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C L Verlinde

Publications and source records attributed to C L Verlinde.

34 records · Page 2Linked to original sources
PubMed1995

Synthesis and structure-activity relationships of analogs of 2'-deoxy-2'-(3-methoxybenzamido)adenosine, a selective inhibitor of trypanosomal glycosomal glyceraldehyde-3-phosphate dehydrogenase.

In continuation of a project aimed at the structure-based design of drugs against sleeping sickness, analogs of 2'-deoxy-2'-(3-methoxybenzamido)adenosine (1) were synthesized and tested to establish structure-activity relationships for inhibiting glycosomal glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Compound 1 was recently designed using the NAD:GAPDH complexes of the human enzyme and that of Trypanosoma brucei, the causative agent of sleeping sickness. In an effort to exploit an extra hydrophobic domain due to Val 207 of the parasite enzyme, several new 2'-amido-2'-deoxyadenosines were synthesized. Some of them displayed an interesting improvement in inhibitory activity compared to 1. Carbocyclic or acyclic analogs showed marked loss of activity, illustrating the importance of the typical (C-2'-endo) puckering of the ribose moiety. We also describe the synthesis of a pair of compounds that combine the beneficial effects of a 2- and 8-substituted adenine moiety on potency with the beneficial effect of a 2'-amido moiety on selectivity. Unfortunately, in both cases, IC50 values demonstrate the incompatibility of these combined modifications. Finally, introduction of a hydrophobic 5'-amido group on 5'-deoxyadenosine enhances the inhibition of the protozoan enzyme significantly, although the gain in selectivity is mediocre.

Animals↗
PubMed1995

Three-dimensional structure of the diphtheria toxin repressor in complex with divalent cation co-repressors.

BACKGROUND: When Corynebacterium diphtheriae encounters an environment with a low concentration of iron ions, it initiates the synthesis of several virulence factors, including diphtheria toxin. The diphtheria toxin repressor (DtxR) plays a key role in this iron-dependent, global regulatory system and is the prototype for a new family of iron-dependent repressor proteins in Gram-positive bacteria. This study aimed to increase understanding of the general regulatory principles of cation binding to DtxR. RESULTS: The crystal structure of dimeric DtxR holo-repressor in complex with different transition metals shows that each subunit comprises an amino-terminal DNA-binding domain, an interface domain (which contains two metal-binding sites) and a third, very flexible carboxy-terminal domain. Each DNA-binding domain contains a helix-turn-helix motif and has a topology which is very similar to catabolite gene activator protein (CAP). Molecular modeling suggests that bound DNA adopts a bent conformation with helices alpha 3 of DtxR interacting with the major grooves. The two metal-binding sites lie approximately 10 A apart. Binding site 2 is positioned at a potential hinge region between the DNA-binding and interface domains. Residues 98-108 appear to be crucial for the functioning of the repressor; these provide four of the ligands of the two metal-binding sites and three residues at the other side of the helix which are at the heart of the dimer interface. CONCLUSIONS: The crystal structure of the DtxR holorepressor suggests that the divalent cation co-repressor controls motions of the DNA-binding domain. In this way the metal co-repressor governs the distance between operator recognition elements in the two subunits and, consequently, DNA recognition.

Amino Acid Sequence↗
PubMed1994

Selective inhibition of trypanosomal glyceraldehyde-3-phosphate dehydrogenase by protein structure-based design: toward new drugs for the treatment of sleeping sickness.

Within the framework of a project aimed at rational design of drugs against diseases caused by trypanosomes and related hemoflagellate parasites, selective inhibitors of trypanosomal glycolysis were designed, synthesized, and tested. The design was based upon the crystallographically determined structures of the NAD:glyceraldehyde-3-phosphate dehydrogenase complexes of humans and Trypanosoma brucei, the causative agent of sleeping sickness. After one design cycle, using the adenosine part of the NAD cofactor as a lead, the following encouraging results were obtained: (1) a 2-methyl substitution, targeted at a small pocket near Val 36, improves inhibition of the parasite enzyme 12.5-fold; (2) an 8-(thien-2-yl) substitution, aimed at Leu 112 of the parasite enzyme, where the equivalent residue in the mammalian enzyme is Val 100, results in a 167-fold better inhibition of the trypanosomal enzyme, while the inhibition of the human enzyme is improved only 13-fold; (3) exploitation of a "selectivity cleft" created by a unique backbone conformation in the trypanosomal enzyme near the adenosine ribose yields a considerable improvement in selectivity: 2'-deoxy-2'-(3-methoxybenzamido)adenosine inhibits the human enzyme only marginally but enhances inhibition of the parasite enzyme 45-fold when compared with adenosine. The designed inhibitors are not only better inhibitors of T. brucei GAPDH but also of the enzyme from Leishmania mexicana.

