Finding Needles in a Haystack: Determining Key Molecular Descriptors Associated with the Blood-brain Barrier Entry of Chemical Compounds Using Machine Learning.

In this paper we used two sets of calculated molecular descriptors to predict blood-brain barrier (BBB) entry of a collection of 415 chemicals. The set of 579 descriptors were calculated by Schrodinger and TopoCluj software. Polly and Triplet software were used to calculate the second set of 198 descriptors.

Cube-Related Corner Coalesced Nets.

Finite or periodic structures containing the cube motif can be synthesized and transformed into a variety of structures both at the theoretical and real, experimental level. The rhombellation topo-geometric operation may be used to transform the cube-shape into larger units and then build light (spongy) structures with larger voids. Hyper-clusters are polyhedral structures which nodes are polyhedral structures (the same or different ones).

Cube-Rhombellane Related Structures: A Drug Perspective.

Rhombellanes represent a new class of structures, of which homeomorphs may be synthesized as real molecules. Cube-rhombellane is a double-shell structure, with vertices of degree 3 and 6, respectively. Several hypothetical structures/molecules were proposed and computed using molecular graph theory and coordination chemistry principles.

Binding Site and Potency Prediction of Teixobactin and other Lipid II Ligands by Statistical Base Scoring of Conformational Space Maps.

Background: Lipid II, a peptidoglycan, is a precursor in bacterial cell synthesis. It has both hydrophilic and lipophilic properties. The molecule translocates a bacterial membrane to deliver and incorporate "building blocks" from disaccharide-pentapeptide into the peptidoglican wall.

Ligand Shaping in Induced Fit Docking of MraY Inhibitors. Polynomial Discriminant and Laplacian Operator as Biological Activity Descriptors.

Docking-i.e., interaction of a small molecule (ligand) with a proteic structure (receptor)-represents the ground of drug action mechanism of the vast majority of bioactive chemicals.

Spongy Nanostructures.

Spongy structures are hollow-containing materials, encountered in natural or synthesized zeolites, spongy carbon, etc. The design and topological study of some hypothetical spongy nanostructures is presented in terms of map operations and genus calculation of their associated graphs, respectively. Among the discussed structures one remarks some novel spongy polyhedra that can evolve with 1-periodicity or radially, to provide multi-shell cages.

Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase.

Glucose oxidase (GOx) is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state) to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H₂O₂).

Understanding the Action of Indolizines as Biologically Active Moieties: A Molecular Dynamics Study.

Background: Indolizines represent a class of heteroaromatic compounds, of pharmacological importance, containing two condensed 5- and 6-memebered rings bridged by a nitrogen atom. Despite indolizine is an important medicinal moiety, a detailed view on the mechanism of action of biologically active indolizines is unavailable.

Objective: The study of ligand-enzyme affinity is of high interest; description of characteristics (energetic and geometric ones) of ligand binding to the active sites of an enzyme could be useful in understanding the action mechanism of a given ligand on the concerned enzyme.

Linear and Branched PEIs (Polyethylenimines) and Their Property Space.

A chemical property space defines the adaptability of a molecule to changing conditions and its interaction with other molecular systems determining a pharmacological response. Within a congeneric molecular series (compounds with the same derivatization algorithm and thus the same brute formula) the chemical properties vary in a monotonic manner, i.e.

Molecular Docking Studies of Flavonoids Derivatives on the Flavonoid 3- O-Glucosyltransferase.

A study of 30 flavonoid derivatives, taken from PubChem database and docked on flavonoid 3-O-glucosyltransferase 3HBF, next submitted to a QSAR study, performed within a hypermolecule frame, to model their LD50 values, is reported. The initial set of molecules was split into a training set and the test set (taken from the best scored molecules in the docking test); the predicted LD50 values, computed on similarity clusters, built up for each of the molecules of the test set, surpassed in accuracy the best model. The binding energies to 3HBF protein, provided by the docking step, are not related to the LD50 of these flavonoids, more protein targets are to be investigated in this respect.

QSAR and docking studies of anthraquinone derivatives by similarity cluster prediction.

Forty anthraquinone derivatives have been downloaded from PubChem database and investigated in a quantitative structure-activity relationships (QSAR) study. The models describing log P and LD50 of this set were built up on the hypermolecule scheme that mimics the investigated receptor space; the models were validated by the leave-one-out procedure, in the external test set and in a new version of prediction by using similarity clusters. Molecular docking approach using Lamarckian Genetic Algorithm was made on this class of anthraquinones with respect to 3Q3B receptor.

Quantum-mechanical calculations on molecular substructures involved in nanosystems.

In this review article, four ideas are discussed: (a) aromaticity of fullerenes patched with flowers of 6-and 8-membered rings, optimized at the HF and DFT levels of theory, in terms of HOMA and NICS criteria; (b) polybenzene networks, from construction to energetic and vibrational spectra computations; (c) quantum-mechanical calculations on the repeat units of various P-type crystal networks and (d) construction and stability evaluation, at DFTB level of theory, of some exotic allotropes of diamond D5, involved in hyper-graphenes. The overall conclusion was that several of the yet hypothetical molecular nanostructures herein described are serious candidates to the status of real molecules.

