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PubMed2001

Conformational analysis of carboxyphenylglycine (CPG) derivatives: insight into bioactive and bioselective conformations of group-I mGluRs antagonists.

A series of carboxyphenylglycine (CPG) derivatives, endowed with diverse activity and selectivity at metabotropic glutamate receptors (mGluRs), were subjected to an extensive conformational analysis by employing molecular mechanics, semiempirical and ab initio methods. The comparison of the conformational profiles of active and inactive CPGs suggests a possible bioactive conformation characterized by a value of 10 degrees for the N-Calpha-C1Ph-C2Ph angle, with this conformation characterized by ammonium group of the amino acid moiety lying on the plane defined by the aromatic ring.

Glycine↗
PubMed1994

Conformational analysis of 5-lipoxygenase inhibitors: role of the substituents in chiral recognition and on the active conformations of the (methoxyalkyl)thiazole and methoxytetrahydropyran series.

The investigation of the SAR of 5-lipoxygenase (5-LO) inhibition of a series of racemic (methoxyalkyl)thiazoles, exemplified by compound 7 (ZM-211965), has led to other active, racemic derivatives in which the thiazole moiety has been replaced by an ester or an ether. Furthermore, the cyclization of the ethers has given a highly potent, but achiral series, the methoxytetrahydropyrans (methoxyTHP), exemplified by 41 (ZD-2138) presently under clinical evaluation. More recent structural investigations have led to chiral members of this series bearing a 2-methyl substituent in the tetrahydropyran ring. The potential for enantioselectivity in each of the three noncyclic, racemic series led us to synthesize the pure enantiomers ((R)-13c, (S)-13c, (R)-13d, (S)-13d, (R)-15c, (S)-15c, (R)-16b, (S)-16b, and (R)-16c, (S)-16c) and to determine their absolute configuration. The biological activity of each enantiomer was evaluated in intact mouse macrophages and in human whole blood and showed that, of these three series, only the thiazole is enantioselective and that the active configuration is (S) (being between 2 and 3 orders of magnitude more potent than the (R) isomer in mouse macrophages). Conformational analysis using systematic conformational searching, molecular mechanics, and semiempirical methods has been performed on the chiral compounds, and the results have helped to explain the enantioselectivity in the thiazole series and to define the role of the substituents around the quaternary carbon. Simultaneously in the achiral tetrahydropyran (THP) series, the critical role of the methoxy substituent has been examined through the synthesis of the ethyl (24b), ester (22b), methoxymethyl ether (26), hydroxymethyl (25b), aldehyde (27b), ketone (29b), hydroxy (31b), and methyl (23b) analogues and by analysis of their biological and conformational properties. This approach, complemented by the results of a similar study carried out on the Z and E isomers of the chiral ethyl-2-methylTHP derivative (39b and 40b), has also led to the characterization of the active conformation in this series. The whole study has identified new elements to clarify the 3D structural requirements of the 5-LO active site.

Animals↗
PubMed1993

Hemophilia B carrier determination based on family-specific mutation detection by DNA single-strand conformation analysis.

Single-strand conformation (SSC) analysis can distinguish normal from variant DNA fragments containing single point mutations by conformation-induced electrophoretic mobility shifts in non-denaturing polyacrylamide gels. We studied 25 hemophilia B kindreds by using SSC analysis after polymerase chain reaction (PCR) amplification of the eight factor IX exons and their intron boundaries. Variant SSC fragments were unambiguously identified in 24 kindreds, and direct DNA sequencing of variant PCR fragments identified 20 different hemophilia B mutations. This technique was used for rapid and accurate carrier determination in female family members without the need for additional sequencing studies, because carriers have both normal and hemophilia family-specific SSC fragments. Of 25 obligate carriers from 15 kindreds, 24 were confirmed to carry variant fragments. The exception, a patient's daughter homozygous for the normal allele, was demonstrated by subsequent PCR genotyping to be the result of non-paternity. In the additional 32 at-risk females from 16 kindreds studied, 19 were identified as carriers and 13 as non-carriers. Eleven of the unique mutations affected restriction enzyme digestion sites, and carriers could then be identified by appropriate restriction enzyme digestion of amplified DNA. Our study, with hemophilia B as a model system, demonstrates the accuracy and efficiency of SSC analysis in screening and tracking unknown mutations in monogenic inherited disorders with known gene sequences.

