Predicting bioactive conformations and binding modes of macrocycles

Macrocyclic compounds experience increasing interest in drug discovery. It is often thought that these large and chemically complex molecules provide promising candidates to address difficult targets and interfere with protein–protein interactions. From a computational viewpoint, these molecules are difficult to treat. For example, flexible docking of macrocyclic compounds is hindered by the limited ability of current docking approaches to optimize conformations of extended ring systems for pose prediction. Herein, we report predictions of bioactive conformations of macrocycles using conformational search and binding modes using docking. Conformational ensembles generated using specialized search technique of about 70 % of the tested macrocycles contained accurate bioactive conformations. However, these conformations were difficult to identify on the basis of conformational energies. Moreover, docking calculations with limited ligand flexibility starting from individual low energy conformations rarely yielded highly accurate binding modes. In about 40 % of the test cases, binding modes were approximated with reasonable accuracy. However, when conformational ensembles were subjected to rigid body docking, an increase in meaningful binding mode predictions to more than 50 % of the test cases was observed. Electrostatic effects did not contribute to these predictions in a positive or negative manner. Rather, achieving shape complementarity at macrocycle-target interfaces was a decisive factor. In summary, a combined computational protocol using pre-computed conformational ensembles of macrocycles as a starting point for docking shows promise in modeling binding modes of macrocyclic compounds.     

Emerging chemical patterns: a new methodology for molecular classification and compound selection

A concept termed Emerging Chemical Patterns (ECPs) is introduced as a novel approach to molecular classification. The methodology makes it possible to extract key molecular features from very few known active compounds and classify molecules according to different potency levels. The approach was developed in light of the situation often faced during the early stages of lead optimization efforts: too few active reference molecules are available to build computational models for the prediction of potent compounds. The ECP method generates high-resolution signatures of active compounds. Predictive ECP models can be built based on the information provided by sets of only three molecules with potency in the nanomolar and micromolar range. In addition to individual compound predictions, an iterative ECP scheme has been designed. When applied to different sets of active molecules, iterative ECP classification produced compound selection sets with increases in average potency of up to 3 orders of magnitude.     

Carbon-13 chemical shifts and conformations of dimethylcyclohexanols

Carbon-13 chemical shifts of all twenty-two dimethylcyclohexanols, formed by the hydrogenation of isomeric xylenols, have been measured and assigned. Conformational peculiarities of dimethylcyclohexanols are discussed on the basis of their carbon-13 chemical shifts.     

Local switching of chemical patterns through light-triggered unfolding of creased hydrogel surfaces

Visible light induces switching of surface chemical patterns based on hybrid gels of thermally responsive poly(N-isopropyl acrylamide) copolymer networks containing iron oxide nanoparticles. The swelling of these hybrid gels is reduced upon illumination (see picture), allowing controlled unfolding of creased features formed owing to an elastic surface instability.     

An efficient and versatile chemical synthesis of bioactive glyco-glycerolipids

Synthesis of β-glyco-1,2-diacylglycerols is achieved by a versatile and simple procedure based on trichloro-acetimidate methodology and use of peracetate sugar substrates. The chemical strategy was tested through stereoselective preparation of β-galacto- and β-gluco-lipid derivatives capable to trigger immune system response. The synthetic approach is designed to obtain enantiomerically pure regio- and stereo-isomers including derivatives containing poly-unsaturated fatty acids.     

Nonlinear chemical reaction between Na2S2O3 and Peroxide compound

Kinetics of reaction between Na₂S₂0₃ and peroxide compound (H₂0₂ or Na₂S₂O₃) in a batch reactor and in a continuous stirring tank reactor (CSTR) were studied. Steady oscillations in uncatalyzed reactions in a CSTR were first discovered. In Na₂S₂0₃-H₂O₂-H₂S0₄ reaction system, Pt potential and pH of higher and lower flow rates beyond oscillation flow rates were in around the same extreme values. The reaction catalyzed by Cu²⁺ consists of the catalyzed oscillation process and the uncatalyzed osciliation one. On the basis of experiment, a reaction mechanism consisting of three stages was put forward. The three stages are H⁺ positive-feedback reactions, proton negative-feedback (uncatalyzed negative-feedback and catalyzed negative-feedback) reactions and transitional reactions. The mechanism is able to explain reasonably the nonlinear chemical phenomena appearing in the thiosulfate oxidation reaction by peroxide compounds. Project supported by the National Natural Science Foundation of China.     

