Classical Potential Energy Calculations Research Articles

Conformational Studies of Thyroid Hormones. I. The Diphenyl Ether Moiety

Conformational flexibility round the diphenyl ether linkage in the thyroid hormones has been investigated by means of molecular orbital (AM1) and classical potential-energy calculations. The results obtained from these theoretical approaches are in qualitative agreement with those from n.m.r. spectroscopy, i.e., the barrier to rotation around this structural feature is sufficiently low to allow rapid interconversion between two stable conformers to occur at room temperature. Two pathways of rotation around the diphenyl ether bridge were explored and were both calculated to be approximately 14-15 kJ mol-1 by the AM1 method. This compares with the experimental barrier of 36 kJ mol-1. The potential-energy calculations gave barriers up to an order of magnitude larger which were inconsistent with experimental observations. A comparison of the AM1 data with results from previous studies with CNDO/2, which predicted a larger barrier, is also given. The detailed mode of interconversion around the two torsion angles involved in diphenyl ether rotation is investigated, as is the interplay of the bulky iodo substituents with the second aromatic ring during such conformational changes. The nature of torsion angle cooperation during rotations around this linkage is discussed.

Conformational requirements for convulsant compounds

The conformations of a structurally diverse series of convulsant drugs sharing a common binding site with picrotoxinin were studied to give some clues as to the mechanisms of epilepsy and thus to the design of anti-convulsant drugs. Both classical potential energy calculations and molecular orbital calculations were used to determine low energy conformations able to bind at the receptor. In addition, electrostatic potential energy surfaces were calculated to establish the most likely sites of electrostatic interaction. This information was then used to determine a common pharmacophore for these compounds.

Molecular Modelling of the Active Site of Enkephalin‐Degrading Neutral Endopeptidase‐24.11 (Enkephalinase) An Active Site Model for Neutral Endopeptidase‐24.11

AbstractThe active site regions of thermolysin (TLN) and carboxypeptidase A (CPA) are directly compared by superimposition of the published crystal structures of eight TLN/inhibitor complexes and four CPA‐inhibitor complexes. There is a remarkable similarity in the S′1 region of these two zinc metalloenzymes, and it is suggested that this may be a common feature among other enzymes of this class, including the enkephalin‐degrading neutral endopeptidase or “enkephalinase” (NEP‐24.11). Assuming this common feature, the possible geometry of the S′2 region of enkephalinase was determined by performing classical potential energy calculations on potent NEP‐24.11 inhibitors. The active conformation of these inhibitors was thus identified as similar to that found in the X‐ray crystal structure of TLN/inhibitor complexes. It is proposed that the active site region of TLN should serve as a reasonable model for that of NEP‐24.11. Extension of the model to the case of angiotensin‐converting enzyme (ACE) showed that this enzyme might have a similar S′1 region to the other three enzymes, and allowed further definition of the ACE model previously developed in our laboratory.

ChemInform Abstract: Conformational Analysis of Clinically Active Anticonvulsant Drugs.

A series of ureides active against grand mal epilepsy have been studied by using classical potential energy calculations. The series includes phenyl ethyl and diphenyl derivatives of hydantoins, succinimides, glutarimides, oxazolidine-2,4-diones, pyrimidine-2,6-diones, barbituric acids, and phenacemide. A thorough examination of the conformational possibilities did not reveal an exclusive conformation that could account for their activity. However, comparisons with diazepam and other benzodiazepines known to have the ability to competitively bind with drugs such as diphenylhydantoin at some sites show that there is a distinct conformational preference that may well account for their activity against grand mal epilepsy. The conformational studies led to the proposal of a general model for anticonvulsant activity comprising two aromatic rings or their equivalent in a favored orientation and a third region, usually a cyclic ureide, comprising a number of hydrogen-bond-forming functional groups. The specific placement of hydrogen-bonding groups in this region appears to be of less importance than the correct conformational arrangement of the hydrophobic elements.

Conformational energy calculations and electrostatic potentials of dihydrofolate reductase ligands: relevance to mode of binding and species specificity.

