Incorporating real time velocity map image reconstruction into closed-loop coherent control

We report techniques developed to utilize three-dimensional momentum information as feedback in adaptive femtosecond control of molecular dynamics. Velocity map imaging is used to obtain the three-dimensional momentum map of the dissociating ions following interaction with a shaped intense ultrafast laser pulse. In order to recover robust feedback information, however, the two-dimensional momentum projection from the detector must be inverted to reconstruct the full three-dimensional momentum of the photofragments. These methods are typically slow or require manual inputs and are therefore accomplished offline after the images have been obtained. Using an algorithm based upon an "onion-peeling" (also known as "back projection") method, we are able to invert 1040 × 1054 pixel images in under 1 s. This rapid inversion allows the full photofragment momentum to be used as feedback in a closed-loop adaptive control scheme, in which a genetic algorithm tailors an ultrafast laser pulse to optimize a specific outcome. Examples of three-dimensional velocity map image based control applied to strong-field dissociation of CO and O2 are presented.

Novel omega-conotoxins from Conus catus discriminate among neuronal calcium channel subtypes

omega-Conotoxins selective for N-type calcium channels are useful in the management of severe pain. In an attempt to expand the therapeutic potential of this class, four new omega-conotoxins (CVIA-D) have been discovered in the venom of the piscivorous cone snail, Conus catus, using assay-guided fractionation and gene cloning. Compared with other omega-conotoxins, CVID has a novel loop 4 sequence and the highest selectivity for N-type over P/Q-type calcium channels in radioligand binding assays. CVIA-D also inhibited contractions of electrically stimulated rat vas deferens. In electrophysiological studies, omega-conotoxins CVID and MVIIA had similar potencies to inhibit current through central (alpha(1B-d)) and peripheral (alpha(1B-b)) splice variants of the rat N-type calcium channels when coexpressed with rat beta(3) in Xenopus oocytes. However, the potency of CVID and MVIIA increased when alpha(1B-d) and alpha(1B-b) were expressed in the absence of rat beta(3), an effect most pronounced for CVID at alpha(1B-d) (up to 540-fold) and least pronounced for MVIIA at alpha(1B-d) (3-fold). The novel selectivity of CVID may have therapeutic implications. (1)H NMR studies reveal that CVID possesses a combination of unique structural features, including two hydrogen bonds that stabilize loop 2 and place loop 2 proximal to loop 4, creating a globular surface that is rigid and well defined.

Drugs from the peptide venoms of marine cone shells

Australian cone shell venoms are being investigated as an exciting new source of bioactive peptides as part of a new collaborative project between the 3D Centre and AMRAD. Initial studies have already revealed a number of new and novel acting peptides amongst the hundred or so small, heavily constrained peptides present in the venom of each cone shell. The aim of the project is to develop peptidomimetic drugs based on a selection of these native peptides.

The role of delineation and spatial frequency in the perception of the colours of the spectrum

The observations of the spectrum made by Newton, Young, Wollaston and Helmholtz are approximated and accounted for. Increasing the number of delineations allows progressively more bands differing in colour to be perceived, in addition to the three blocks of colour seen in the undelineated spectrum. The rate at which further delineation permits more colours to be observed decreases, however, so that up to 30 colours can be perceived in the subdivided spectrum. The wavelength discrimination measurements agree well with previous data. Enhanced colour discrimination is shown to require luminance contrast transients containing only the first few Fourier harmonics.

Verification of the interaction between peptide T and CD4 using surface plasmon resonance

Peptide T is currently in phase II clinical trials for the treatment of AIDS-associated dementia. Its putative mode of action is inhibition of binding of the HIV envelope protein (gp120) to its cellular receptor (CD4), thus preventing viral infectivity and gp120-induced neuronal toxicity. However, a number of reports have appeared in the literature which have failed to observe any inhibitory activity of Peptide T on CD4-gp120 binding, thus casting doubt on this hypothesis. This study uses a novel biosensor technique to demonstrate that Peptide T does bind to CD4 and that this binding can be specifically inhibited by an anti-CD4 monoclonal antibody. A detailed analysis of the kinetics of the interaction is presented.

