ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions

The article presents a Web-based platform for collecting and storing toxicological structural alerts from literature and for virtual screening of chemical libraries to flag potentially toxic chemicals and compounds that can cause adverse side effects. An alert is uniquely identified by a SMARTS template, a toxicological endpoint, and a publication where the alert was described. Additionally, the system allows storing complementary information such as name, comments, and mechanism of action, as well as other data. Most importantly, the platform can be easily used for fast virtual screening of large chemical datasets, focused libraries, or newly designed compounds against the toxicological alerts, providing a detailed profile of the chemicals grouped by structural alerts and endpoints. Such a facility can be used for decision making regarding whether a compound should be tested experimentally, validated with available QSAR models, or eliminated from consideration altogether. The alert-based screening can also be helpful for an easier interpretation of more complex QSAR models. The system is publicly accessible and tightly integrated with the Online Chemical Modeling Environment (OCHEM, http://ochem.eu ). The system is open and expandable: any registered OCHEM user can introduce new alerts, browse, edit alerts introduced by other users, and virtually screen his/her data sets against all or selected alerts. The user sets being passed through the structural alerts can be used at OCHEM for other typical tasks: exporting in a wide variety of formats, development of QSAR models, additional filtering by other criteria, etc. The database already contains almost 600 structural alerts for such endpoints as mutagenicity, carcinogenicity, skin sensitization, compounds that undergo metabolic activation, and compounds that form reactive metabolites and, thus, can cause adverse reactions. The ToxAlerts platform is accessible on the Web at http://ochem.eu/alerts , and it is constantly growing.     

Nematic ordering in dilute solutions of rodlike polyelectrolytes

Quantitative theory of orientational behavior of rodlike polyelectrolytes in dilute solution is developed. We find that in salt-free solutions many-body Coulomb interactions between macro- and counterions favor nematic ordering. It is shown that the orientationally isotropic phase of the solution becomes unstable toward nematic ordering at polymer concentration smaller than the overlap concentration. Our predictions are consistent with experimental observations for synthetic polyelectrolytes poly(p-phenylene)sulfonates in aqueous solutions.     

X-ray and conformation analysis of the new trinuclear cluster of osmium Os3(μ,η2-OCC6H5)(η3-C3H5)(CO)9

The crystal structure of the Os₃(μ,η²-O=CC₆H₅)(η³-C₃H₅)(CO)₉ cluster synthesized by the reaction of the (μ-H)Os₃(μ-O=CC₆H₅)(CO)₁₀ complex with allylamine in chloroform was determined by X-ray analysis. Prolonged storage of the reaction mixture led to N-C bond cleavage in allylamine and η³-addition of the allyl fragment at one of the Os atoms (Os-C 2.246 ?, 2.248 ?, and 2.273 ?). The unit cell parameters of the complex are a = 9.494(1) ?, b = 10.479(1) ?, c = 12.474(2) ?, α = 84.55(1)°, β = 70.08(1)°, γ = 70.72(1)°, V = 1255.8(4), ?³, space group P , Z = 2; C₁₉H₁₀O₁₀Os₃; d _calc = 2.922 g/cm³, 3085 I _hkl > 2σ _I of 3611 collected reflections; R = 0.0252. The structure of Os₃(μ,η²-O=CC₆H₅)(η³-C₃H₅)(CO)₉ is molecular. The plane of the Os₃ triangle and the OsCOOs plane are connected according to the “butterfly” principle with an angle of 103.4° between them. The Os-Os distances in the cluster core vary from 2.836(1) ? to 2.844(1) ?; the Os-C_carb distances are 1.88(1)–1.97(1) ?; the distances to the atoms of the bridging ligands are Os-C 2.11(1) ?, Os-O 2.14(1) ?; the O-C bridging bond is 1.24(1) ?. of the Os₃(μ,η²-O=CC₆H₅)(η³-C₃H₅)(CO)₉ triosmium cluster were studied theoretically. The potential curve of the internal rotation of the allyl ligand relative to the Os(1)-C(9) bond was determined. The rotation barrier of the allyl ligand in crystal relative to the Os(1)-C(9) bond is 8.38 kJ/mol, and the rotation of the ligand is not hindered. The effects of the intra-and intermolecular interactions on the conformation state of the cluster complex are considered. Original Russian Text Copyright ? 2008 by V. A. Maksakov, N. V. Pervukhina, N. V. Podberezskaya, M. Yu. Afonin, V. A. Potemkin, and V. P. Kirin __________ Translated from Zhurnal Strukturnoi Khimii, Vol. 49, No. 5, pp. 926–932, September–October, 2008.     

