Conformational analysis of cocaine,the potent analog 2β-carbomethoxy-3β-(4-fluorophenyl)tropane (CFT), and other dopamine reuptake blockers

Using the MM2-87 program and parameter set, conformational analyses have been performed on cocaine ( 1 ), the potent analog 2β-carbomethoxy-3β-(4-fluorophenyl)tropane (CFT, 2 ), and a group of dopamine reuptake blockers that contain two phenyl rings. The latter includes LU 19-005 ( 3 ), a 1-amino-4-phenyltetralin ( 4 ), a hexahydropyrrolo[2,1-a]isoquinoline ( 5 ), diclofensine ( 6 ), and a hexahydro[1,2-b]pyridine ( 7 ). Using different values for the dielectric constant, the global minimum of 1 and 2 is a conformer in which there is a favorable electrostatic interaction between the ammonium hydrogen and the carbonyl of the carbomethoxy group. The N-methyl groups in 1 and 2 are found to strongly prefer the equatorial position of the piperidine ring. These results were also related to four crystal structures of 1 and its close derivatives. Compounds 3–7 are found to have a common conformation that was used to define the pharmacophore for dopamine reuptake blockers including the required orientation of the ammonium hydrogen. The pharmacophore provides an explanation for why the tertiary amine analogs of 3 and 4 are less potent than the secondary amines because the added N-methyl group occupies the position required for the ammonium hydrogen. This explanation, however, does not work for 7 , in which the tertiary amine is again less active than the secondary amine. However, this last series appears to have a number of anomalous features. Superposition of 2 with the pharmacophore suggests that its carbomethoxy may occupy the same region of the receptor as the second phenyl ring in compounds 3–7 . © 1993 John Wiley & Sons, Inc.     

Substrate-assisted antibody catalysis

A new strategy in transition-state analog design is demonstrated to elicit catalytic antibodies. The strategy is based on substrate-assisted antibody catalysis and utilizes analogs designed to mimic the transition-state for intramolecular catalysis and thereby favor antibodies that can recruit catalytic groups from substrate. The hydrolysis of the benzoyl ester of cocaine provides an illustration. The benzoyl ester of cocaine is distant from the protonated nitrogen in the stable chair conformer but proximate in the strained boat form. An antibody stabilizing the boat form and approximating ester and amine could catalyze ester hydrolysis. To mimic the transition-state for the intramolecular catalysis, we synthesized a cocaine analog that replaces this ester with a methylenephenylphosphinate bridge to the tropane nitrogen. This bridged analog elicited 85 cocaine esterases out of 450 anti-analog antibodies-a performance markedly superior to that of a simple phosphonate ester-based analog with an identical tether. The correspondence of the analog to a "high energy" conformer eliminated product inhibition. For certain polyfunctional targets, substrate assistance can be an effective strategy for eliciting catalytic antibodies.     

Formation of the C ring in the lanosterol biosynthesis from squalene

[reaction: see text] Ab initio calculations were performed on a cyclohexane derivative to elucidate the mechanism of the formation of the five-membered C ring in the biosynthesis of lanosterol from squalene. A conformational analysis of the side chain containing the double bond indicated that the conformer that should give rise to the cyclized C ring is not a minimum on the potential surface. Consequently, it is suggested that it is very likely that C-ring formation occurs in concert with formation of the A and B rings.     

Structural aspects of phencyclidines: crystal structure and quantum mechanical calculations for 1-[1-(2-thienyl)cyclohexyl] piperidine and its hydrochloride

Crystal structure determinations for neutral and protonated phencyclidine, 1-[1-(2-thienyl)cyclohexyl] piperidine, show that the piperidine-axial conformer on the cyclohexane ring is present in the neutral compound, and that the piperidine-equatorial conformer in the protonated species. Quantum mechanical calculations in vacuo using ab initio techniques also arrive at the same conclusion. A search of the crystallographic literature via the Cambridge structural database reveals that all protonated phencyclidines assume the piperidine-equatorial conformation, and most neutral phencyclidines assume the piperidine-axial conformation.     

Synthetic Routes to a Constrained Ring Analog of Didemnin B

The didemnin class of biologically active cyclodepsipeptides, isolated from a marine tunicate, has shown antitumor, antiviral, and immunosuppressive activities. Synthetic studies were undertaken to prepare a modified analog of one of the most potent congeners, didemnin B (1). The side chain of the isostatine unit was tethered into the macrocycle viaa cyclohexane ring in order to provide a more rigid conformation and determine the importance of this unit in bioactive compounds. This modification created a new macrocycle core and generated a diastereomeric mixture of a constrained analog of didemnin B (2).     