Central nervous system receptor binding profiles of some 2-amino-4-phenyl quinolines: a novel class of alpha 2-adrenoceptor selective ligands

The 2-amino-4-phenyl quinoline moiety is a structural motif common to a number of central nervous system active agents. Extensive radio-ligand receptor binding profiles for several derivatives of this common structural feature have been determined. A high base level of central nervous system receptor affinity was observed with a distinct preference for the alpha-, and in particular the alpha 2-, adrenoceptors.

Motion reveals spatial visual defects

The question of how we can be unaware of the deficit in our (monocular) visual field, equivalent in size to 76 full moons, is examined. A new method of investigating the response to moving images on and near the blind spot has been found. The image of a computer-generated line, which is made to lengthen with time and pass over the blind spot, is seen as shorter than that of a similar, parallel line which passes outside the blind spot. This perceived difference in length corresponds to the actual width of the blind spot. Our unawareness of blind spots and scotomata is often described as involving some form of 'filling in' process. The rapid variation in cortical receptive field size, recently found to occur in response to stabilized images, may provide a general filling-in mechanism for the removal from perception of otherwise-distracting, stabilizing image regions (such as the shadows of blood vessels and clinical scotomata).

A one-variable topographical descriptor for the beta-turns of peptides and proteins

The beta-turn is a common secondary structure in biologically active peptides and globular proteins, where it is widely thought to serve as a molecular recognition site for many biological processes. Although the primary beta-turn recognition requirements are thought to be straightforward, relating mainly to the relative positions of the peptide sidechains, current classifications of beta-turns are complex and are based solely upon the very variable geometry of the peptide backbone. We demonstrate here that beta-turns can be described in terms of a single dihedral angle, which we have called beta, which provides a complete description of the spatial relationship between the entry and exit peptide bonds as well as the relative orientations of the intervening sidechains for any beta-turn. This description should prove particularly useful in the development and application of novel peptide mimetic drugs, compounds for which a classification based on a peptide backbone geometry may be entirely irrelevant.

Aspartate aminotransferase: investigation of the active sites

An investigation of the crystal structure of cytosolic pig-heart aspartate aminotransferase (AAT, E.C.2.6.1.1) was carried out to determine the structural requirements for ligand recognition by the active site. Structural differences were observed between the two active sites of the AAT dimer. The natural ligand, L-aspartate, was docked into both active sites using various methods. However, due to structural differences, the ligand was able to form all the necessary interactions for initial binding in only one of the active sites. The program GRID (P.J. Goodford, J. Med. Chem. 1985, 28, 849-857) was used to predict favorable binding sites for the functional groups of the aspartate ligand. These binding sites corresponded to the position of the docked aspartate ligand, indicating that substrate recognition takes place before any major conformational changes occur within the enzyme.

Conformational analysis of cyproheptadine hydrochloride

A nuclear magnetic resonance and theoretical study on the conformations and molecular flexibility of cyproheptadine hydrochloride (1) is reported. In the 1H NMR spectrum of 1 in CDCl3, two conformational forms are observed to occur in an approximate ratio of 1:4. In both forms, NOE and coupling constant measurements suggested that the terminal N-methyl group is equatorial. NOE experiments identified the more populated conformer (labeled D) as similar to the form seen in the X-ray crystal structure of cyproheptadine. The other form observed (A) may in principle be converted to D via either inversion of the central ring (T(inv)) or concerted nitrogen (N(inv)) and piperidine ring inversion (P(inv)). Chemical-exchange peaks in the 400-MHz 2D NOESY/chemical-exchange spectrum suggested that the latter mechanism is responsible for interconversion between the two forms. A theoretical study of the various interconversion processes using both molecular mechanics (MM2) and molecular orbital (AM1) approaches is also reported.

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.