Base Sequence↗
PubMedDate not supplied

[Study of the spatial organization of the globular fragment of calmodulin. I. Conformational analysis of the domain structure].

Theoretical conformational analysis of dodecapeptide "loop" of one of four domains of CaM is carried out. It's shown that one of the lowest energy conformations of the "loop" can bring about together E(i)- and F(i)-hands till van-der-waals contacts. Predominance and advantages of the calculated conformations are discussed in connection with structural organization of the domains and their capability to bind Ca(2+)-ions. The proposed "alpha-hairpin" structure of the domains is a part of a supersecondary structure of globular lobe of CaM.

Amino Acid Sequence↗
PubMed1987

[Conformation analysis of modified tetrasaccharide sequences of the N-glycoprotein type--problem of the alpha-(1 to 6)-glycosidic bond].

The conformational analysis of the recently synthesized tetrasaccharides alpha-D-Manp (1----3)-[alpha-D-Manp-(1----6)]-4-deoxy-beta-D-lyx-hexp+ ++-(1----4)-D-GlcNAc (2) and alpha-D-Manp-(1----3)-[alpha-D-Manp-(1----6)]-beta-D-Talp -(1----4)-D-GlcNAc (3) will be described. The preferred solution conformation of 2 and 3 is a gt-conformation, which is nearly identical with the preferred conformation of the naturally occurring tetrasaccharide alpha-D-Manp-(1----3)-[alpha-D-Manp-(1----6)]-beta-D-Manp -(1----4)-D-GlcNAc (1). The main structural feature is the backfolding of the alpha-(1----6)-linked D-Man to the reducing D-GlcNAc unit. Conformational analysis of the tetrasaccharides alpha-D-Manp-(1----3)-[alpha-D-Manp-(1----6)]-beta-D-Manp -(1----4)-1,6- anhydro-beta-D-GlcNAc (4), alpha-D-Manp-(1----3)-alpha-D-Manp-(1----6)]-4-deoxy-beta-D- lyx-hexp-(1----4)- 1,6-anhydro-beta-D-GlcNAc (5), and alpha-D-Manp-(1----3)-[alpha-D-Manp-(1----6)]-beta-D-Talp -(1----4)- 1,6-anhydro-beta-D-GlcNAc (6) gave additional proof for this backfolding. The substitution of the reducing unit leads to a smaller amount of gt- and a greater amount of gg-conformers. The method used for conformational analysis of 2-6 is a combination of n.m.r.-experiments and HSEA-calculations with the program GESA. Concerning the application of new 2D-techniques, the COLOC-experiment turned out to be extremely useful in sequencing oligosaccharides.

Carbohydrate Conformation↗
PubMed2005

Focal-point conformational analysis of ethanol, propanol, and isopropanol.

Conformational analysis of three small alcohols--ethanol, propanol, and isopropanol--was carried out by systematically improving the basis set and the level of electron correlation. Correlation energy contributions to conformational energies are strongly basis-set-dependent but accurate energy contributions can be obtained by extrapolation to the basis-set limit. At the basis-set limit, second- and third-order electron correlation effects play a significant role for rotations around the CC-OH, HC-CO, and CC-CO bonds. Specifically, second- and third-order correlation effects strongly stabilize structures in which the hydroxylic hydrogen eclipses with the adjacent carbon; a lesser stabilization is present in structures where the CC-OH moiety is in the gauche form. Fourth-order correlation effects to the CC-OH rotation are small due to a partial cancellation of the singles, doubles, and quadruples contribution by the triples contribution. Electron correlation significantly lowers barriers for methyl-group rotations in ethanol and isopropanol, and in these cases the fourth-order correlation effects are noticeable. The relatively large overall importance of third-order correlation energy contributions raises a concern that the inability to accurately estimate this slowly converging contribution may become a limiting factor when highly accurate conformational energies in larger molecules are sought.

