V. A. Palyulin

Virtual computational chemistry laboratory - design and description

Internet technology offers an excellent opportunity for the development of tools by the cooperative effort of various groups and institutions. We have developed a multi-platform software system, Virtual Computational Chemistry Laboratory, http://www.vcclab.org, allowing the computational chemist to perform a comprehensive series of molecular indices/properties calculations and data analysis. The implemented software is based on a three-tier architecture that is one of the standard technologies to provide client-server services on the Internet. The developed software includes several popular programs, including the indices generation program, DRAGON, a 3D structure generator, CORINA, a program to predict lipophilicity and aqueous solubility of chemicals, ALOGPS and others. All these programs are running at the host institutes located in five countries over Europe. In this article we review the main features and statistics of the developed system that can be used as a prototype for academic and industry models.

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information.

The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records. The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community. Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu.

Molecular Field Topology Analysis Method in QSAR Studies of Organic Compounds

A new method of QSAR analysis for organic compounds, molecular field topology analysis (MFTA), is considered that involves the topological superposition of the training set structures and the construction of a molecular supergraph (MSG). This enables the creation of the uniform descriptor vectors based on the local physicochemical parameters (atom and bond properties) of the molecules. The application of this technique is illustrated by a number of examples, and its features are discussed. The MFTA is especially suitable for solving the problems where the analysis of three-dimensional structure is either unnecessary or complicated.

GAG-binding variants of tick-borne encephalitis virus.

Previously different authors described various flavivirus mutants with high affinity to cell glycosaminoglycans and low neuroinvasiveness in mice that were obtained consequently passages in cell cultures or in ticks. In present study the analysis of TBEV isolates has shown existence of GAG-binding variants in natural virus population. Affinity to GAG has been evaluated by sorption on heparin-Sepharose. GAG-binding phenotype corresponds to such virus properties, like small plaque phenotype in PEK cells, absence of hemagglutination at pH 6.4, and low neuroinvasiveness in mice. Mutations increasing charge of E protein were necessary but not sufficient for acquisition of GAG-binding phenotype. Molecular modeling and molecular dynamics simulation have shown that the flexibility of E protein molecule could bear influence on the phenotypic manifestation of substitutions increasing charge of the virions.

RICON-The Computer Program for the Quantitative Investigations of Cyclic Organic Molecule Conformations.

The methods of quantitative conformational analysis of cyclic fragments in molecules and the computer program RICON (RIng CONformations) developed by us for this purpose are considered. Program RICON uses atomic coordinates obtained from X-ray studies or force field/quantum chemical computations and allows one to analyze geometric parameters of a molecule, to compute the puckering parameters of rings in the molecule using various methods, and to obtain a verbal description of a ring conformation. The abilities of the program are described, and the examples of its application are given.

Inhibitors of tick-borne flavivirus reproduction from structure-based virtual screening.

Flaviviruses form a large family of enveloped viruses affecting millions of people over the world. To date, no specific therapy was suggested for the infected people, making the treatment exclusively symptomatic. Several attempts were performed earlier for the design of fusion inhibitors for mosquito-borne flaviviruses, whereas for the tick-borne flaviviruses such design had not been performed. We have constructed homology models of envelope glycoproteins of tick-transmitted flaviviruses with the detergent binding pocket in the open state. Molecular docking of substituted 1,4-dihydropyridines and pyrido[2,1-b][1,3,5]thiadiazines was made against these models, and 89 hits were selected for the in vitro experimental evaluation. Seventeen compounds showed significant inhibition against tick-borne encephalitis virus, Powassan virus, or Omsk hemorrhagic fever virus in the 50% plaque reduction test in PEK cells. These compounds identified through rational design are the first ones possessing reproduction inhibition activity against tick-borne flaviviruses.

Neuroprotective and cognition-enhancing properties of MK-801 flexible analogs. Structure-activity relationships.

