Methodological developments and strategies for a fast flexible superposition of drug-size molecules

An alternative to experimental high through-put screening is the virtual screening of compound libraries on the computer. In absence of a detailed structure of the receptor protein, candidate molecules are compared with a known reference by mutually superimposing their skeletons and scoring their similarity. Since molecular shape highly depends on the adopted conformation, an efficient conformational screening is performed using a knowledge-based approach. A comprehensive torsion library has been compiled from crystal data stored in the Cambridge Structural Database. For molecular comparison a strategy is followed considering shape associated physicochemical properties in space such as steric occupancy, electrostatics, lipophilicity and potential hydrogen-bonding. Molecular shape is approximated by a set of Gaussian functions not necessarily located at the atomic positions. The superposition is performed in two steps: first by a global alignment search operating on multiple rigid conformations and then by conformationally relaxing the best scored hits of the global search. A normalized similarity scoring is used to allow for a comparison of molecules with rather different shape and size. The approach has been implemented on a cluster of parallel processors. As a case study, the search for ligands binding to the dopamine receptor is given.     

Quality of approximate electron densities and internal consistency of molecular alignment algorithms in molecular quantum similarity

The calculation of molecular quantum similarity measures using the molecular electron density requires the electron density and molecular alignment between two molecules. To obtain meaningful quantum similarity matrices, the electron density should be calculated efficiently and accurately and the alignment should be internally consistent. The internal consistency of the alignment for a series of molecules is investigated through distance geometry concepts. The calculation of the quantum similarity matrix requires the calculation of a quadratic number of similarity integrals, and a scheme to obtain these efficiently is developed. Both the alignment procedure and the ASA method for approximate molecular electron densities are tested for a set of steroid molecules.     

Use of electron density critical points as chemical function-based reduced representations of pharmacological ligands

In this paper, we propose a reduced representation of molecules of pharmacological interest based on their chemical functions. The proposed representations of the molecules are obtained by a topological analysis of their electron density maps at medium resolution, leading to graphs of critical points. The distribution of the different types of critical points are compared at various levels of resolution for a training set of 22 molecules in order to define the optimal resolution level leading to the best representation of the various chemical functions. The reduced representations can in the future be used for molecular similarity research and pharmacophore proposals.     

Estimation of molecular similarity based on 4D-QSAR analysis: formalism and validation

The 4D-QSAR paradigm has been used to develop a formalism to estimate molecular similarity measures as a function of conformation, alignment, and atom type. It is possible to estimate the molecular similarity of pairs of molecules based upon the entire ensemble of conformational states each molecule can adopt at a given temperature, normally room temperature. Molecular similarity can be measured in terms of the types of atoms composing each molecule leading to multiple measures of molecular similarity. Multiple measures of molecular similarity can also arise from using different alignment rules to perform relative molecular similarity, RMS, analysis. An alignment independent method of determining molecular similarity measures, referred to as absolute molecular similarity, AMS, analysis has been developed. Various sets and libraries of compounds, including the amino acids, are analyzed using 4D-QSAR molecular similarity analysis to demonstrate the features of the formalism. Exploration of molecular similarity as a function of chirality, identification of common embedded 3D pharmacophores in compounds, and elucidation of 3D-isosteric compounds from structurally diverse libraries are carried out in the application studies.     

Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities

Summary Exploitation of protein structures for potential drug leads by molecular docking is critically dependent on methods for scoring putative protein-ligand interactions. An ideal function for scoring must exhibit predictive accuracy and high computational speed, and must be tolerant of variations in the relative protein-ligand molecular alignment and conformation. This paper describes the development of an empirically derived scoring function, based on the binding affinities of protein-ligand complexes coupled with their crystallographically determined structures. The function's primary terms involve hydrophobic and polar complementarity, with additional terms for entropic and solvation effects. The issue of alignment/conformation dependence was solved by constructing a continuous differentiable nonlinear function with the requirement that maxima in ligand conformation/alignment space corresponded closely to crystallographically determined structures. The expected error in the predicted affinity based on cross-validation was 1.0 log unit. The function is sufficiently fast and accurate to serve as the objective function of a molecular-docking search engine. The function is particularly well suited to the docking problem, since it has spatially narrow maxima that are broadly accessible via gradient descent.     