Effect of ring size on the tautomerization and ionization reaction of cyclic 2-nitroalkanones: an experimental and theoretical study

The keto-enol tautomerism of some cyclic 2-nitroalkanones was studied in cyclohexane. Keto-enol equilibrium constants, K(T), at 25 °C were obtained from (1)H NMR spectra. The relative enol content for the investigated ketones as a function of ring size decreases in the order 6 > 7 > 11 > 12 > 15. This trend apparently is different from that observed in water. Density functional theory (DFT) calculations have been performed to rationalize the effects of ring size and of the solvent on tautomerism. The acidity constants, K(a)(KH), for the different keto tautomers were measured spectrophotometrically at 25 °C in buffered aqueous solutions. No simple correlations between K(a)(KH) and ring size was observed, and this is in agreement with a DFT analysis performed on the same compounds.     

First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine

We have performed a series of first-principles electronic structure calculations to examine the reaction pathways and the corresponding free energy barriers for the ester hydrolysis of protonated cocaine in its chair and boat conformations. The calculated free energy barriers for the benzoyl ester hydrolysis of protonated chair cocaine are close to the corresponding barriers calculated for the benzoyl ester hydrolysis of neutral cocaine. However, the free energy barrier calculated for the methyl ester hydrolysis of protonated cocaine in its chair conformation is significantly lower than for the methyl ester hydrolysis of neutral cocaine and for the dominant pathway of the benzoyl ester hydrolysis of protonated cocaine. The significant decrease of the free energy barrier, approximately 4 kcal/mol, is attributed to the intramolecular acid catalysis of the methyl ester hydrolysis of protonated cocaine, because the transition state structure is stabilized by the strong hydrogen bond between the carbonyl oxygen of the methyl ester moiety and the protonated tropane N. The relative magnitudes of the free energy barriers calculated for different pathways of the ester hydrolysis of protonated chair cocaine are consistent with the experimental kinetic data for cocaine hydrolysis under physiologic conditions. Similar intramolecular acid catalysis also occurs for the benzoyl ester hydrolysis of (protonated) boat cocaine in the physiologic condition, although the contribution of the intramolecular hydrogen bonding to transition state stabilization is negligible. Nonetheless, the predictability of the intramolecular hydrogen bonding could be useful in generating antibody-based catalysts that recruit cocaine to the boat conformation and an analog that elicited antibodies to approximate the protonated tropane N and the benzoyl O more closely than the natural boat conformer might increase the contribution from hydrogen bonding. Such a stable analog of the transition state for intramolecular catalysis of cocaine benzoyl-ester hydrolysis was synthesized and used to successfully elicit a number of anticocaine catalytic antibodies.     

A carbon-13 cp/mas NMR investigation of the conformation of substituted cyclohexanes in thiourea inclusion compounds

Inclusion compounds of several monosubstituted cyclohexanes and thiourea have been studied using high-resolution ¹³C CP/MAS NMR spectroscopy. The ¹³C NMR chemical shifts of the substituted cyclohexane ring are sensitive to the conformation of the substituent and allow one to predict qualitatively the relative populations of the axial and equatorial conformers. For methylcyclohexane trapped in thiourea the methyl substituent prefers the equatorial conformation while for the cyclohexyl halides (Cl, Br and I) the axial conformer is preferred. In the case of fluorocyclohexane the equatorial conformer appears to predominate; however, this conformer is in rapid equilibrium with the axial conformer.     

Hierarchical clustering analysis of flexible GBR 12909 dialkyl piperazine and piperidine analogs

Pharmacophore modeling of large, drug-like molecules, such as the dopamine reuptake inhibitor GBR 12909, is complicated by their flexibility. A comprehensive hierarchical clustering study of two GBR 12909 analogs was performed to identify representative conformers for input to three-dimensional quantitative structure–activity relationship studies of closely-related analogs. Two data sets of more than 700 conformers each produced by random search conformational analysis of a piperazine and a piperidine GBR 12909 analog were studied. Several clustering studies were carried out based on different feature sets that include the important pharmacophore elements. The distance maps, the plot of the effective number of clusters versus actual number of clusters, and the novel derived clustering statistic, percentage change in the effective number of clusters, were shown to be useful in determining the appropriate clustering level.Six clusters were chosen for each analog, each representing a different region of the torsional angle space that determines the relative orientation of the pharmacophore elements. Conformers of each cluster that are representative of these regions were identified and compared for each analog. This study illustrates the utility of using hierarchical clustering for the classification of conformers of highly flexible molecules in terms of the three-dimensional spatial orientation of key pharmacophore elements.     