Morpheus: a conformation-activity relationships and receptor modeling package

Our molecular modeling software package, MORPHEUS, allows the study of the interactions between biologically active molecules and their receptors. The package is capable of exploring the multidimensional conformational space accessible to each molecule of the data set under study. By specifying distance constraints or hypothetical receptor binding points, the package is able to filter the biologically accessible conformations of each active compound and deduce a three-dimensional model of the binding sites consistent with the properties of the agonists (or antagonists) under scrutiny. The electrostatic potentials in the environment of a putative binding site can also be investigated using the MORPHEUS package. The molecular modeling module CRYS-X, which is written in FORTRAN 77 for IBM PC machines, is capable of building, displaying and manipulating molecules.

Synthesis and Conformational Analysis of the Slime-Mold Acrasin Glorin

The chemotactic dipeptide for the slime-mould Polysphondylium violaceum, glorin (N- propionyl-y-L-glutamyl-L-ornithine-δ-lac ethyl ester) (8), was synthesized convergently in five steps with 41% overall yield, starting from L- ornithine hydrochloride (1) and L- glutamic acid γ-benzyl ester (4). -1H n.m.r. spectral analysis led to the conclusion that the propionamide and the γ-L- glutamyl amide bonds both undergo slow cis-trans isomerism in solution at room temperature. From a Karplus-type analysis of the values of the Cα,Cβ coupling constants at the lactam chiral carbon, it was concluded that the six-membered ring can adopt either a half-chair or half-boat conformation, but it is not clear which. Similar calculations for the glutamyl Ca,Cβ coupling constants were performed and, from these, significantly different relative populations for the three staggered conformations about the Glu-Ca,Cβ bond were suggested. Receptor binding studies showed that glorin did not bind significantly to any of the six receptors studied, including opioid, dopamine, central benzodiazepine, peripheral benzodiazepine, α1-adrenoceptor and α2-adrenoceptor sites.

Receptor site topographies for phencyclidine-like and sigma drugs: predictions from quantitative conformational, electrostatic potential, and radioreceptor analyses

Computer-assisted molecular modelling techniques and electrostatic analyses of a wide range of phenycyclidine (PCP) and sigma ligands, in conjunction with radioreceptor studies, were used to determine the topographies of the PCP and sigma receptors. The PCP receptor model was defined using key molecules from the arylcyclohexylamine, benzomorphan, bridged benz[f]isoquinoline, and dibenzocycloalkenimine drug classes. Hypothetical receptor points (R1, R2) were constructed onto the aromatic ring of each compound to represent hydrophobic interactions with the receptor, along with an additional receptor point (R3) representing a hydrogen bond between the nitrogen atom and the receptor. The superimposition of these key molecules gave the coordinates of the receptor points and nitrogen defining the primary PCP pharmacophore as follows: R1 (0.00, 3.50, 0.00), R2 (0.00, -3.50, 0.00), R3 (6.66, -1.13, 0.00), and N (3.90, -1.46, -0.32). Additional analyses were used to describe secondary binding sites for an additional hydrogen bonding site and two lipophilic clefts. Similarly, the sigma receptor model was constructed from ligands of the benzomorphan, octahydrobenzo[f]quinoline, phenylpiperidine, and diphenylguanidine drug classes. Coordinates for the primary sigma pharmacophore are as follows: R1 (0.00, 3.50, 0.00), R2 (0.00, -3.50, 0.00), R3 (6.09, 2.09, 0.00), and N (4.9, -0.12, -1.25). Secondary binding sites for sigma ligands were proposed for the interaction of aromatic ring substituents and large N-substituted lipophilic groups with the receptor. The sigma receptor model differs from the PCP model in the position of nitrogen atom, direction of the nitrogen lone pair vector, and secondary sigma binding sites. This study has thus demonstrated that the differing quantitative structure-activity relationships of PCP and sigma ligands allow the definition of discrete receptors. These models may be used in conjunction with rational drug design techniques to design novel PCP and sigma ligands of high selectivity and potency.