Predicting drug pharmacokinetic properties using molecular interaction fields and SIMCA

We have developed a method that combines molecular interaction fields with soft independent modeling of class analogy (SIMCA) Wold:1977 to predict pharmacokinetic drug properties. Several additional considerations to those made in traditional QSAR are required in order to develop a successful QSPR strategy that is capable of accommodating the many complex factors that contribute to key pharmacokinetic properties such as ADME (absorption, distribution, metabolism, and excretion) and toxicology. An accurate prediction of oral bioavailability, for example, requires that absorption and first-pass hepatic elimination both be taken into consideration. To accomplish this, general properties of molecules must be related to their solubility and ability to penetrate biological membranes, and specific features must be related to their particular metabolic and toxicological profiles. Here we describe a method, which is applicable to structurally diverse data sets while utilizing as much detailed structural information as possible. We address the issue of the molecular alignment of a structurally diverse set of compounds using idiotropic field orientation (IFO), a generalization of inertial field orientation Clark:1998. We have developed a second flavor of this method, which directly incorporates electrostatics into the molecular alignment. Both variations of IFO produce a characteristic orientation for each structure and the corresponding molecular fields can then be analyzed using SIMCA. Models are presented for human intestinal absorption, blood-brain barrier penetration and bioavailability to demonstrate ways in which this tool can be used early in the drug development process to identify leads likely to exhibit poor pharmacokinetic behavior in pre-clinical studies, and we have explored the influence of conformation and molecular field type on the statistical properties of the models obtained.     

Light-Driven Flipping of Azobenzene Assemblies—Sparse Crystal Structures and Responsive Behaviour to Polarised Light

For creation of autonomous microrobots, which are able to move under conditions of a constant environment and a constant energy supply, a mechanism for maintenance of mechanical motion with a capacity for self-control is required. This requirement, known as self-organisation, represents the ability of a system to evade equilibrium through formation of a spatio-temporal pattern. Following our previous finding of a self-oscillatory flipping motion of an azobenzene-containing co-crystal, we present here regulation of the flipping motion by a light-receiving sensor molecule in relation to the alignment and role of azobenzene molecules in crystals. In the anisotropic structure, a specific azobenzene molecule acts as a reaction centre for the conversion of light to a mechanical function process, whereas the other molecules act as modulators for spatio-pattern regulation. The present results demonstrate that autonomously drivable molecular materials can exhibit information-responsive, self-sustainable motion by incorporating stimulus-responsive sensors.     

Molecular Dynamics Simulations of the First Steps of the Formation of Polysiloxane Layers at a Zinc Oxide Surface

Three different dissolved silane molecules adsorbed at a polar ZnO surface (000&1macr;) are studied by means of constant temperature molecular dynamics simulations. The adsorbed single silane molecules exhibit a different behavior depending on the chemical nature of their tail. For octyltrihydroxysilane molecules with their rather unpolar tail an orthogonal orientation at the polar metal oxide surface is statistically favored with all three polar hydroxide groups of the head being in contact with the polar ZnO surface and the unpolar tail remaining in the isopropanol phase. On the contrary, due to their highly polar tail, aminopropyltrihydroxysilane molecules show a more or less parallel orientation at the surface. Apart from some minor fluctuations two hydroxide groups as well as the amino group of the tail are in contact with the surface. The behavior of the thiolpropyltrihydroxysilane molecules is somehow located in between resulting in parallel as well as orthogonal orientations of the molecule at the surface. Though many of the results obtained for single adsorbed silane molecules can also be transferred to adsorbed silane molecules within whole layers a remarkable difference appears: Now even for aminopropyltrihydroxysilane molecules a mixture of parallel and orthogonal alignment of the molecules can be observed whereas some of the octyltrihydroxysilane molecules also show a parallel orientation.     

MOLECULAR CLOSE-PACKING METHOD AND ITS APPLICATION TO CRYSTAL STRUCTURE DETERMINATION OF DESHEXAPEPTIDE (B25--B30) INSULIN

Based on the molecule-packing theory, we defined a molecule-packing function express-ing the compatibility of packing among the symmetry-related molecules in a unit cell. Acomputer program imitating the close-packing of molecules in the objective crystal latticeand giving the function value of each rotation and translation of the molecule in the unitcell was performed, and it therefore made the close-packing of molecules expressquantitatively. This method not only could judge a correct solution from several peaks ofthe rotation or translation function but it may also independently, quantitatively and quicklysolve some specific problems of rotation and translation. Using known structure of despenta-peptide (B26--B30) insulin as an example, the effectiveness of this method and its programwas inspected, and this method was successfully applied to solving the translation problem ofthe unknown structure of deshexapeptide (B25--B30) insulin. The molecular close-packingmethod proved by the results of R--search     

Alignment of molecules by the Monte Carlo optimization of molecular similarity indices