Nitrogen bridgehead compounds VIII . Ring transformations IV . Synthesis and reactions of 2,3-Cycloalkylene-4H-pyrido [1,2-a] pyrimidin-4-ones

By condensing alicyclic β-ketocarboxylates with substituted 2-aminopyridines in polyphosphoric acid or phosphoryl chloride-polyphosphoric acid, numerous 2,3-tri-, tetra-, penta- and hexamethylene-4H-pvrido[1,2-a]pyrimidin-4-ones were synthesized for pharmacological purposes. The stability and several reactions of the title compounds were studied. The 6-substituted-4H-pyrido[1,2-a]pyrimidin-4-ones were transformed into 1,8-naphthyridines in good yields independent of the ring size of ring C . The characteristic differences in the ir and uv spectra of the pyrido-pyrimidines and the corresponding naphthyridines are discussed. Catalytic hydrogenation of the pyrido[1,2-a]pyrimidin-4-ones furnished the corresponding 6,7,8,9-tetrahydropyrido-[1,2-a]pyrimidin-4-one derivatives. It was found that the A and C rings attached to the pyrirnidinone ring in solutions of unsubstituted tetrahydropyrido[1,2-a]pyrimidin-4-ones are flexible, whereas in the 6-methyl derivatives the conformer containing the 6-methyl group in axial position predominates.     

Study of the dative bond in 2-aminoethoxydiphenyl borate at various levels of theory: another poor performance of the B3LYP method for B-N dative bonds

Aminoethoxydiphenyl borate (2-APB), 1, is a potent inhibitor of store-operated calcium entry channels (SOCCs). Other SOCC inhibitors are being investigated as promising pharmacological agents for a variety of conditions. Though toxic, 2-APB could be useful in the development of additional inhibitors, but its preferred binding structure must first be determined. Thus, we performed ab initio calculations to study the conformers and the strength of the dative bond of 2-APB. As a first step, we performed a series of computations at various levels of theory. We obtained vastly different dissociation energies for the dative bond depending on whether we used MP2 or B3LYP (7-10 kcal/mol different). This discrepancy has previously been observed for other B-N dative bonds by Gilbert, who found that the MP2 values were in much better agreement with experimental values (Gilbert, T. M. J. Phys. Chem. A 2004, 108, 2550-2554). Since we lacked experimental data for comparison, we performed CCSD(T) calculations and found them to have similar results to those from MP2. Thus, we conclude that MP2 is more accurate for 2-APB. The dissociation free energy at the MP2 level is 7 kcal/mol and indicates that the dative bond conformer will be the predominant structure in the gas phase. The dissociation energy is comparatively low due to the electron donation from the oxygen atom to the boron atom and due to the ring strain in the dative bond conformer.     

Dimers of boroglycine and methylamine boronic acid: a computational comparison of the relative importance of dative versus hydrogen bonding

Boronic acids are widely used in materials science, pharmacology, and the synthesis of biologically active compounds. In this Article, geometrical structures and relative energies of dimers of boroglycine, H2N-CH2-B(OH)2, and its constitutional isomer H3C-NH-B(OH)2, were computed using second-order M?ller-Plesset perturbation theory and density functional theory; Dunning-Woon correlation-consistent cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ basis sets were employed for the MP2 calculations, and the Pople 6-311++G(d,p) basis set was employed for a majority of the DFT calculations. Effects of an aqueous environment were incorporated into the results using PCM and COSMO-RS methodology. The lowest-energy conformer of the H2N-CH2-B(OH)2 dimer was a six-membered ring structure (chair conformation; Ci symmetry) with two intermolecular B:N dative-bonds; it was 14.0 kcal/mol lower in energy at the MP2/aug-cc-pVDZ computational level than a conformer with the classic eight-centered ring structure (Ci symmetry) in which the boroglycine monomers are linked by a pair of H-O...H bonds. Compared to the results of MP2 calculations with correlation-consistent basis sets, DFT calculations using the PBE1PBE and TPSS functionals with the 6-311++G(d,p) basis set were significantly better at predicting relative conformational energies of the H2N-CH2-B(OH)2 and H3C-NH-B(OH)2 dimers than corresponding calculations using the BLYP, B3LYP, OLYP, and O3LYP functionals, particularly with respect to dative-bonded structures.     

