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.

Adaptive strong-field control of chemical dynamics guided by three-dimensional momentum imaging.

Shaping ultrafast laser pulses using adaptive feedback can manipulate dynamics in molecular systems, but extracting information from the optimized pulse remains difficult. Experimental time constraints often limit feedback to a single observable, complicating efforts to decipher the underlying mechanisms and parameterize the search process. Here we show, using two strong-field examples, that by rapidly inverting velocity map images of ions to recover the three-dimensional photofragment momentum distribution and incorporating that feedback into the control loop, the specificity of the control objective is markedly increased. First, the complex angular distribution of fragment ions from the nω+C2D4→C2D3++D interaction is manipulated. Second, isomerization of acetylene (nω+C2H2→C2H2(2+)→CH2++C+) is controlled via a barrier-suppression mechanism, a result that is validated by model calculations. Collectively, these experiments comprise a significant advance towards the fundamental goal of actively guiding population to a specified quantum state of a molecule.

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.

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.

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.

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.

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.

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.