Abstract: Neuroprotective and biobehavioral properties of a series of novel open chain MK‐801 analogs, as well as their structure‐activity relationships have been investigated. Three groups of compounds were synthesized: monobenzylamino, benzhydrylamino, and dibenzylamino (DBA) analogs of MK‐801. It was revealed that DBA analogs exhibit pronounced glutamate‐induced calcium uptake blocking properties and anti‐NMDA activity. The hit compound of DBA series, NT‐1505, was investigated for its ability to improve cognition functions in animal model of Alzheimers disease type dementia, simulated by treating animals with cholinotoxin AF64A. The results from an active avoidance test and a Morris water maze test showed that experimental animals, treated additionally with NT‐1505, exhibited much better learning ability and memory than the control group (AF64A treated) and close to that of the vehicle group of animals (treated with physiological solution). Study of NT‐1505 influence on locomotor activity revealed that it is characterized by a spectrum of behavioral activity radically different from that of MK‐801, and in contrast to the latter one does not produce any psychotomimetic side effects in the therapeutically significant dose interval. The computed docking of MK‐801 and its flexible analogs on the NMDA receptor elucidated the crucial role of the hydrogen bond formed between these compounds and the asparagine residue for magnesium binding in the NMDA receptor. It was suggested that strong hydrophobic interaction between MK‐801 and the hydrophobic pocket in the NMDA receptor‐channel complex determines much higher irreversibility of this adduct compared to the intermediates formed between this site and Mg ions or flexible DBA derivatives, which might explain the absence of PCP‐like side effects of the latter compounds.

Theoretical scales of hydrogen bond acidity and basicity for application in QSAR/QSPR studies and drug design. Partitioning of aliphatic compounds.

Phenomenological analysis of existing hydrogen bond (HB) donor and acceptor scales and apparent physical considerations have enabled the establishment of new quantitative scales of hydrogen bond basicity and acidity. Chemical structures represented by molecular graphs and the orbital electronegativities of Hinze and Jaffe are utilized as an input data. The scales obtained correlate well with several experimental solvent polarity scales such as and, pK(HB), and E(T)(30). To demonstrate the applicability of the new quantities, we have applied them to seven equilibrium partitioning data sets: octanol-water, hexadecane-water, chloroform-water, gas-water, gas-octanol, gas-hexadecane, and gas-chloroform partition coefficients. The hydrogen bond descriptors when supplemented by a cavity-forming term and a dipolarity term show high performance in correlations of the partition coefficients of aliphatic compounds. These new HB descriptors can be used in studying hydrogen bonding and fluid phase equilibria as well as scoring functions in ligand docking and descriptors in ADME evaluations.

A Neural Device for Searching Direct Correlations between Structures and Properties of Chemical Compounds

A scheme of a neural device intended for searching direct correlations between structures and properties of organic compounds without preliminary computation of molecular descriptors (that are invariant with respect to renumbering atoms in a molecule) is suggested. The invariance of a property with respect to renumbering atoms in a molecule is ensured by the architecture of the neural device, which is constructed by analogy with biological vision systems. A model software of the neural device was tested on several examples. The descriptive and predictive performances of the device are shown to be comparable and even overcome the performances of using molecular descriptors, such as topological indexes and substructural descriptors, especially for analyzing heterogeneous data sets including inorganic compounds. The neural device can be advantageously used in the cases when more traditional approaches fail to work or “good” molecular descriptors have not been devised yet.

Combined QSAR studies of inhibitor properties of O-phosphorylated oximes toward serine esterases involved in neurotoxicity, drug metabolism and Alzheimer's disease

Oxime reactivation of serine esterases (EOHs) inhibited by organophosphorus (OP) compounds can produce O-phosphorylated oximes (POXs). Such oxime derivatives are of interest, because some of them can have greater anti-EOH potencies than the OP inhibitors from which they were derived. Accordingly, inhibitor properties of 58 POXs against four EOHs, along with pair-wise selectivities between them, have been analysed using different QSAR approaches. EOHs (with their abbreviations and consequences of inhibition in parentheses) comprised acetylcholinesterase (AChE: acute neurotoxicity; cognition enhancement), butyrylcholinesterase (BChE: inhibition of drug metabolism or stoichiometric scavenging of EOH inhibitors; cognition enhancement), carboxylesterase (CaE: inhibition of drug metabolism or stoichiometric scavenging of EOH inhibitors), and neuropathy target esterase (NTE: delayed neurotoxicity). QSAR techniques encompassed linear regression and backpropagation neural networks in conjunction with fragmental descriptors containing labelled atoms, Molecular Field Topology Analysis (MFTA), Comparative Molecular Similarity Index Analysis (CoMSIA), and molecular modelling. All methods provided mostly consistent and complementary information, and they revealed structural features controlling the ‘esterase profiles’, i.e. patterns of anti-EOH activities and selectivities of the compounds of interest. In addition, MFTA models were used to design a library of compounds having a cognition-enhancement esterase profile suitable for potential application to the treatment of Alzheimers disease.