QSAR in flavonoids by similarity cluster prediction.

Quantitative Structure-Activity Relationships based on molecular descriptors calculated with correlation weights within the hypermolecule, considered to mimic the investigated correlational space, was performed on a set of 40 flavonoids (PubChem database). The best models describing log P and LD50 of this set of flavonoids were validated by the leave-one-out procedure, in the external test set and in a new version of prediction by using clusters of similar molecules. The best prediction was provided by the similarity cluster procedure.

Multistructural biomimetic substrates for controlled cellular differentiation.

Multidimensional scaffolds are considered to be ideal candidates for regenerative medicine and tissue engineering based on their potential to provide an excellent microenvironment and direct the fate of the cultured cells. More recently, the use of stem cells in medicine has opened a new technological opportunity for controlled tissue formation. However, the mechanism through which the substrate directs the differentiation of stem cells is still rather unclear.

Polybenzene revisited.

Polybenzene was described by O'Keeffe et al., as an embedding of a 6.82 net in the infinite periodic minimal D-surface, with a single type of carbon atoms and was predicted to have a substantially lower energy per atom in comparison to C60, the reference structure in Nanoscience.

Hyper-diamonds and dodecahedral architectures by tetrapodal carbon nanotube junctions.

Tetrapodal junctions are used to construct diamond-like networks and dodecahedral architectures. They can be associated with the already synthesized spongy carbon, consisting only of sp2 covalent carbon atoms, and the zeolites, periodic structures in the Euclidean space. In this paper, the structure and stability of two zigzag tetrapodal junctions are discussed.

Molecular design and QSARs/QSPRs with molecular descriptors family.

The aim of the present paper is to present the methodology of the molecular descriptors family (MDF) as an integrative tool in molecular modeling and its abilities as a multivariate QSAR/QSPR modeling tool. An algorithm for extracting useful information from the topological and geometrical representation of chemical compounds was developed and integrated to calculate MDF members. The MDF methodology was implemented and the software is available online (http://l.

Deposition of DLC Film on Stainless Steel Substrates Coated by Nickel Using PECVD Method.

Research on diamond-like carbon (DLC) films has been devoted to find both optimized conditions and characteristics of the deposited films on various substrates. In the present work, we investigate the quality of the DLC films grown on stainless steel substrates using different thickness of the nickel nanoparticle layers on the surface. Nickel nanoparticles were sputtered on the stainless steel substrates at 200 °C by a DC-sputtering system to make a good adherence between DLC coating and steel substrates.

Nanotube junctions and the genus of multi-tori.

Carbon nanotube junctions can be modeled by fullerene spanning or by using some operations on map. They can self-assemble into more complex structures, such as finite or infinite high genera multi-tori. Four junctions of tetrahedral and octahedral symmetry, covered by patches consisting only of hexagons, were designed.

Sumanene Units in P-type Surface Networks.

Sumanene is a synthesized circulene molecule, with formula: 6:(5,6)3. We propose here units for periodic P-type surface networks, based on their stability, evaluated at the Hartree-Fock HF level of theory. Design of the yet hypothetical lattices was performed by using operations on maps, as provided by CVNET and Nano Studio software.

Electrically conductive gold-coated collagen nanofibers for placental-derived mesenchymal stem cells enhanced differentiation and proliferation.

Gold-coated collagen nanofibers (GCNFs) were produced by a single-step reduction process and used for the growth and differentiation of human adult stem cells. The nanomaterials were characterized by a number of analytical techniques including electron microscopy and spectroscopy. They were found to be biocompatible and to improve the myocardial and neuronal differentiation process of the mesenchymal stem cells isolated from the placental chorionic component.

Omega polynomial revisited.

Omega polynomial was proposed by Diudea (Omega Polynomial, Carpath. J. Math.

Shell-polynomials and cluj-tehran index in tori t(4,4)s[5,n].

Weighted Hosoya polynomials have been developed by Diudea, in ref. Studia Univ. "Babes-Bolyai", 2002, 47, 131-139.

Counting Polynomials in Tori T(4,4)S[c,n].

A counting polynomial P(x) is a description of a graph property P(G) in terms of a sequence of numbers so that the exponents express the extent of its partitions while the coefficients are related to the number of partitions of a given extent. Basic definitions and some properties are given for two classes of polynomials, called here polynomials of vertex proximity and edge proximity, respectively. Formulas to calculate these polynomials in T(4,4)[c,n] tori are derived by a cutting procedure.

Kekulé structure count in corazulenic fullerenes.

Tiling modification in fullerene modeling can be achieved by some map operations. In this respect, sequences of classical operations, or single generalized operations, were used to obtain corannulene-like azulenic patterns. The aromaticity of such cages tessellated by "corazulenic" supra-faces is discussed in terms of several criteria.