Cis-trans isomerization of the proline residue in insulin studied by 13C NMR spectroscopy

The natural abundance 13C NMR spectrum of bovine insulin contains two resonances at 49.6 and 48.9 ppm which have a 7:3 intensity ratio at 298 K. Use of the DEPT spectral editing technique shows them to be of CH2 multiplicity. On the basis of their chemical shifts, which are well-resolved from other peaks, they are assigned as the C delta carbon of proline in trans and cis forms respectively. Since insulin contains only a single proline residue, the site of the isomerization can be localized at the peptide bond linking Thr-27 and Pro-28. On heating, the two peaks broaden, coalesce at 308 K, and then sharpen to yield a single peak at higher temperatures. The barrier for this process was calculated to be 64 kJ mol-1 (at the coalesce temperature), which is at the lower end of the range observed for proline isomerization in small peptides. Computer-graphic studies based on the X-ray crystal structure of insulin were used to deduce the structural implications of the cis-trans isomerism in this globular protein.

Synthesis and Biological Evaluation of a Series of Substituted 4,5-Diphenylpyridine-2,6(1H,5H)-diones

We report the synthesis of a series of disubstituted 4,5- diphenylpyridine-2,6(1H,5H)- diones (8),(10),(12)-(21), their characterization by 1H and 13C n.m.r . spectroscopy and their receptor binding affinities for catecholamine and benzodiazepine receptors.

Anisatin: a Crystallographic, N.M.R. and Theoretical Conformation Study

The convulsant compound anisatin has been studied by 1H n.m.r ., and X- ray crystallography, to establish its molecular geometry. The n.m.r . measurements included an analysis of proton-proton vicinal coupling constants and saturation transfer experiments which monitored exchange of the hydroxy groups of anisatin. The former analysis was used to obtain a solution conformation via the Karplus equation while the latter experiments yield information on intramolecular hydrogen bonding. The experimental geometry is compared to that obtained by several theoretical methods, including MINDO/3, MNDO, AM1 and MM2. The AM1 optimized geometry was closest to that of the crystal structure.

Structure and Conformations of GABA-Transaminase Inhibitors. V. 4-[(2-Hydroxy-3,6-dimethylbenzyl)-methylamino]butanoic Acid Monohydrate

As part of a program to define conformational detail of potential inhibitors based on the calculated transition state of GABA-T, we report the crystal structure of the title compound. Crystals were triclinic and belong to the space group Pī with a 10.110(1), b 9.358(1), c 13.933Ǻ, α 90.37(1), β 93.27(1), γ 88.12(1)? and Z 4. Refinement on 3505 data measured with Cu Kα radiation converged at R 0.052. The two independent inhibitor molecules are essentially identical in conformation detail and are in a dipolar form. There is no intramolecular hydrogen bonding between the GABA nitrogen and phenolic oxygen but extensive intermolecular hydrogen bonding links the molecules into a three-dimensional network in the crystal.

Structure and Conformations of GABA-Transaminase Inhibitors. IV. Transition State Analogs

Crystal structures of three potential inhibitors [salicylamide derivative C16H15NO4 (5), pyridoxazine C11H16N2O5S (6) and benzoxazone C12H13NO4 (7).H2O] of GABA- transaminase (E.C.2.6.1.19, GABA-T) based on the calculated transition state of GABA-T were determined. The conformational analyses of these structures (non-bonded energies, MNDO,AM1) indicate that they can all fit the transition state in relatively low energy conformations. The crystal structures appear to be close to the calculated minimum energy conformations, except for the salicylamide derivative (5), which features internal hydrogen-bonding. The AM1 parametrization has been used successfully to predict two possible hydrogen-bonded conformations of (5), one of which is found in the crystal structure.

Transition-state analogues as inhibitors of L-dopa decarboxylase

1. A series of compounds has been prepared which are analogues of the transition state of the reaction catalysed by L-dopa decarboxylase (EC 4.1.1.28). 2. These compounds are reduced adducts of the substrate (L-dopa) and coenzyme (pyridoxal phosphate), as well as analogues of these substances (D-dopa, pyridoxal and salicaldehyde). 3. Compounds were also prepared with an oxazine link between the 3'-oxygen and the nitrogen attached to the 4'-carbon of the aldehyde moiety. 4. None of the D-dopa adducts produced any significant inhibition, but the L-dopa adducts were all active at millimolar levels, with the oxazine derivatives being more active than their parent compounds. 5. Inhibition was competitive with respect to L-dopa, but was neither competitive nor non-competitive with respect to pyridoxal phosphate. 6. The most active compound tested was the oxazine derivative of the L-dopa/salicaldehyde adduct, with an estimated Ki of 58.0 microM. 7. Increased inhibitory activity was observed when enzyme depleted of pyridoxal phosphate was used.