Regioselective dehydration of axial and equatorial tertiary alcohols with α-methyl group in the cyclohexane ring by Swern’s reagent

Swern’s reagent (a complex of oxalyl chloride with DMSO) was shown to dehydrate tertiary alcohols containing an α-methyl group in the cyclohexane ring. Dehydration of equatorial alcohols affords mixtures of isomeric compounds where isomers with an exocyclic double bond dominate, whereas isomers with an endocyclic double bond prevail in the products of dehydration of axial tertiary alcohols. Thus, Swern’s reagent can serve as a chemical test to determine the configuration of tertiary alcohols containing an α-methyl group in cyclohexane ring. The composition of the products of dehydration of these alcohols with Swern’s reagent is similar to that obtained by their dehydration with POCl₃ in pyridine. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 800–803, April, 1997.     

Conformational equilibrium in 8-methyl-cis-2-thiahydrindane and 8-methyl-cis-2-oxahydrindane by 13C NMR spectroscopy

The preferred conformation of 8-methyl-cis-thiahydrindane has been both estimated by ¹³C NMR chemical shifts and determined by low temperature ¹³C NMR spectroscopy to be the conformer with the methyl group equatorial with respect to the cyclohexane ring. This result is in disagreement with the interpretation of the temperature dependence of the CD spectra of (+) and (?) 8-methyl-cis-2-thiahydrindane, whereby the conformation with the methyl group axial with respect to the cyclohexane ring was claimed to be the preferred conformation. The preferred conformation of the related oxygen heterocycle, 8-methyl-cis-2-oxahydrindane, has been estimated by ¹³C NMR chemical shifts to be the conformer with the methyl group axial with respect to the cyclohexane ring. Possible reasons for these observations are discussed.     

Azoles and azines. 62. Structure of 2-aryl-1,3-oxazine-4,6-diones

¹H,¹³C NMR, IR, and UV spectra have been studied for solutions of a number of potentially tautomeric 2-aryl-1,3-oxazine-4,6-diones and their 5-methyl substituted analogs with variation of substituent at the para position of the benzene ring, as well as compounds with a fixed structure that simulates possible tautomeric forms. The data have been compared with the results of quantum chemical calculations carried out in SSO MO LCAO approximation by the CNO, CNDO/2, and MPNDO/3 methods. In DMSO and THF solution the test compounds exist predominantly as 2-aryl-4-hydroxy-6H-1,3-oxazin-6-ones. The para substituent in the benzene ring does not affect the composition of the tautomer mixture significantly.For Communication 61, see [1].Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 386–394, March, 1987.     

Computer-aided drug design: A free energy perturbation study on the binding of methyl-substituted pterins and N5-deazapterins to dihydrofolate reductase

Summary Molecular dynamics simulation and free energy perturbation techniques have been used to study the relative binding free energies of 8-methylpterins and 8-methyl-N5-deazapterins to dihydrofolate reductase (DHFR). Methyl-substitution at the 5, 6 and 7 positions in the N-heterocyclic ring gives rise to a variety of ring substituent patterns and biological activity: several of these methyl derivatives of the 8-methyl parent compounds (8-methylpterin and 8-methyl-N5-deazapterin) have been identified as substrates or inhibitors of vertebrate DHFR in previous work. The calculated free energy differences reveal that the methyl-substituted compounds are thermodynamically more stable than the primary compounds (8-methylpterin and 8-methyl-N5-deazapterin) when bound to the enzyme, due largely to hydrophobic hydration phenomena. Methyl substitution at the 5 and/or 7 positions in the 6-methyl-substituted compounds has only a small effect on the stability of ligand binding. Furthermore, repulsive interactions between the 6-methyl substituent and DHFR are minimal, suggesting that the 6-methyl position is optimal for binding. The results also show that similarly substituted 8-methylpterins and 8-methyl-N5-deazapterins have very similar affinities for binding to DHFR. The computer simulation predictions are in broad agreement with experimental data obtained from kinetic studies, i.e. 6,8-dimethylpterin is a more efficient substrate than 8-methylpterin and 6,8-dimethyl-N5-deazapterin is a better inhibitor than 8-methyl-N5-deazapterin.     