3D-QSAR uses statistical techniques to correlate calculated structural properties with target properties like biological activity. The comparison of calculated structural properties is dependent upon the relative orientations of molecules in a given data set. Typically molecules are aligned by performing an overlap of common structural units. This “alignment rule” is adequate for a data set, that is closely related structurally, but is far more difficult to apply to either a diverse data set or on the basis of some structural property other than shape, even for sterically similar molecules. In this work we describe a new algorithm for molecular alignment based upon optimization of molecular similarity indices. We show that this Monte Carlo based algorithm is more effective and robust than other optimizers applied previously to the similarity based alignment problem. We show that QSARs derived using the alignments generated by our algorithm are superior to QSARs derived using the more common alignment of fitting of common structural units. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18 : 1344–1353, 1997     

Investigation of a molecular morphology effect on polyphenylazomethine dendrimers; physical properties and metal-assembling processes

A series of novel dendritic polyphenylazomethines (DPA) with asymmetric morphologies was synthesized. Their physical properties, such as encapsulating effect, molecular dynamics, and metal assembly, are strongly dependent on the entire conformation of the molecules. The most important property is layer-by-layer metal assembly in the dendrimer structure from the core to the outside. Bis- and tris-substituted DPAs of the fourth generation also act as frameworks for stepwise assembly of a metal component (SnCl2), like the fully substituted symmetric DPA. However, extensive investigation of metal assembly in specific DPAs revealed that they do not follow the stepwise process. The molecular density calculated from the experimental hydrodynamic volume indicated that bis- and tris-substituted DPAs with asymmetric morphology still retain a free space similar to that of fully substituted symmetric DPA. The monosubstituted DPA, however, displayed a slightly higher density (smaller space) than the other DPAs. The experimental results suggest a bent conformation of the dendrimer in which the core moiety is folded into the dendron structure. In addition, the molecular dynamics were probed by means of the 1H NMR signals of the porphyrin core. It was demonstrated that the conformation is not fixed at room temperature in solvated DPAs, especially in monosubstituted DPA. A similar observation was for the smaller DPAs (third generations) with asymmetric morphologies. These dendrimers do not follow the stepwise complexation process. The structures of bis- and tris-substituted dendrimers which accurately follow the stepwise process are fixed. These observations provide a new insight into the finely controlled metal-assembly chemistry of dendritic macromolecules, and a rigid and fixed conformation is one of important factors for their unique properties.     

Alignment of liquid crystals on ultrathin organized molecular films

Liquid crystal (LC) alignment techniques based on various kinds of ultrathin organized molecular films are reviewed. The mechanisms of LC alignment on the organized films are discussed. For the homeotropic alignment of LCs the main anchoring mechanism is due to the dipole–dipole interaction between polar groups of an aligning agent and LC molecules while the homogeneous alignment is mainly attributed to the orientation of polymer chains or polymer aggregates. An experimental system for an anchoring transition induced by a conformation change of aligning molecules is introduced. Finally the AFM experimental observations on the rubbed polymer films and its mechanisms are summarized.     

Orientation Control of Molecularly Functionalized Surfaces Applied to the Simultaneous Alignment and Sorting of Carbon Nanotubes

Self‐assembly has been relied upon for molecular alignment in many advanced technological applications. However, although effective, it is inherently limited in its capability for optimization. Despite the potential benefits, the seemingly fundamental strategy of external orientation control has yet to be realized. Herein we demonstrate an approach that allows control of the orientation of small molecules covalently bound to a surface. The method exploits an alignment relay technique, passing alignment information through a liquid‐crystal medium to small molecules to control surface functionalization events. The method is technically simple and can be carried out on a bench top without the need for specialized equipment. Moreover, we demonstrate the utility of the resulting surfaces to address two long‐standing problems in nanoscience: the sorting and alignment of single‐walled carbon nanotubes. This new method enabled significant alignment of the nanotubes as well as length and diameter sorting.     

Simultaneous formation behaviour of surface structures and molecular alignment by patterned photopolymerisation

ABSTRACT

Highly functional soft materials with fine control of molecular alignment are of great interest for the applications in various fields. However, the current method of molecular alignment still has some challenges. Recently, we have developed a new alignment process based on a concept of scanning wave photopolymerisation (SWaP). When a sample is irradiated with spatially selected light, a polymerisation occurs only in an irradiated region, leading to a molecular motion between the irradiated and unirradiated regions. Such molecular motion generates the alignment of liquid crystal molecules. Moreover, a surface relief structure is formed in the polymer film by the molecular motion. In this study, we simultaneously formed the surface structure and molecular alignment by the patterned photopolymerisation. We compared the degree of molecular alignment with the shape of the created surface structure, and revealed that the degree of molecular alignment was maximized at the boundary of irradiated and unirradiated regions. This method enables one to form both molecular alignment patterning and surface structuring in a single step.     