Adenosine↗
PubMed1994

Protein crystallography and infectious diseases.

The current rapid growth in the number of known 3-dimensional protein structures is producing a database of structures that is increasingly useful as a starting point for the development of new medically relevant molecules such as drugs, therapeutic proteins, and vaccines. This development is beautifully illustrated in the recent book, Protein structure: New approaches to disease and therapy (Perutz, 1992). There is a great and growing promise for the design of molecules for the treatment or prevention of a wide variety of diseases, an endeavor made possible by the insights derived from the structure and function of crucial proteins from pathogenic organisms and from man. We present here 2 illustrations of structure-based drug design. The first is the prospect of developing antitrypanosomal drugs based on crystallographic, ligand-binding, and molecular modeling studies of glycolytic glycosomal enzymes from Trypanosomatidae. These unicellular organisms are responsible for several tropical diseases, including African and American trypanosomiases, as well as various forms of leishmaniasis. Because the target enzymes are also present in the human host, this project is a pioneering study in selective design. The second illustrative case is the prospect of designing anti-cholera drugs based on detailed analysis of the structure of cholera toxin and the closely related Escherichia coli heat-labile enterotoxin. Such potential drugs can be targeted either at inhibiting the toxin's receptor binding site or at blocking the toxin's intracellular catalytic activity. Study of the Vibrio cholerae and E. coli toxins serves at the same time as an example of a general approach to structure-based vaccine design. These toxins exhibit a remarkable ability to stimulate the mucosal immune system, and early results have suggested that this property can be maintained by engineered fusion proteins based on the native toxin structure. The challenge is thus to incorporate selected epitopes from foreign pathogens into the native framework of the toxin such that crucial features of both the epitope and the toxin are maintained. That is, the modified toxin must continue to evoke a strong mucosal immune response, and this response must be directed against an epitope conformation characteristic of the original pathogen.

Amino Acid Sequence↗
PubMed1993

Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma brucei determined from Laue data.

The three-dimensional structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase [D-glyceraldehyde-3-phosphate:NAD+ oxidoreductase (phosphorylating), EC 1.12.1.12] from the sleeping-sickness parasite Trypanosoma brucei was solved by molecular replacement at 3.2-A resolution with an x-ray data set collected by the Laue method. For data collection, three crystals were exposed to the polychromatic synchrotron x-ray beam for a total of 20.5 sec. The structure was solved by using the Bacillus stearothermophilus enzyme model [Skarzyński, T., Moody, P. C. E. & Wonacott, A. J. (1987) J. Mol. Biol. 193, 171-187] with a partial data set which was 37% complete. The crystals contain six subunits per asymmetric unit, which allowed us to overcome the absence of > 60% of the reflections by 6-fold density averaging. After molecular dynamics refinement, the current molecular model has an R factor of 17.6%. Comparing the structure of the trypanosome enzyme with that of the homologous human muscle enzyme, which was determined at 2.4-A resolution, reveals important structural differences in the NAD binding region. These are of great interest for the design of specific inhibitors of the parasite enzyme.

Animals↗
PubMed1992

Structure of the complex between trypanosomal triosephosphate isomerase and N-hydroxy-4-phosphono-butanamide: binding at the active site despite an "open" flexible loop conformation.

The structure of triosephosphate isomerase from Trypanosoma brucei complexed with the competitive inhibitor N-hydroxy-4-phosphono-butanamide was determined by X-ray crystallography to a resolution of 2.84 A. Full occupancy binding of the inhibitor is observed only at one of the active sites of the homodimeric enzyme where the flexible loop is locked in a completely open conformation by crystal contacts. There is evidence that the inhibitor also binds to the second active site of the enzyme, but with low occupancy. The hydroxamyl group of the inhibitor forms hydrogen bonds to the side chains of Asn 11, Lys 13, and His 95, whereas each of its three methylene units is involved in nonpolar interactions with the side chain of the flexible loop residue Ile 172. Interactions between the hydroxamyl and the catalytic base Glu 167 are absent. The binding of this phosphonate inhibitor exhibits three unusual features: (1) the flexible loop is open, in contrast with the binding mode observed in eight other complexes between triosephosphate isomerase and various phosphate and phosphonate compounds; (2) compared with these complexes the present structure reveals a 1.5-A shift of the anion-binding site; (3) this is the first phosphonate inhibitor that is not forced by the enzyme into an eclipsed conformation about the P-CH2 bond. The results are discussed with respect to an ongoing drug design project aimed at the selective inhibition of glycolytic enzymes of T. brucei.

