, EC 2.4.2.1) have been designed by using the three-dimensional structure of the enzyme as determined by x-ray crystallography. The process was an iterative one that utilized interactive computer graphics, Monte Carlo-based conformational searching, energy minimization, and x-ray crystallography. The proposed compounds were synthesized and tested by an in vitro assay. Among the compounds designed and synthesized are the most potent competitive inhibitors of purine nucleoside phosphorylase thus far reported.

Amino Acid Sequence↗
PubMed1991

Crystallization and preliminary X-ray investigation of a sarcoplasmic calcium-binding protein from amphioxus.

Crystals of a sarcoplasmic Ca(2+)-binding protein from the protochordate amphioxus have been grown from solutions of ammonium sulfate. The crystals are orthorhombic, space group C222(1), with unit cell axes a = 59.6(1) A, b = 81.3(1) A and c = 82.4(1) A. There is one molecule in the asymmetric unit. The crystals diffract beyond 2.5 A and show less than 20% decline in diffraction intensities after a three day exposure to X-rays from a laboratory rotating anode source.

Ammonium Sulfate↗
PubMed1991

Crystallization and preliminary X-ray investigation of factor D of human complement.

Human factor D, an essential enzyme of the alternative pathway of complement activation, has been crystallized. Crystals were grown by vapor diffusion using polyethylene glycol 6000 and NaCl as precipitants. The factor D crystals are triclinic and the space group is P1 with unit cell dimensions a = 40.8 A, b = 64.7 A, c = 40.3 A, alpha = 101.0 degrees, beta = 109.7 degrees, gamma = 74.3 degrees. The unit cell contains two molecules of factor D related by a non-crystallographic 2-fold axis. The crystals grow to dimensions of 0.8 mm x 0.5 mm x 0.2 mm within five days, are stable in the X-ray beam and diffract beyond 2.5 A.

Complement Factor D↗
PubMed1991

Purification, crystallization and preliminary crystallographic analysis of porcine aldose reductase.

Large crystals of porcine aldose reductase have been grown from polyethylene glycol solutions. The crystals are triclinic, space-group P1, with a = 81.3 A, b = 85.9 A, c = 56.6 A, alpha = 102.3 degrees, beta = 103.3 degrees and gamma = 79.0 degrees. The crystals grow within ten days to dimensions of 0.6 mm x 0.4 mm x 0.2 mm and diffract to at least 2.5 A. There are four molecules in the unit cell related by a set of three mutually perpendicular non-crystallographic 2-fold axes.

Aldehyde Reductase↗
PubMed1991

Three-dimensional structure of a sarcoplasmic calcium-binding protein from Nereis diversicolor.

The three-dimensional structure of a sarcoplasmic Ca2(+)-binding protein from the sandworm Nereis diversicolor has been determined at 3.0 A resolution using multiple isomorphous replacement techniques. The NH2-terminal half of the molecule contains one variant Ca2(+)-binding domain with a novel helix-loop-helix conformation and one Ca2(+)-binding domain that is no longer functional because of amino acid changes. The overall conformation of this pair of domains is different from any previously described Ca2(+)-binding protein. The COOH-terminal half of the protein contains two Ca2(+)-binding domains with the usual helix-loop-helix configuration and is similar to calmodulin and troponin C. Unlike calmodulin or troponin C, there is no exposed alpha-helix connecting the two halves of the molecule, so the overall structure is much more compact.

Amino Acid Sequence↗
PubMed1990

Rotation function studies of human C-reactive protein.

Rotation function studies of two tetragonal crystal forms of human C-reactive protein have confirmed the pentameric structure of the molecule. The two crystal forms have space groups P4122 (I) and P4222 (II) with closely similar unit cells and are often twinned together. Investigation of the crystallization conditions indicates that dissociation heterogeneity has been a major limiting factor in the reproducible growth of good single crystals. The orientation of the pentameric molecule is shown to be almost identical in both forms, about the axial direction omega = 57 degrees, phi = 45 degrees, i.e. 57 degrees away from c in the (110) plane.

C-Reactive Protein↗
PubMed1990

Three-dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2 A resolution.