Structural and conformational analogy between cholecystokinin and ergopeptines

The central nervous system (CNS) peptide cholecystokinin (CCK) and the ergopeptine alkaloids exhibit common pharmacology in the brain, particularly via catecholaminergic systems. We report here structural similarities between CCK and the ergot alkaloids, and the subsequent conformational analysis of the peptide undertaken to establish whether or not a three-dimensional relationship exists between the compounds. Two low-energy conformations of CCK that mimic the ergopeptine ergotamine are identified, one arising from an X-ray crystal structure and the other from a Dreiding model-based, computer-assisted search. The pharmacological, structural and conformational observations strongly support the hypothesis that CCK and the ergopeptines share common sites of action in the CNS.

Structure and Conformations of GABA-Transaminase Inhibitors. III. Synthesis and Crystal Structure of a Novel Tetracyclic Benzoxazaborinone

Reduction of the substituted Schiff base (1) with sodium borohydride gave a product which was found by X-ray crystallographic analysis to be a mixture of two unexpected tetracyclic benzoxazaborinones (3a,b). X-ray analysis showed that, in the dipolar molecules, the pyridine nitrogen is protonated and the boron carries the negative charge. The crystals have site disorder, the exocyclic attachment at the boron being 73% methoxy (3a) and 27% hydroxy (3b). The stability, conformational rigidity and potential biology activity of these cyclic boron chelates all combine to give them particular interest as targets for further chemical and biological studies.

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.

A common structural model for central nervous system drugs and their receptors

On the basis of the hypothesis that there is a common structural basis for central nervous system (CNS) drug action consisting primarily of an aromatic group and a nitrogen atom, a four-point model for a common pharmacophore is defined with use of five semirigid CNS-active drug molecules: morphine, strychnine, LSD, apomorphine, and mianserin. Two of the points of the model represent possible hydrophobic interactions between the aromatic group and the receptor, while the other two represent hydrogen bonding between the nitrogen atom and the receptor. The model is then extended by the inclusion of nine additional CNS-active drug molecules: phenobarbitone, clonidine, diazepam, bicuculline, diphenylhydantoin, amphetamine, imipramine, chlorpromazine, and procyclidine, each being chosen as a key representative of a different CNS-active drug class or neurotransmitter system. Consideration of all phenyl group and nitrogen atom combinations, as well as all feasible conformations, shows that all nine molecules closely fit the common model in low-energy conformations. It is proposed that the model may eventually be used to design CNS-active drugs by mapping the relative locations of secondary binding sites. It can also be used to predict whether a given structure is likely to show CNS activity: a search over 1000 entries in the Merck Index shows a high probability of CNS activity in compounds fitting the common structural model.

13C NMR studies of the molecular flexibility of antidepressants

The solution dynamics of a series of clinically potent antidepressants have been investigated by measuring 13C NMR relaxation parameters. Correlation times and internal motional rates were calculated from spin-lattice relaxation times and nuclear Overhauser effects for the protonated carbons in mianserin, imipramine-like antidepressants, and amitriptyline-like antidepressants. These data were interpreted in terms of overall molecular tumbling, internal rotations, and inherent flexibility of these structures. Of particular interest was the conformational variability of the tricyclic nucleus of the tricyclic antidepressants, where the data indicated a fivefold difference in mobility of the dimethylene bridge of imipramine-like antidepressants relative to amitriptyline-like compounds. The implications of such a difference in internal motions is discussed in relation to previous NMR studies and to the reported differences in pharmacological activity of these antidepressants.