Nonlinear chemical reaction between Na_2S_2O_3 and Peroxide compound

Kinetics of reaction between Na2S2O3 and peroxide compound ( H2O2 or Na2S2O8) in a batch reactor and in a continuous stirring tank reactor (CSTR) were studied.Steady oscillations in uncatalyzed reactions in a CSTR were first discovered.In Na2S2O3-H2O2-H2SO4 reaction system,Pt potential and pH of higher and lower flow rutes beyond oscillation flow rates were in around the same extreme values.The reaction catalyeed by Cu2+ corsist of the catalyzed oscillation process and the uncatalyzed osciliation one.On the basis of experiment,a reaction mechanism consisting of three stages was put forward.The three stages are H positive-feedback reactions,proton negative-feedba k (uncatalyzed negative-feedback and catalyzed negative-feedback) reactions and transitional reactions.The mechanism is able to explain reasonably the nonlinear chemical phenomena appearing in the thiosulfatc oxidation reaction by peroxide-compounds.     

Correlated ab initio quantum chemical calculations of di- and trisaccharide conformations

High level correlated quantum chemical calculations, using MP2 and local MP2 theory, have been performed for conformations of the disaccharide, beta-maltose, and the trisaccharide, 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose. For beta-maltose, MP2 and local MP2 calculations using the 6-311++G** basis set are in good agreement, predicting a global minimum gas-phase conformation with a counterclockwise hydrogen bond network and the experimentally-observed intersaccharide hydrogen bonding arrangement. For conformations of 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose, MP2/6-311++G**, and local MP2/6-311++G** calculations do not provide a consensus prediction of relative energetics, with the MP2 method finding large differences in stability between extended and folded trisaccharide conformations. Local MP2 calculations, less susceptible to intramolecular basis set superposition errors, predict a narrower range of trisaccharide energetics, in line with estimates from Hartree-Fock theory and B3LYP and BP86 density functionals. All levels of theory predict compact, highly hydrogen-bonded conformations as lowest in energy on the in vacuo potential energy surface of the trisaccharide. These high level, correlated local MP2/6-311++G** calculations of di- and trisaccharide energetics constitute potential reference data in the development and testing of improved empirical and semiempirical potentials for modeling of carbohydrates in the condensed phase.     

Macromolecular conformations at the water-air interface: Interactions between alpha and beta conformations of polypeptides

Bidimensional miscibility between alpha and beta conformations of polypeptides was investigated at the water-air interface in the 15°–30°C temperature range. The polypeptides were poly--methyl-L-glutamate (PGMG), poly--benzyl-L-glutamate (PGBG) and poly--benzyl-L-aspartate (PBBA). The polypeptide conformations, alpha or beta, were checked by IR spectroscopy using the MIR technique.The spreading isotherms for mixed monolayers alpha-PGMG/alpha-PGBG and beta-PGMG/beta-PBBA showed bidimensional miscibility both for alpha-alpha and beta-beta mixtures.For the alpha-alpha system, attractive interactions among the polypeptide alphahelices were found (G_mix<0) and the driving factor appeared to be the entropic one (packing). Compressibility moduli and surface potential measurements showed a fluidification effect of alpha-PGBG on mixed monolayers. In the case of beta-beta mixed monolayers, ideal behaviour was observed and no fluidification effect detected.Scanning electron micrographs made on collapsed monolayers showed hexagonal structures for alpha-alpha mixtures and no well-defined or characterized features for the beta-beta system.     

Conformational and docking studies of acyl homoserine lactones as a robust method to investigate bioactive conformations