Similarity measures based on Gaussian-type promolecular electron density models: alignment of small rigid molecules

Various molecular similarity measures (overlap, Coulomb, kinetic, electrostatic energy) and similarity indices (Carbó, Hodgkin-Richards, Kulczynski, Shape Tanimoto) are applied to the superposition of 3D promolecular electron density (PED) distributions. The original aspect of the paper lies in the consideration of smoothed PEDs, which allow to decrease the number of local solutions to a superposition problem, together with the use of the less common kinetic and electrostatic energy similarity measures. Results are obtained for a family of five rigid endothiapepsin ligands that were already considered in previous applications, based on graph representations of their PED. In the present work, it is observed that the use of smoothed PED and the kinetic similarity measure, together with the Kulczynski or Shape Tanimoto index, performed the best to align molecules of different sizes.     

Is the alignment of nematics on a polymer slab always along the rubbing direction? A molecular dynamics study

ABSTRACT

We have studied the alignment and molecular organisation within a thin film of the popular nematic 5CB sandwiched between two flat polymer slabs, examining the effect of polymer chemical nature and morphology with atomistic molecular dynamics simulations. We have chosen two common polymers: polystyrene (PS) and polymethylmethacrylate (PMMA), either with their chains in random coil conformation (disordered) or with chains unidirectionally stretched (ordered). We found that, independently on the arrangement of the chains, both surfaces align planarly the liquid crystal, in accord with experimental observation. Moreover, while 5CB molecules align along the chains stretching direction of the PMMA ordered surface, on the combed PS surface they arrange on average perpendicularly to the stretching direction. This behaviour is attributed to the chemically specific interactions between the respective aromatic moieties of PS and 5CB.     

A Green and Wide-Scope Approach for Chiroptical Sensing of Organic Molecules through Biomimetic Recognition in Water

Optical chirality sensing has attracted a lot of interest due to its potential in high-throughput screening in chirality analysis. A molecular sensor is required to convert the chirality of analytes into optical signals. Although many molecular sensors have been reported, sensors with wide substrate scope remain to be developed. Herein, we report that the amide naphthotube-based chirality sensors have an unprecedented wide scope for chiroptical sensing of organic molecules. The substrates include, but are not limited to common organic products in asymmetric catalysis, chiral molecules with inert groups or remote functional groups from their chiral centers, natural products and their derivatives, and chiral drugs. The effective chirality sensing is based on biomimetic recognition in water and on effective chirality transfer through guest-induced formation of a chiral conformation of the sensors. Furthermore, the sensors can be used in real-time monitoring on reaction kinetics in water and in determining absolute configurations and ee values of the products in asymmetric catalysis.     

水团簇构象稳定性起源和本质的密度泛函理论与量子分子动力学研究

寻找确定分子体系构象稳定性的关键因素是至关重要的, 但即使对最简单的分子, 其稳定性的起源和本质仍存在很大的争议. 本文以水团簇为例, 采用量子分子动力学产生185个八聚水分子团簇模型, 并运用基于密度泛函理论的两个能量分解方法寻找其稳定性的决定因素. 我们发现不同水团簇的稳定性与其立体排斥能和交换相关能成良好的线性关系.本文还采用双变量模型模拟水团簇的稳定性, 取得了更好的结果(相关系数大于0.99). 本工作对揭示包括水分子团簇在内的通过弱相互作用组成的分子络合物的稳定性起源和本质提供了有益启示.     

The Influence of Two‐Dimensional Organization on Peptide Conformation

Molecular crowding plays a significant role in regulating molecular conformation in cellular environments. It is also likely to be important wherever high molecular densities are required, for example in surface‐phase studies, in which molecular densities generally far exceed those observed in solution. Using on‐surface circular dichroism (CD) spectroscopy, we have investigated the structure of a synthetic peptide assembled into a highly packed monolayer. The immobilized peptide undergoes a structural transition between α‐helical and random coil conformation upon changes in pH and ionic concentration, but critically the threshold for conformational change is altered dramatically by molecular crowding within the peptide monolayer. This study highlights the often overlooked role molecular crowding plays in regulating molecular structure and function in surface‐phase studies of biological molecules.