Carboxyl-modified amino acids and peptides as protease inhibitors

Several types of carboxyl-modified amino acids and peptides were prepared in forms having N-terminal modifications (carrier fragments) suitable for one of several representative protease enzymes, and their inhibitory action toward those enzymes were evaluated. The carboxyl modifications (inhibitory units) included (b) CONH2, (c) CSNH2, (d) CN, (e) trans-CH = CHCO2Me, and (f) trans-CH = CHSO2Me. The carrier fragments included NH2(PhCH2)CHX (1), AcNH(PhCH2)CHX (2), H2NCH2CONH(PhCH2)CHX (3), and AcNH(PhCH2)CHCONHCH2X (4). Compounds 1b, 1d, 1e, and 1f were competitive inhibitors of both microsomal and cytosolic leucine aminopeptidase (Ki = 14.8, 67, 61, and 3.7 mM with the former and 14.1, 26.4, 27.3, and 8.8 mM with the latter, respectively). Neither compound 1c nor leucine thioamide had any detectable effect on either enzyme. Compounds 2b-f were also competitive inhibitors toward chymotrypsin (Ki = 13.9, 23.0, 5.3, 30.8, and 29.4 mM, respectively). While 4b, 4c, and 4d were competitive inhibitors of papain (Ki = 4.7, 0.095, and 0.0011 mM, respectively), 4e proved to be an irreversible affinity label (Ki = 0.026 mM and k2 = 0.0018 s-1). Inactivation of papain by 4e was retarded in the presence of 4d and could not be reversed by dialysis. Similarly 3b and 3d were competitive inhibitors of dipeptidyl aminopeptidase I (DPP-I, EC 3.4.14.1) (Ki = 6.2 and 0.0027 mM, respectively), while 3e and 3f were irreversible affinity labels (Ki = 0.22 and 0.18 mM, and k2 = 0.015 and 0.010 s-1, respectively). Inhibition of DPP-I by 3d provides only the second example of a cysteine protease which is strongly inhibited by a nitrile analogue of a specific substrate. Further studies are needed to determine the generality and potential utility of this finding. Compounds 3e, 3f, and 4e exemplify a new class of specific affinity labels for cysteine proteases whose activity probably derives from irreversible Michael addition of the catalytic cysteine to the activated double bond.

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.

Structure and Conformations of Gaba-Transaminase Inhibitors. II. Transition-State Analogs

Crystal structures of two benzoxazine derivatives designed as transition state analogue inhibitors of GABA-T were determined. These cyclic oxazine structures are shown to be more similar to the proposed transition state than the pyridoxal derivatives reported in the preceding article.1 Conformational analyses (non-bonded energy, MINDO/3, MNDO) show that the crystal structures are close to the calculated energy minima. The MNDO parameterization gives geometries close to the crystal structure, with the configuration at the nitrogen of the oxazine ring in particular being better reproduced than by the MINDO/3 method, which tends to prefer planar (sp2) nitrogen.

Design, synthesis, and testing of insulin hexamer-stabilizing agents

The addition of zinc to insulin solution leads to a long-acting insulin preparation because the zinc stabilizes the less soluble hexameric form of the hormone. It is clear from the crystal structure of dizinc insulin that there is a space at the center of the hexamer, between the two zinc atoms, that could accommodate a small organic molecule. It should thus be possible to design a structure that could further stabilize the insulin hexamer by binding at this site. Computer graphic techniques have been used to design several molecules capable of forming multiple bonds to the six histidine residues surrounding the site. Synthesis and testing of one of these compounds, benzene-1,4-disulfonic acid, show a significant increase in weight-average molecular weight of insulin in solution, and control experiments with related structures suggest that this effect is due to the proposed binding mechanism.

Conformational analysis and active site modelling of angiotensin-converting enzyme inhibitors

The discovery of captopril as a potent, orally active inhibitor of angiotensin-converting enzyme (ACE) led to the recent development of many series of novel structures with similar biological activity. To date, however, all of these inhibitors are flexible or semiflexible molecules, and there is therefore no clear definition of the conformational requirements for ACE inhibition. In an effort to solve this problem, we have carried out conformational energy calculations on a series of eight structurally diverse ACE inhibitors. Comparison of the low-energy conformations available to these molecules leads to the conclusion that there is a common low-energy conformation throughout the series. The calculations thus define the structural and conformational requirements for ACE inhibition. Expansion of this model to the receptor level has been achieved by considering possible alternative receptor sites for each of the molecules in its proposed biologically active conformation and leads to an active-site model for ACE which may be useful for the design of further inhibitors.