Journal Article↗
PubMed1977

Conformational analysis of cyclo (L-cystine).

Conformational analysis of cyclo(L-cystine) shows that the diketopiperazine ring has to exist only in the boat form. With this geometry, the molecule can adopt two distinct forms differing mainly in the chirality of the disulphide bridge. In both the P- and M-models, corresponding to dihedral angles of nearly +90 degrees and -90 degrees respectively about the S-S- bond, the molecule displays an approximate two-fold symmetry. According to our semi-empirical energy calculations, the minimum energy of the M-model is --9.2 kcal/mol, only 0.3 kcal/mol lower than that of the P-model. Because the difference between the two minima is so small, neither form is clearly superior to the other. However, the number of low energy conformations of the M-model in the allowed conformational space is significantly larger than that of the P-model by a ratio of 3 to 1, and therefore the former is likely to be thermodynamically favoured.

Cystine↗
PubMed1990

Automated conformational analysis and structure generation: algorithms for molecular perception.

Many methodologies for performing automated conformational analysis require some means of "perceiving" a molecule to determine features of interest. Algorithms for finding rings, bond orders, and stereocenters and detecting the presence of substructural fragments have been developed. These algorithms are described, emphasizing their importance in conformational analysis.

Artificial Intelligence↗
PubMed1996

Conformational analysis of D1 dopamine receptor agonists: pharmacophore assessment and receptor mapping.

Compute-aided conformational analysis was used to characterize the agonist pharmacophore for D1 dopamine receptor recognition and activation. Dihydrexidine (DHX), a high-affinity full agonist with limited conformational flexibility, served as a structural template that aided in determining a molecular geometry that would be common for other more flexible, biologically active agonists. The intrinsic activity of the drugs at D1 receptors was assessed by their ability to stimulate adenylate cyclase activity in rat striatal homogenates (the accepted measure of D1 receptor activation). In addition, affinity data on 12 agonists including six purported full agonists (dopamine, dihydrexidine, SKF89626, SKF82958, A70108, and A77636), as well as six less efficacious structural analogs, were obtained from D1 dopamine radioreceptor-binding assays. The active analog approach to pharmacophore building was applied as implemented in the SYBYL software package. Conformational analysis and molecular mechanics calculations were used to determine the lowest energy conformation of the active analogs (i.e., full agonists), as well as the conformations of each compound that displayed a common pharmacophoric geometry. It is hypothesized that DHX and other full agonists may share a D1 pharmacophore made up of two hydroxy groups, the nitrogen atom (ca. 7 A from the oxygen of m-hydroxyl) and the accessory ring system characterized by the angle between its plane and that of the catechol ring (except for dopamine and A77636). For all full agonists (DHX, SKF89626, SKF82958, A70108, A77636, and dopamine), the energy difference between the lowest energy conformer and those that displayed a common pharmacophore geometry was relatively small (< 5 kcal/mol). The pharmacophoric conformations of the full agonists were also used to infer the shape of the receptor binding site. Based on the union of the van der Waals density maps of the active analogs, the excluded receptor volume was calculated. Various inactive analogs (partial agonists with D1 K0.5 > 300 nM) subsequently were used to define the receptor essential volume (i.e., sterically intolerable receptor regions). These volumes, together with the pharmacophore results, were integrated into a three-dimensional model estimating the D1 receptor active site topography.

Adenylyl Cyclases↗
PubMed2000

Solution conformational study of Scyliorhinin I analogues with conformational constraints by two-dimensional NMR and theoretical conformational analysis.