The three-dimensional structure of human erythrocytic purine nucleoside phosphorylase has been determined at 3.2 A resolution using x-ray diffraction data. Intensity data were measured using radiation from the Synchrotron Radiation Source, Daresbury, England, and oscillation film techniques. Phases were determined by using multiple isomorphous replacement methods with four heavy-atom derivatives and were improved using solvent flattening techniques. Purine nucleoside phosphorylase exists in the crystal as a trimer in which subunits are related by a crystallographic 3-fold axis. Each subunit contains an eight-stranded mixed beta-sheet and a five-stranded mixed beta-sheet which join to form a distorted beta-barrel structure. This core beta-structure is flanked by seven alpha-helices in a manner that generates a novel folding pattern. The active site, which was characterized from binding of the substrate analogs 8-iodoguanine and 5'-iodoformycin B, is located near the subunit-subunit boundary within the trimer and involves seven different segments from one subunit and an additional short segment from an adjacent subunit. In the crystal, the phosphate-binding site is probably occupied by a sulfate ion. The specificity of purine nucleoside phosphorylase for guanine, hypoxanthine, and their analogs can be explained on the basis of the arrangement of hydrogen bond donors and acceptors in the active site.

Amino Acid Sequence↗
PubMed1988

Structure of calmodulin refined at 2.2 A resolution.

The crystal structure of mammalian calmodulin has been refined at 2.2 A (1 A = 0.1 nm) resolution using a restrained least-squares method. The final crystallographic R-factor, based on 6685 reflections in the range 2.2 A less than or equal to d less than or equal to 5.0 A with intensities exceeding 2.5 sigma, is 0.175. Bond lengths and bond angles in the molecule have root-mean-square deviations from ideal values of 0.016 A and 1.7 degrees, respectively. The refined model includes residues 5 to 147, four Ca2+ and 69 water molecules per molecule of calmodulin. The electron density for residues 1 to 4 and 148 is poorly defined, and they are not included in the model. The molecule is shaped somewhat like a dumbbell, with an overall length of 65 A; the two lobes are connected by a seven-turn alpha-helix. Prominent secondary structural features include seven alpha-helices, four Ca2+-binding loops, and two short, double-stranded antiparallel beta-sheets between pairs of adjacent Ca2+-binding loops. The four Ca2+-binding domains in calmodulin have a typical EF hand conformation (helix-loop-helix) and are similar to those described in other Ca2+-binding proteins. The X-ray structure determination of calmodulin shows a large hydrophobic cleft in each half of the molecule. These hydrophobic regions probably represent the sites of interaction with many of the pharmacological agents known to bind to calmodulin.

Amino Acid Sequence↗
PubMed1988

Crystallization and preliminary X-ray analyses of two neuraminidases from influenza B virus strains B/Hong Kong/8/73 and B/Lee/40.

Crystals of neuraminidase heads from two different influenza B virus strains have been grown. Neuraminidase crystals of influenza B/Hong Kong/8/73 were grown from solutions of potassium phosphate. The crystals are tetragonal prisms, space group I422; the axes are a = 123 A and c = 165 A. Influenza B/Lee/40 neuraminidase crystals were grown from solutions of polyethylene glycol 4000. The crystals are tetragonal pyramids, space group P4(1)2(1)2 or its enantiomorph P4(3)2(1)2; the axes are a = 125 A and c = 282 A.

Crystallization↗
PubMed1988

Crystallization and preliminary X-ray analysis of type B influenza virus neuraminidase complexed with antibody Fab fragments.

Fab fragments from four different monoclonal antibodies have been complexed with influenza B virus neuraminidase (B/Lee/40) and the complexes have been crystallized. Three of the complex crystals are, so far, not suitable for X-ray diffraction studies, but the fourth (B/Lee/40 NA-B1Fab) forms large crystals which diffract X-rays to 3.0 A resolution. The crystals have a space group of F432, a = 441.21 A. Vm calculations show that the asymmetric unit contains two monomeric complexes.

Antibodies, Monoclonal↗
PubMed1987

Crystallization and preliminary x-ray investigation of sarcoplasmic calcium-binding protein from Nereis diversicolor.

Crystals of sarcoplasmic calcium-binding proteins from Nereis diversicolor have been grown from solutions of ammonium sulfate. The crystals are monoclinic, space group P2(1); the axes are a = 43.65 (1), b = 56.05 (1), c = 65.77 (1) A, and beta = 92.58 (2) degrees. The crystals are quite stable to x-rays and diffract beyond 2.5 A resolution. The asymmetric unit contains two protein molecules.

Animals↗