A method aiming at investigating possible bioactive conformations of acyl homoserine lactone (AHL) quorum sensing (QS) modulators is established. The method relies on the exhaustive conformational analysis of AHLs by varying torsion angles around the amide group then on the selection of the closest conformation to those known from co-crystallized XRD data of AHL-receptor complexes. These latter are then docked as rigid ligand within the receptor binding site, leading to interactions with binding site residues which are highly consistent as compared with the data arising from XRD studies. The method is first validated using AHLs for which XRD data of their complexes with their cognate receptor are available, then extended to examples for which the binding mode is still unknown.Three compounds were used to validate the method: hexanoyl homoserine lactone (HHL) as an example of autoinducer, 3-oxo-butanoyl homoserine lactone (OBHL), as a representative model of 3-oxo-AHLs, and 4-(4-chlorophenoxy)butanoyl homoserine lactone (CPOBHL) as an example of a QS inhibitor. The conformational analysis of these three compounds to their cognate protein (TraR, SdiA, LasR and CviR) provides the data which enable the next rigid docking step. Further rigid docking of the closest conformations compared to the known bioactive ones within the binding sites allows to recover the expected binding mode with high precision (atomic RMSD < 2 Å). This “conformational analysis/torsion angle filter/rigid ligand docking” method was then used for investigating three non-natural AHL-type QS inhibitors without known co-crystallized XRD structures, namely was 2-hexenoyl homoserine lactone (HenHL), 3-oxo-4-phenylbutanoyl homoserine lactone (OPBHL) and 3-(4-bromophenyl)propanoyl homoserine lactone (BPPHL). Results provide insights into their possible binding mode by identifying specific interactions with some key residues within the receptor binding site, allowing discussion of their biological activity.     

Geometric parameters as a criterion for assessment of the bioactive conformations of opiate receptor ligands

The mutual positions of the phenyl fragment and the protonated amino group in the molecules of opiate receptor ligands of various structural classes were studied. It was concluded that two bioactive ligand conformations exist and their implementation does not depend on the structural class of the ligand, selectivity of its action on receptors, or relationship between the agonistic and antagonistic properties. A set of geometric parameters describing the three-dimensional arrangement of the phenyl fragment and the protonated amino group in bioactive conformations was proposed; this can be used as a criterion for the geometric assessment of the opiate activity. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1462–1468, September, 2006.     

Classifying the conformations of a chemical system using matrices of integers

A chemical system is a collection of atomic nuclei and accompanying electrons interacting by electromagnetic forces and organized into one or more molecules, ions, and transient structures. A general problem is to devise a mathematical representation of the conformation of a system which is useful in further mechanical analysis. Through dihedral rotations of bonds and relative motion of structures, many chemical systems can attain an infinite number of conformations. This paper is a theoretical presentation of a scheme to partition these conformations into a finite number of sets. The scheme involves a discrete aspect of chemical kinematics and uses matrices of integers called proximity matrices. The partitioning scheme is anticipated to be useful in studying reaction mechanisms and interactions between molecules, and in finding conformations of particular interest such as that with a potential energy near the global minimum for a molecule.     

Water modeled as an intermediate element between carbon and silicon

Water and silicon are chemically dissimilar substances with common physical properties. Their liquids display a temperature of maximum density, increased diffusivity on compression, and they form tetrahedral crystals and tetrahedral amorphous phases. The common feature to water, silicon, and carbon is the formation of tetrahedrally coordinated units. We exploit these similarities to develop a coarse-grained model of water (mW) that is essentially an atom with tetrahedrality intermediate between carbon and silicon. mW mimics the hydrogen-bonded structure of water through the introduction of a nonbond angular dependent term that encourages tetrahedral configurations. The model departs from the prevailing paradigm in water modeling: the use of long-ranged forces (electrostatics) to produce short-ranged (hydrogen-bonded) structure. mW has only short-range interactions yet it reproduces the energetics, density and structure of liquid water, and its anomalies and phase transitions with comparable or better accuracy than the most popular atomistic models of water, at less than 1% of the computational cost. We conclude that it is not the nature of the interactions but the connectivity of the molecules that determines the structural and thermodynamic behavior of water. The speedup in computing time provided by mW makes it particularly useful for the study of slow processes in deeply supercooled water, the mechanism of ice nucleation, wetting-drying transitions, and as a realistic water model for coarse-grained simulations of biomolecules and complex materials.     

Molecular structure and conformations of benzenesulfonamide: gas electron diffraction and quantum chemical calculations

The molecular structure and conformational properties of benzenesulfonamide, C6H5SO2NH2, were studied by gas electron diffraction (GED) and quantum chemical methods (MP2 and B3LYP with different basis sets). The calculations predict the presence of two stable conformers with the NH2 group eclipsing or staggering the SO2 group. The eclipsed form is predicted to be favored by about 0.5 kcal/mol. According to GED, the saturated vapor over solid benzenesulfonamide at a temperature of 150(5) degrees C consists of the eclipsed conformer. The GED intensities, however, possess a very low sensitivity toward the vapor composition, and contributions of the anti conformer of up to 75% (at the 0.05 level of significance) or up to 55% (at the 0.25 level of significance) cannot be excluded. The molecule possesses C(sS) symmetry with the S-N bond perpendicular to the ring plane.     