Structure formation in heavy metal oxyhydrates at low rates of gel formation

Oxyhydrate gels have a hydrophilic surface, due to which they undergo destruction and secondary polymerization in aqueous media. Prolonged storage in aqueous solution gives rise to regions with selfsimilar helical ordering in gels. Structuring of this kind is also observed when synthesis is conducted under conditions that provide low gelation rates. Electromagnetic UV and visible radiation is another means to change the gel structure; it makes the oligomer species pass into the excited state, due to which one of the directions of structuring becomes dominant. This work summarizes the results of computer simulation of gel agglomerates. For oxyhydrate systems, helical ordering was found to be one of the local energy minima. The units of a macrohelix can lie at various angles relative to one another, and they can change, after absorption of energy, the helix pitch and the order of elements in the helix.     

Modeling of drug molecule orientation within a receptor cavity in the BiS algorithm framework

The BiS algorithm is suggested for modeling the drug molecule orientation within a receptor cavity. It is based on the assumption of complementarity of the field created by biologically active compounds and the field of the responsive receptor. The comparison of predicted orientations of various biologically active compounds on the relevant receptors with the data of X-ray structural studies (Protein Data Bank) reveals that the results obtained with this approach surpasses those reported in the literature. The suggested technique made it possible to elucidate the details of the action mechanism of DNA antimetabolites, dihydrofolate reductase inhibitors. The dependence of the activity on the structural parameters of “ligand-receptor” complexes is determined.     

Two mechanisms of spontaneous curvature of strongly adsorbed (2D) double comblike copolymers

We propose a theory of spontaneous curvature of 2D comblike macromolecules with incompatible side chains of types A and B. It is expected that the side chains of both types are able to change their positions with respect to the backbone. We predict two mechanisms of curvature. In the case of strong incompatibility of the side chains, their complete segregation with respect to the backbone is responsible for the formation of the so-called "energetic" curvature that is a result of the difference in the length (or in the number) of the A and B chains. In the case of moderate incompatibility, partial mixing of the A and B side chains on the convex side of the molecule (a flip of shorter chains to the side of longer chains) can be entropically favorable. In this case, the stretching of the side chains decreases. The radius of the entropic curvature is determined by the length of the longer side chains.     

Theoretical studies of the electronic and structural features of the fragments of dihydropholate reductase inhibitors

The effects of the structural characteristics of dihydrofolate reductase (DHFR) inhibitors on their tuberculostatic activity have been analyzed. It was shown that an increase in the electron density on bonds and atoms in the ring led to an increase in the biological activity of the compounds. A correlation was found between the biological activity and the characteristics of the critical points of electron density of bonds. The 3D- and 4D-QSAR studies with the CiS algorithm revealed the pharmacophore and antipharmacophore fragments of DHFR inhibitors, and regions of the receptor that are responsible for the biological action of dihydropyrimidines were found. Receptor ligand complexes were modeled. For a series of drugs containing a podand chain, it was found that the chain performed only the transport membranotropic function because the increase in the size of molecules due to the podand chain gives rise to steric hindrances when the chain is built in the receptor cavity.     

Electron Density Analysis of SARS-CoV-2 RNA-Dependent RNA Polymerase Complexes

The work is devoted to the study of the complementarity of the electronic structures of the ligands and SARS-CoV-2 RNA-dependent RNA polymerase. The research methodology was based on determining of 3D maps of electron densities of complexes using an original quantum free-orbital AlteQ approach. We observed a positive relationship between the parameters of the electronic structure of the enzyme and ligands. A complementarity factor of the enzyme-ligand complexes has been proposed. The console applications of the AlteQ complementarity assessment for Windows and Linux (alteq_map_enzyme_ligand_4_win.exe and alteq_map_enzyme_ligand_4_linux) are available for free at the ChemoSophia webpage.     

Behavior of PNIPAM Microgels in Different Organic Solvents

In this research, we studied, in detail, the behavior of common PNIPAM microgels, obtained through surfactant-free precipitation polymerization, in a number of organic solvents. We showed that many of the selected solvents serve as good solvents for the PNIPAM microgels and that the size and architecture of the microgels depend on the solvent chosen. Expanding the range of solvents used for PNIPAM microgel incubation greatly enhances the possible routes for microparticle functionalization and modification, as well as the encapsulation of water-insoluble species. In this demonstration, we successfully encapsulated water-insoluble Sudan III dye in PNIPAM microgels and prepared the aqueous dispersions of such composite-colored microparticles.