Classical potential energy calculations are reported for a series of 11 structurally diverse substrates, products, and inhibitors of dihydrofolate reductase. In almost every case, the calculations reveal a range of potential biologically active conformations accessible to the molecule, and geometry optimization with molecular mechanics and molecular orbital calculations further expands the range of accessible conformations. The energy calculations are supplemented with electrostatic potential energy surfaces for the heterocyclic components of each molecule. These data are used in conjunction with the energy calculations and the crystallographically determined enzyme structures to compare two alternative proposed binding modes of folates known to bind with their pteridine rings inverted relative to that of methotrexate. It is shown that the conformational flexibility of the connecting chain between the benzoyl glutamate and pteridine moieties in the folates actually allows the pteridine ring to shift between these alternative binding modes, a combination of which may offer the best explanation for the observed activity. The electrostatic potentials and conformational energy data are also used in an attempt to account for the species specificity of inhibitors of mammalian, bacterial, and protozoal dihydrofolate reductases. The results show that while these techniques can be used to explain many of the observed results, others require recourse to the observed crystal structures to provide a satisfactory explanation.

Conformational analysis of clinically active anticonvulsant drugs.

A series of ureides active against grand mal epilepsy have been studied by using classical potential energy calculations. The series includes phenyl ethyl and diphenyl derivatives of hydantoins, succinimides, glutarimides, oxazolidine-2,4-diones, pyrimidine-2,6-diones, barbituric acids, and phenacemide. A thorough examination of the conformational possibilities did not reveal an exclusive conformation that could account for their activity. However, comparisons with diazepam and other benzodiazepines known to have the ability to competitively bind with drugs such as diphenylhydantoin at some sites show that there is a distinct conformational preference that may well account for their activity against grand mal epilepsy. The conformational studies led to the proposal of a general model for anticonvulsant activity comprising two aromatic rings or their equivalent in a favored orientation and a third region, usually a cyclic ureide, comprising a number of hydrogen-bond-forming functional groups. The specific placement of hydrogen-bonding groups in this region appears to be of less importance than the correct conformational arrangement of the hydrophobic elements.

Structure and Conformations of Gaba-Transaminase Inhibitors. I. Multisubstrate Analogs

Two multisubstrate analogues of the transition state in the reaction catalysed by the enzyme GABA- transaminase (E.C. 2.6.1.19), sulfonic acid pyridoxal dervative , C10H16N2O5S (1) and carboxylic acid pyridoxal derivative, C13H18N2O4 (2), have been characterized by X-ray analyses of crystals of (1). HCl , (1).H2O and (2). HCl . In each structure, the nitrogen on the side chain is the donor in intramolecular hydrogen bonding. However, it is only in (2). HCl that this interaction is with the phenolic oxygen as postulated in the proposed transition state of the reaction catalysed by GABA- transaminase . For both structures of (1), on the other hand, this interaction is with the oxygen of the ring hydroxymethyl substituent, and results in a seven- membered ring. Conformational analysis indicates that both modes of hydrogen bonding may be present in the pyridoxal derivatives, although no quantitative assessment is possible at the MINDO/3 or MNDO levels. Simple classical potential energy calculations indicate significant structural differences between the lowest energy conformations of these compounds and the calculated transition state. However, conformations which match the key features of the transition state are also relatively low in energy.

Conformational Analysis of Nitroglycerin

AbstractThe conformation of the energetic plasticizer, nitroglycerin, has been studied by classical potential energy calculations. The calculations reveal three low energy conformations, each of which has a different dipole moment. The three conformations found are consistent with the published NMR data if an equilibrium between the three conformers is assumed. The results have implications for the interaction of nitroglycerin with solvents and propellant bases.

Conformational analysis of picrotoxinin by N.M.R., X-ray crystallography, and molecular orbital and classical potential-energy calculations

The conformation of the potent convulsant drug picrotoxinin has been studied by proton n.m.r., X-ray crystallography, molecular orbital calculations and classical calculations. The calculations reveal two alternative low-energy conformations, either of which is consistent with the n.m.r. data, and one of which is also observed crystallographically. The energy difference is sufficiently small to suggest that either conformation may be the biologically active form.

Convulsant and anticonvulsant barbiturates. 1. Molecular conformations from classical potential-energy calculations.

Conformational energy calculations are reported for a series of convulsant and anticonvulsant barbiturates derived from 5-ethyl-5-(1'-methylbutyl)barbituric acid (pentobarbital) by minor structural changes to the butyl side chain. A number of low-energy conformations are identified for each barbiturate. In each case substantial barriers to rotation exist between the alternative conformations, and the magnitudes of these barriers suggest that the barbiturates may be conformationally restricted even at physiological temperatures. Fully extended conformations, with both side chains perpendicular to the plane of the barbiturate ring, are favored. In the 1'-methyl derivatives, conformations with the 1'-methyl group located directly above the barbiturate ring are equally low in energy.