Two analogues of Scyliorhinin I (Scyl), a tachykinin with N-MeLeu in position 8 and a 1,5-disubstituted tetrazole ring between positions 7 and 8, introduced in order to generate local conformational constraints, were synthesized using the solid-phase method. Conformational studies in water and DMSO-d6 were performed on these peptides using a combination of the two-dimensional NMR technique and theoretical conformational analysis. The algorithm of conformational search consisted of the following three stages: (i) extensive global conformational analysis in order to find all low-energy conformations; (ii) calculation of the NOE effects and vicinal coupling constants for each of the low energy conformations; (iii) determining the statistical weights of these conformations by means of a nonlinear least-squares procedure, in order to obtain the best fit of the averaged simulated spectrum to the experimental one. In both solvents the three-dimensional structure of the analogues studied can be interpreted only in terms of an ensemble of multiple conformations. For [MeLeu8]Scyl, the C-terminal 6-10 fragment adopts more rigid structure than the N-terminal one. In the case of the analogue with the tetrazole ring in DMSO-d6 the three-dimensional structure is characterized by two dominant conformers with similar geometry of their backbones. They superimpose especially well (RMSD = 0.28 A) in the 6-9 fragments. All conformers calculated in both solvents superimpose in their C-terminal fragments much better than those of the first analogue. The results obtained indicate that the introduction of the tetrazole ring into the Scyl molecule rigidifies its structure significantly more than that of MeLeu.

Algorithms↗
PubMed1989

[Determination of productive conformations of acetylcholinesterase substrates using theoretical conformational analysis].

All equilibrium conformations of twenty-three acetylcholinesterase effectors were calculated by the molecular mechanics method, nonbonded interactions, torsion energy and energy of bond angles deformation being taken into account. In a series of conformationally flexible derivatives of acetylcholine the correlation was found between hydrolysis rate and population of the completely extended tt-conformation. In a series of cyclic analogues of acetylcholine the high hydrolysis rate occurs only for substrates sterically corresponding to tt-conformation of acetylcholine with regard to disposition of ammonium group, carbonyl oxygen and carbonyl carbon. The hydrolysis rate of acetylcholine derivatives with elongated chain between acetyl and cationic groups is directly proportional to the population of the conformations similar to tt-conformation of acetylcholine. It is concluded that tt-conformation of acetylcholine is productive for acetylcholinesterase hydrolysis.

Acetylcholinesterase↗
PubMed1994

Rhenium-labeled somatostatin analog RC-160. 1H NMR and computer modeling conformational analysis.

The solution conformations of RC-160, cyclic D-Phe1-Cys2-Tyr3-D-Trp4-Lys5-Val6-Cys7+ ++-Trp8-NH2, an analog of the tumor antiproliferatory neuropeptide somatostatin, and RC-160 labeled with rhenium (Re-RC-160), have been determined by using two-dimensional 1H NMR spectroscopy (600 MHz) and restrained molecular dynamics simulations. Re-RC-160 yields the same average solution conformation as does the apo form with an antiparallel beta-sheet fold and a type II' beta-turn centered at D-Trp4-Lys5. These results indicate that the spatial topography of the side chains essential for somatostatin receptor binding is maintained in Re-RC-160.

Amino Acid Sequence↗
PubMed2000

Conformational analysis and docking study of potent factor XIIIa inhibitors having a cyclopropenone ring.

A conformational analysis and docking study of potent factor XIIIa inhibitors having a cyclopropenone ring were carried out in an attempt to obtain structural insight into the inhibition mechanism. First, stable conformers of the inhibitors alone were obtained from the conformational analysis by systematic search and molecular dynamics. Next, a binding form model of factor XIIIa was built based on an X-ray crystal structure of the enzyme. Finally, the docking study of the inhibitors into the model's binding site was performed. From the resulting stable complex structures, it was found that the cyclopropenone ring fits the active site located at the base of the binding cavity with high complementarity. The carbonyl oxygen of the cyclopropenone ring formed a hydrogen bond to the indole NH group of Trp279 and the terminal carbon atom of the reactive C=C double bond was in close proximity to the sulfur atom of the catalytic residue, Cys314. This binding mode suggests a possible inhibition mechanism, whereby the cysteine residue reacts with the cyclopropenone ring of the inhibitor, forming an enzyme-ligand adduct. In addition, the higher interaction energies between factor XIIIa and the inhibitors alluded to the probable binding sites of the ligand side chain.