Amino Acid Sequence↗
PubMed1992

In search of new lead compounds for trypanosomiasis drug design: a protein structure-based linked-fragment approach.

A modular method for pursuing structure-based inhibitor design in the framework of a design cycle is presented. The approach entails four stages: (1) a design pathway is defined in the three-dimensional structure of a target protein; (2) this pathway is divided into subregions; (3) complementary building blocks, also called fragments, are designed in each subregion; complementarity is defined in terms of shape, hydrophobicity, hydrogen bond properties and electrostatics; and (4) fragments from different subregions are linked into potential lead compounds. Stages (3) and (4) are qualitatively guided by force-field calculations. In addition, the designed fragments serve as entries for retrieving existing compounds from chemical databases. This linked-fragment approach has been applied in the design of potentially selective inhibitors of triosephosphate isomerase from Trypanosoma brucei, the causative agent of sleeping sickness.

Animals↗
PubMed1991

Anion binding at the active site of trypanosomal triosephosphate isomerase. Monohydrogen phosphate does not mimic sulphate.

The three-dimensional structure of triosephosphate isomerase complexed with the competitive inhibitor SO-4(2) was determined by X-ray crystallography to a resolution of 0.24 nm. A comparison with the native crystal structure, where SO-4(2) is bound, revealed five changes: (a) a 0.10-nm shift of the anion-binding site; (b) a further closing of the flexible loop of the enzyme; (c) a 'swinging in' of the side chain of the catalytic Glu, that is chi 1 changes from (+) to (-) synclinal; (d) an altered water structure; (e) a disappearance of the conformational heterogeneity at the C-terminus of strand beta 7. Some of these changes may be related to the different hydrogen-bond pattern about the two different anions. However, the distance of 0.10 nm between the sulphur and phosphorus positions is unexpected and remains intriguing.

Animals↗
PubMed1991

Crystallographic and molecular modeling studies on trypanosomal triosephosphate isomerase: a critical assessment of the predicted and observed structures of the complex with 2-phosphoglycerate.

In the continuation of a project aimed at the rational design of drugs against diseases caused by trypanosomes, the crystal structure of trypanosomal triosephosphate isomerase in complex with the active site inhibitor 2-phosphoglycerate has been determined. Two alternative modeling protocols have been attempted to predict the mode of binding of this ligand. In the first protocol, certain key interactions were restrained in the modeling procedure. In the second protocol, a full search of ligand conformational space was performed. In both cases the protein scaffold was kept static. Both protocols produced models which were reasonably close to the observed structure (rms difference less than 2.0 A). Nevertheless, some essential features were missed by each of the protocols. The crystallographic structure of the 2-PGA TIM complex shows that the ligand binds fully within the active site of TIM, with partners for all but one of the ligand's strongly hydrogen bonding groups. Several of the interactions between the ligand and the active site of TIM are seen to be common to all of the complexes so far structurally characterized between trypanosomal triosephosphate isomerase and competitive inhibitors. Such key interactions appear to be the best guide in the prediction of the binding mode of a new inhibitor.

Animals↗
PubMed1990

Structure of the neuroleptic drug 4-amino-N-1-[(1-ethyl-2-pyrrolidinyl)methyl]-5-(ethylsulfonyl)-2- methoxybenzamide (amisulpride).

C17H27N3O4S, Mr = 369.48, monoclinic, P2(1)/c, a = 13.333 (7), b = 7.946 (4), c = 17.550 (10) A, beta = 96.99 (4) degrees, V = 1845 (2) A3, Z = 4, Dm = 1.33, Dx = 1.330 Mg m-3, graphite-monochromated Cu K alpha radiation, lambda = 1.54178 A, mu = 1.744 mm-1, F(000) = 792, T = 293 K. Final R = 0.038 for 2405 unique observed reflections. The folded conformation of the molecule with the least-squares planes of the aromatic and the pyrrolidine rings almost perpendicular is essentially determined by intra- and intermolecular hydrogen bonds. In this way, two pseudorings are formed, one linking the amide H with the methoxy O, and a second one involving the 4-amino H and a sulfonyl O. An intermolecular hydrogen bond forces the planar amide group some 28 degrees out of the plane of the aromatic ring.