Stereoselectivity and substrate specificity in the kinetic resolution of methyl-substituted 1-oxaspiro[2.5]octanes by Rhodotorula glutinis epoxide hydrolase

The kinetic resolution of a range of methyl-substituted 1-oxaspiro[2.5]octanes by yeast epoxide hydrolase (YEH) from Rhodotorula glutinis has been investigated. The structural determinants of substrate specificity and stereoselectivity of YEH toward these substrates appeared to be the configuration of the epoxide ring and the substitution pattern of the cyclohexane ring. For all compounds tested, O-axial epoxides were hydrolyzed faster than the corresponding O-equatorial compounds. In concern of the ring substituents, YEH preferred methyl groups on the Re side of the ring. Placement of substituents close to the spiroepoxide carbon decreased the reaction rate but increased enantioselectivity. YEH-catalyzed kinetic resolutions of 4-methyl 1-oxaspiro[2.5]octane epimers were most enantioselective (E > 100).     

Why Doesn't all-trans-1,2,3,4,5,6-Hexaspiro(THF)cyclohexane complex metal ions?

Despite the inherent preference for placing alkyl substituents, rather than alkoxy substituents, in equatorial positions, all-trans-hexaspiro(THF)cyclohexane strongly favors the all-O-equatorial conformer. Ab initio and density functional calculations on a series of cyclohexane derivatives containing one, two, or three spiro(THF) units demonstrate that this preference results from at least two important factors. First, when oxygen atoms are attached to adjacent carbons, the gauche effect favors the di-O-equatorial arrangement. In trans-1,2-dispiro(THF)cyclohexane, the single gauche interaction overcomes the inherent steric preference for projecting the two oxygen atoms axially. Similarly, in the all-trans-hexaspiro(THF)cyclohexane the six gauche interactions in the all-O-equatorial conformer overpower the inherent conformational biases of the six isolated spiro(THF) moieties. Nevertheless, the gauche effect only partially accounts for the more than 20 kcal/mol conformational bias calculated for this molecule. There is also another factor, the high energetic cost associated with projecting multiple alkoxy substituents axially on the same face of a cyclohexane scaffold. The calculations find the energetic cost of each 1,3-diaxial interaction is about 2 kcal/mol larger between alkoxy substituents than between alkyl substituents.     

Synthetic and structural studies on macrocyclic amino cyclitols--conformational chameleons

Starting from quinic acid the synthesis of 1,4-butanediol-linked macrocyclic aminocyclitols 30, 32, 34, 36 and 38 is described. Assembly was achieved by olefin cross-metathesis of appropriate cyclohexyl allyl ethers followed by ring-closing metathesis of bis-O-allyl homodimers. In all five cases studied, the only products that were formed were those resulting from direct ring-closing metathesis; the formation of larger rings was not detected. These macrocycles exhibited diverse conformational behaviour which included formation of stable separable conformers 31a and 31b as well as conformationally dynamic macrocycles 35 in which a ring flip in one cyclohexane chair conformer induces a ring flip of the other cyclohexane ring through the linking chains of the macrocycles. The activation energy for the inversion of the chair conformation in this process was determined to be about 38 kJ mol(-1), which is about 7 kJ mol(-1) lower than the activation energy for the ring flip of the unsubstituted cyclohexane ring. In all cases, the conformational studies strongly suggest that intramolecular H-bonding between 1,3-diaxially oriented amido and alcohol or ether groups exerts a decisive contribution to the overall stabilisation of the preferred cyclohexane chair conformation.     

1H NMR spectra and ring shapes of the 4,5,8-trimethyl and 4-methyl derivatives of 1-tetralone

The 220 MHz spectra of the title compounds are reported and values for the internal ring dihedral angle, Ψ, formed between the C-2? C-1 and C-3? C-4 bonds, calculated using the R-value method. The trimethyltetralone exists in a conformer having Ψ = 51° and the 4-methyl group in the axial position. 4-Methyl-1-tetralone exists in a conformational equilibrium where the mean value of Ψ for the conformers adopted is 56°.