Cyclopropanes↗
PubMed1997

Detection of somatic mutations in the mitochondrial DNA control region of colorectal and gastric tumors by heteroduplex and single-strand conformation analysis.

Each entire hypervariable region of the mitochondrial DNA control region was screened for mutations from paired normal and tumor DNA corresponding to a group of 21 patients (13 colorectal and 8 gastric adenocarcinomas) using both heteroduplex analysis and single-strand conformation analysis. These two mutation scanning strategies allowed the identification of sequence alterations in 3/13 (23%) colorectal tumors and in 3/8 (37%) gastric tumors. Heteroduplex analysis showed the heteroplasmic state of the majority of these tumor mutations. Sequence analysis revealed two A:T/G:C transitions (nucleotide positions: 16241 and 16166) in hypervariable region 1 (HV1) and two C:G/T:A transitions (nucleotide positions: 76 and 312), one A:T/G:C transition (nucleotide position: 93), a 1-basepair C:G deletion (nucleotide position: 309), and a 2-base-pair CC:GG insertion (nucleotide position: 309) in the HV 2 region. A considerable proportion of these mutations was found in homopolymeric regions which are highly polymorphic among humans. Different mechanisms (clonal expansion, increased oxidative damage, and nuclear mutator mutations) were suggested to explain the increased mitochondrial DNA mutation rate observed in cancer.

Adenocarcinoma↗
PubMedDate not supplied

Comparison of conformational analysis techniques to generate pharmacophore hypotheses using catalyst.

Generation of reliable pharmacophore models is a key strategy in drug design. The quality of a pharmacophore model is known to depend on several factors, with the quality of the conformer sets used perhaps being one of the most important. The goal of this study was to compare different conformational analysis methods to determine if one was superior to the others for pharmacophore generation using Catalyst/HypoGen. The five methods selected were Catalyst/Fast, Catalyst/Best, Omega, Chem-X and MacroModel. Data sets for which Catalysts models had previously been published were selected using defined quality measures. Hypotheses were generated for each of the data sets and the performance of the different conformational analysis methods was compared using both quantitative (cost and correlation coefficients) and qualitative measures (by comparing the hypotheses in terms of the features present and their spatial relationships). Two main conclusions emerged from the study. First, it was not always possible to replicate the literature results. The reasons for these failures are explored in detail, and a template for use in publications that apply the Catalyst methodology is proposed. Second, the faster rule-based methods for conformational analysis give pharmacophore models that are just as good as, and in some cases better than, the models generated using the slower, more rigorous approaches.

Catalysis↗
PubMed1995

Conformational analysis of molecular chains using nano-kinematics.

We present algorithms for 3-D manipulation and conformational analysis of molecular chains, when bond lengths, bond angles and related dihedral angles remain fixed. These algorithms are useful for local deformations of linear molecules, exact ring closure in cyclic molecules and molecular embedding for short chains. Other possible applications include structure prediction, protein folding, conformation energy analysis and 3D molecular matching and docking. The algorithms are applicable to all serial molecular chains and make no assumptions about their geometry. We make use of results on direct and inverse kinematics from robotics and mechanics literature and show the correspondence between kinematics and conformational analysis of molecules. In particular, we pose these problems algebraically and compute all the solutions making use of the structure of these equations and matrix computations. The algorithms have been implemented and perform well in practice. In particular, they take tens of milliseconds on current workstations for local deformations and chain closures on molecular chains consisting of six or fewer rotatable dihedral angles.

Algorithms↗
PubMed1999

5-Substituted pyrimidine 1,5-anhydrohexitols: conformational analysis and interaction with viral thymidine kinase.

Conformational analysis of anhydrohexitol nucleosides using a combination of experimental (X-ray crystallography) and computational methods indicates that those antiviral compounds occur in an equilibrium between two forms, one conformation being adopted in solid phase and in solution, the other found when the nucleosides are in complex with HSV-1 thymidine kinase. The conformational change induced by the enzyme has been investigated.

Crystallography↗