Influence of ribose 2′‐O‐methylation on GpC conformation by classical potential energy calculations

AbstractPotential energy calculations were employed to examine the effect of ribose 2′‐O‐methylation on the conformation of GpC. Minimum energy conformations and allowed conformational regions were calculated for 2′MeGpC and Gp2′MeC. The two lowest energy conformations of 2′MeGpC and Gp2′MeC are similar to those of GpC itself. The helical RNA conformation (sugar pucker‐C(3′)‐endo, ω′ and ω,g−g−, bases‐anti) is the global minimum, and a helix‐reversing conformation with ω′, ω in the vicinity of 20°, 80° is next in energy. However, subtle differences between the three molecules are noted. When the substitution is on the 5′ ribose (Gp2′MeC), the energy of the helical conformation is less than that of GpC, due to favorable interactions of the added methyl group. When the substitution is at the 3′ ribose (2′MeGpC) these stabilizing interactions are outweighed by steric restrictions, and the helical conformation is of higher energy than for GpC. Furthermore, the statistical weight of the 2′MeGpC g− g− helical region is substantially less than the corresponding weight for Gp2′MeC. In addition, 2′MeGpC′s methoxy group is conformationally restricted to a narrow range centered at 76°. This group has a broadly allowed region between 50 and 175° in Gp2′MeC. These differences occur because the appended methyl group in 2′MeGpC is located in the interior of the helix cylinder, as it would be in polynucleotide, while it hangs unimpeded in Gp2′MeC. These findings suggest that 2′‐O‐methylation has both stabilizing and destabilizing influences on the helical conformation of RNA. For 2′MeGpC the destabilizing steric hindrance imposed by the nature of the guanine base dominates.

The conformational analysis of adenosine triphosphate by classical potential energy calculations

AbstractThe conformational analysis of adenosine triphosphate was conducted by using classical potential energy calculations. All rotatable bonds were examined, i.e., no dihedral angles were fixed at predetermined conformations except for the ribofuranose ring, which was held in the C(3′)‐endo conformation—the conformation observed for adenosine in the crystal state.The energy terms included in the total energy expression consist of nonbonded pairwise interaction, electrostatic pairwise interaction, free energy of solvation, and torsional bond potentials.Two separate approaches were used in the conformational analyses. The first consisted of a sequential fragment approach were four bonds were rotated simultaneously at 30° increments. Each fragment overlapped the preceding one by at least one bond. All rotors were then simultaneously examined at their minima and at ±15°. The second approach consisted of a coarse grid search where all rotors were examined simultaneously, but only at staggered positions. The low‐energy conformations thus obtained were then used as starting conformations for a minimization routine based on the method of conjugate directions. The first approach required about 40 hr of central processing unit (CPU) computer time, while the coarse grid/minimization approach required about 4 hr of CPU time.Both the sequential fragment approach and the minimization approach yielded lowest‐energy conformations which are remarkably similar to the solid‐state conformation of C(3′)‐endo ATP.

Conformational adaptability at GABA-sensitive inhibitory synapses

Receptors for γ-aminobutyric acid (GABA) and its agonists display a considerable tolerance to the size of the agonist molecule. By considering the potencies of four rigid GABA analogues, it is possible to construct a model for the elasticity of the receptor. Using this model in conjunction with the probability distributions of the charge separations of 12 GABA agonists, based on classical potential energy calculations, interaction probabilities are calculated which enable the molecular structure of the agonists to be correlated with their pharmacological activity.

Classical potential energy calculations for ApA, CpC, GpG, and UpU. The influence of the bases on RNA subunit conformations.

AbstractClassical potential energy calculations have been made for the ribodinucleoside monophosphates ApA, CpC, GpG, and UpU. Van der Waal's, electrostatic, and torsional contributions to the energy were calculated, and the energy was minimized with the seven backbone conformational angles as simultaneously variable parameters. At the global minimum, ApA and CpC have conformations like double helical RNA: the angles ω′ and ω are g−g−, the sugar pucker is C3′‐endo, and the bases are anti. GpG and UpU, on the other hand, have the ω′,ω angle pair g−t at the global minimum, and for GpG the bases are syn. Energy contour maps for ω′ and ω show two broad, low energy regions for ApA, CpC, and UpU: one is g−g−, and the second encompasses g−t and g+g+ within a single lowenergy contour. The two regions are connected by a path at 10–13 kcal./mole. For GpG, with bases syn, however, only a small low‐energy region at g−t is found. The helical ‘A’ RNA conformation is 8.5 kcal/mole higher for this molecule. Thus, the base composition is shown to influence the conformations adopted by dinucleoside phosphates. Comparison of calculations with experimetal data, where available, show good agreement.