Amisulpride↗
PubMed1989

Structure and absolute configuration of two stereoisomers of alpha,alpha'-[iminobis-(methylene)]bis(3,4-dihydro-2H-1-benzopyran-2- methanol) hydrobromide.

alpha,alpha'-1,1'-Bis(3,4-dihydro-2H-benzopyran-2-yl)-2,2'-iminodieth anol hydrobromide. (I) C22H28NO4+.Br-, Mr = 450.37, orthorhombic, P2(1)2(1)2(1), a = 5.1278(1), b = 13.1699(6), c = 30.858(2) A, V = 2083.9(2)A3, Z = 4, Dm = 1.44, D chi = 1.436 Mg m-3, lambda(Cu K alpha) = 1.54178 A, mu(Cu K alpha) = 2.915 mm-1, F(000) = 936, room temperature, final R = 0.054 for 2086 observed reflections. (II) C22H28NO4+.Br-, Mr = 450.37, orthorhombic, P2(1)2(1)2(1), a = 5.1292(2), b = 13.1764(9), c = 30.847(3) A, V = 2084.8(3)A3 lambda(Cu K alpha) = 1.54178A, mu(Cu K alpha) = 2.915 mm-1, F(000) = 936, room temperature, final R = 0.054 for 2676 observed reflections. The two structures are mirror images and the central C--C--N--C--C chain adopts the anti-periplanar-synclinal conformation. The active beta 1-selective adrenergic receptor blocker [isomer (I)] has the S,R,R,S absolute configuration while the inactive isomer (II) has the R,S,S,R configuration. Endless chains are formed by (N-)H...Br hydrogen bonds in the a direction and by (O-)H...Br hydrogen bonds in the b direction.

Adrenergic beta-Antagonists↗
PubMed1989

Structure and conformational analysis of the opioid antagonist (-)-(1R,5R,9R)-5,9-diethyl-2-(3-furylmethyl)-2'-hydroxy-6,7-benzomorpha n (Mr2266).

C21H27NO2, Mr = 325.449, monoclinic, P2(1), a = 16.3916 (7), b = 12.7460 (5), c = 8.9806 (5) A, beta = 107.191 (4) degrees, V = 1792.5 (2) A3, Z = 4, Dm = 1.22 (2), D chi = 1.206 Mg m-3, lambda(Cu K alpha) = 1.54178 A, mu(Cu K alpha) = 0.566 mm-1, F(000) = 704, T = 291 K, final R = 0.048 for 4225 observed reflections. The two molecules present in the asymmetric unit adopt a different conformation with respect to the N-side chain. Starting from the asymmetric carbon and proceeding along the allyl moiety the conformations are antiperiplanar/(-)-anticlinal for molecule 1 and antiperiplanar/(+)-synclinal for molecule 2. The furyl rings engage in aromatic-aromatic interactions which are compared with results from a theoretical study from the literature. Finally, the 3-furyl geometry is evaluated through a Cambridge Structural Database search and CNDO/2 calculations.

Benzomorphans↗
PubMed1989

Structure of a kappa-opioid receptor misfit: (1S,5R,8R,9R)-2'-hydroxy-5,9-dimethyl-8,2-epoxyethano-6,7-benzomorphan hydrochloride.

C16H22NO+2.Cl-, Mr = 295.808, monoclinic, P2(1), a = 11.967 (1), b = 12.529 (1), c = 9.9369 (9) A, beta = 93.00 (1) degrees, V = 1487.8 (2) A3, Z = 4, Dm = 1.32 (2), Dx = 1.321 Mg m-3, lambda(Cu K alpha) = 1.54178 A, mu(Cu K alpha) = 2.289 mm-1, F(000) = 632, T = 291 K, final R = 0.040 for 2448 observed reflections. The two molecules present in the asymmetric unit are linked by an extensive network of hydrogen bonds, including several of the less common (C-)H...O and (C-)-H...Cl types. This interpretation is substantiated by a Mulliken population analysis resulting from CNDO/2 calculations. The major effect of the presence of the epoxyethano bridge is a marked flattening about the N atom of the piperidinium ring. Whether this is sufficient to explain the inactivity of the compound at the opioid kappa receptor is not clear.

Benzomorphans↗