Exploration of the relationship between topology and designability of conformations

Protein structures are evolutionarily more conserved than sequences, and sequences with very low sequence identity frequently share the same fold. This leads to the concept of protein designability. Some folds are more designable and lots of sequences can assume that fold. Elucidating the relationship between protein sequence and the three-dimensional (3D) structure that the sequence folds into is an important problem in computational structural biology. Lattice models have been utilized in numerous studies to model protein folds and predict the designability of certain folds. In this study, all possible compact conformations within a set of two-dimensional and 3D lattice spaces are explored. Complementary interaction graphs are then generated for each conformation and are described using a set of graph features. The full HP sequence space for each lattice model is generated and contact energies are calculated by threading each sequence onto all the possible conformations. Unique conformation giving minimum energy is identified for each sequence and the number of sequences folding to each conformation (designability) is obtained. Machine learning algorithms are used to predict the designability of each conformation. We find that the highly designable structures can be distinguished from other non-designable conformations based on certain graphical geometric features of the interactions. This finding confirms the fact that the topology of a conformation is an important determinant of the extent of its designability and suggests that the interactions themselves are important for determining the designability.     

Design and synthesis of a conformationally restricted trans peptide isostere based on the bioactive conformations of saquinavir and nelfinavir

The design and synthesis of a new peptide isostere which contains a trans alkene core is described. The key step involves a Wadsworth-Emmons reaction between chiral aldehyde (2S)-9a and chiral phosphonate 7 under base-sensitive conditions to give a chiral enone (2R)-24a which was reduced to afford the desired trans alkene isosteres (2R,5R)-6a and (2R,5S)-6b (Scheme 6). A potential application of this isostere in the synthesis of HIV protease inhibitors is also discussed.     

Distinguishing between R- and S-antcin C and their cytotoxicity

Antcin C is a bioactive compound isolated from Antrodia cinnamomea, a rare and expensive medicinal fungus endemic to Taiwan. Up to date, the absolute structure of antcin C has not been solved. In this study, the phenylglycine methyl ester (PGME) derivatives of antcin C were prepared. From NMR analysis the absolute configuration of(S)-antcin C (1) and (R)-antcin C (2) were determined. By MTT assay, (S)-antcin C presented cytotoxicity against Hep G2 and MCF-7 cells, with IC50 values of 14.5 and 12.8 microg/mL, respectively. However, (R)-antcin C did not show significant cytotoxicity. Our results showed that the configuration at C25 for antcin C is very important for its cytotoxicity. From a quality control point of view, it is necessary to identify and quantify the R- and S- enantiomers in the A. cinnamomea products.     

Experiments on temporal and spatial chemical patterns

Two examples of bifurcation sequences observed in experiments on nonequilibrium reactions in continuous flow stirred reactors are discussed: one experiment demonstrates that bifurcation diagrams can serve as a tool for elucidating chemical mechanisms, and another experiment illustrates that even very complex bifurcation sequences need not include chaotic states. A discussion of chemical spatial patterns emphasizes the need for the development of spatially extended reactors in which patterns can be maintained indefinitely. Three such recently developed reactors are described.     

Spectroscopic and quantum chemical study of the novel compound cyclopropylmethylselenol

An investigation into the properties of the novel compound cyclopropylmethylselenol has been undertaken by use of Stark-modulation microwave spectroscopy and high-level quantum chemical calculations. Ground-state spectra belonging to six isotopomers of a single conformer of the molecule were recorded and assigned. This conformer, predicted to be the lowest in energy by a series of quantum chemical calculations, possesses a synclinal arrangement of the H-C-C-Se atoms. In addition to the assignment of these ground-state spectra, transitions attributable to vibrationally excited states of the 78Se- and 80Se-containing isotopomers were identified. A tentative assignment of these excited-state spectra to specific vibrational modes has been made with the assistance of a density functional theory calculation at the B3LYP/6-311++G(3df,2pd) level of theory. Close agreement was found between experimental ground-state rotational constants and ab initio equilibrium values calculated at the MP2/aug-cc-pVTZ level of theory. Good agreement was also noted between certain r(s) principal axis coordinates of atoms in the molecule and the corresponding ab initio r(e) values. Limited evidence in favor of the formation of a weak intramolecular hydrogen bond between the H atom of the selenol group and electron density associated with the cyclopropyl ring is discussed.