Design, Synthesis and Testing of Transition State Analogues of Alanine Racemase as Antibacterials

Transition state analogues have been designed for alanine racemase , an important enzyme target for the development of bacterial cell wall inhibitors. These analogues are based on the transition state structure obtained from MINDO/3 calculations on the reaction pathway of a model alanine racemization . A number of analogues have been synthesized and are shown to have weak anti-bacterial activity, but results from microbiological assays indicate that their antibacterial activity is not due to inhibition of alanine racemase . Subsequent n.m.r .studies have shown that they are unstable in aqueous environments. Formaldehyde has been identified as one of the degradation products, and the likely source of antibacterial activity.

Functional group contributions to drug-receptor interactions

The binding constants and structural components of 200 drugs and enzyme inhibitors have been used to calculate the average binding energies of 10 common functional groups. As expected, charged groups bind more strongly than polar groups, which in turn bind more tightly than nonpolar groups. The derived intrinsic binding energies (in kcal/mol) are (i) charged groups, CO-2, 8.2; PO2-4, 10.0; N+, 11.5; (ii) polar groups, N, 1.2; OH, 2.5; CO, 3.4; O or S ethers, 1.1; halogens, 1.3; (iii) nonpolar groups, C (sp2), 0.7; C (sp3), 0.8. These values may be used to determine the goodness of fit of a drug to its receptor. This is done by comparing the observed binding constant to the average binding energy calculated by summing the intrinsic binding energies of the component groups and then subtracting two entropy related terms (14 kcal/mol for the loss of overall rotational and translational entropy and 0.7 kcal/mol for each degree of conformational freedom). Drugs that match their receptors exceptionally well have a measured binding energy that substantially exceeds this calculated average value--examples include diazepam and biotin. Conversely, if the observed binding energy is very much less than the calculated average value, then the drug apparently matches its receptor less well than average. Examples of this type include methotrexate and buprenorphine.

Actions of pentobarbitone and derivatives with modified 5-butyl substituents on GABA and diazepam binding to rat brain synaptosomal membranes

The effects of a variety of factors known to influence the enhancement of GABA binding by diazepam, were studied upon pentobarbitone stimulation of GABA binding to washed synaptosomal membranes prepared from whole rat brains. The differential kinetics of, and effects of temperature, chloride ions, a benzodiazepine receptor antagonist (Ro15-1788) and picrotoxinin upon pentobarbitone and diazepam enhancement of GABA binding, suggest that these drugs exert their actions upon GABA binding at different loci. The degree of enhancement of diazepam binding and of high affinity GABA binding in chloride-containing media at 25 degrees C by members of a series of twelve side chain methyl substituted and/or unsaturated derivatives of 5-butyl-5-ethyl-barbituric acid (pentobarbitone analogs) correlated significantly. For the sedative members of the series, enhancement of high affinity GABA binding correlated with their anaesthetic but not their anticonvulsant activities. It appears likely that the anaesthetic and anticonvulsant activities of barbiturates arise from different molecular actions.

Structure-activity relationships of convulsant and anticonvulsant barbiturates: a computer-graphic-based pattern-recognition analysis

A computer-graphic-based pattern-recognition study of two series of 5-ethyl-5-substituted barbiturates has been undertaken in an attempt to find a correlation between molecular conformation and convulsant and anticonvulsant activity. Studies of a first (trial) set of barbiturates related to pentobarbital revealed a region of space in which at least one low-energy conformation of the hydrocarbon side chain of each of the anticonvulsant barbiturates resides. Another region was occupied by a low-energy conformation of each of the convulsant barbiturates. These regions of space are, thus, possible pharmacophores for convulsant and anticonvulsant activity. Analysis of a second (test) set of barbiturates related to phenobarbital has shown that the activities and structures of these molecules are consistent with the above model. These pharmacophores thus provide a basis for the design of rigid, new analogues with potent convulsant or anticonvulsant activities.

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.