Designing sedative/hypnotic compounds from a novel substructural graph-theoretical approach

A novel approach to computer-aided molecular design is illustrated. This approach is based on the calculation of the spectral moments of the bond adjacency matrix of graphs representing molecular structures. Spectral moments are then expressed as linear combinations of the different sub-structures present in molecules. Two series of compounds, one containing sedative/hypnotic and the other containing different classes of drugs were used to find a discriminant function with the present approach. Several compounds from the Merck Index were identified by the model as sedative/hypnotic, five of them were found in the recent literature as possessing this activity. The critical fragments, actives and inactive ones, were detected.     

Quantum-chemical foundations of the topological substructural molecular design

The topological substructural molecular design (TOPS-MODE) approach is formulated as a tight-binding quantum-chemical method. The approach is based on certain postulates that permit to express any molecular property as a function of the spectral moments of certain types of molecular and environment-dependent energies. We use several empirical potentials to account for these intrinsic and external molecular energies. We prove that any molecular property expressed in terms of a quantitative structure-property and structure-activity relationships (QSPR/QSAR) model developed by using the TOPS-MODE method can be expressed as a bond additivity function. In addition, such a property can also be expressed as a substructural cluster expansion function. The conditions for such bond contributions being transferable are also analyzed here. Several new statistical-mechanical electronic functions are introduced as well as a bond-bond thermal Green's function or a propagator accounting for the electronic hopping between pairs of bonds. All these new concepts are applied to the development and application of a new QSAR model for describing the toxicity of polyhalogenated-dibenzo-1,4-dioxins. The QSAR model obtained displays a significant robustness and predictability. It permits an easy structural interpretation of the structure-activity relationship in terms of bond additivity functions, which display some resemblances with other theoretical parameters obtained from first principle quantum-chemical methods.     

Intramolecular energy transfer through charge transfer state in lanthanide compounds: a theoretical approach

A theoretical approach for the intramolecular energy transfer process involving the ligand-to-metal charge transfer (LMCT) state in lanthanide compounds is developed. Considering a two-electron interaction, both the direct Coulomb and exchange interactions are taken into account, leading to expressions from which selection rules may be derived and transfer rates may be calculated. These selection rules show that the direct Coulomb and exchange mechanisms are complementary, in the same way as obtained in previous works for the case of ligand-lanthanide ion energy transfer processes. An important result from numerical estimates is that the channel ligand-LMCT state is by far the dominant case, leading to transfer rates higher than for the channel lanthanide ion-LMCT state by several orders of magnitude. The analysis of the emission quantum yield as a function of the relative energy position of the LMCT state in a typical Eu(3+) compound allows the identification of two quenching regions, the most pronounced one occurring close to the lower ligand triplet level.     

On topological charge stabilization in heterocyclic compounds

According to Gimarc's principle of topological chargestabilization, heteroatomic molecules are topologically stabilized when more electronegative atoms are placed in those positions where atom-atom connectivity and the electron-filling level provide the highest electron charge in the reference hydrocarbon frame. Recently, we showed that the relative atomic moments of energy (the frequencies of atomic self-returning walks) in such uniform molecular skeletons are equal to the respective squared principal eigenvector coefficients. We show here that for conjugated heteroryclic molecules these partial atomic charges follow closely the patterns mirrored by topological charge stabilization and, by producing a nonuniform charge distribution in alternant molecules, enable the broader application of this principle to such molecules.Texas A&M university, Galveston, Texas. Published in Khimiya Geterotsiklicheskikh Soedinenii, No. 8, pp. 1011–1022,August, 1995. Original article submitted May 19, 1995.Dedicated to N. S. Zefirov for his important contributions to mathematical chemistry, as well as for his friendly help to those who need it.     

Preparation of active antibacterial LDPE surface through multistep physicochemical approach: I. Allylamine grafting, attachment of antibacterial agent and antibacterial activity assessment

Low-density polyethylene (LDPE) samples were treated in air plasma discharge, coated by polyallyamine brush thought copolymeric grafting surface-from reaction and deposited four common antibacterial agents (benzalkonium chloride, bronopol, chlorhexidine and triclosan) to gain material with active antibacterial properties. Surface characteristics were evaluated by static contact angle measurement with surface energy evaluation ATR-FTIR, X-ray Photoelectron Spectroscopy (XPS) and SEM analysis. Inhibition zone on agar was used as in vitro test of antibacterial properties on two representative gram positive Staphylococcus aureus (S. aureus) and gram negative Escherichia coli (E. coli) strains. It was confirmed, that after grafting of polyallyamine, more antibacterial agent is immobilized on the surface. The highest increase of antibacterial activity was observed by the sample containing triclosan. Samples covered by bronopol did not show significant antibacterial activity.     

Understanding topological symmetry: a heuristic approach to its determination

An algorithm based on heuristic rules for topological symmetry perception of organic structures having heteroatoms, multiple bonds, and any kind of cycle, and configuration, is presented. This algorithm identifies topological symmetry planes and sets of equivalent atoms in the structure, named symmetry atom groups (SAGs). This approach avoids both the need to explore the entire graph automorphism groups, and to encompass cycle determination, resulting in a very effective computer processing. Applications to several structures, some of them highly symmetrical such as dendrimers, are presented.     

Isomer discrimination by topological information approach

A comparative analysis of ten topological indices is made. No index is found to discriminate isomers uniquely. A combined topological index, named the superindex, consisting of a number of topological indices is proposed. Information theory is applied to express all components of the superindex on a common quantitative scale. The superindex is tested on the sample of 427 graphs consisting of all acyclic, monocyclic, and bicyclic graphs with 4–8 vertices.     

Small organometallic compounds as antibacterial agents

The emergence of bacterial resistance to commercial antibiotics is an issue of global importance. During the last two decades, the number of antibacterial agents that have been discovered and introduced into the market has steadily declined and failed to meet the challenges posed by rapidly increasing resistance of the pathogens against common antibacterial drugs. The development of new classes of compounds to control the virulence of the pathogens is therefore urgently required. This perspective describes the historical development in brief and recent advances on the preparation of small organometallic compounds as new classes of antibacterial agents with potential for clinical development.     

Design of topological indices: computer-oriented approach

A novel method is suggested for constructing topological indices (TIs) of molecular graphs which models human logic. This method is described in terms of a block scheme, consisting of the mutually connected elementary blocks. In each block the simple transformations of a molecular graph are fulfilled. A variant of the transformation is selected from the list of possible variants. Every TI is obtained as a result of the sequential execution of a number of operations, corresponding to some ‘walk’ on the block scheme. This walk can be selected both randomly and by the investigator. The suggested method can serve as a basis for the development of the respective computer program which may be used for the automatic construction of any number of TIs of differing nature. By this process one can also obtain the TIs that are unlikely to be constructed manually, due to their complexity. The set of obtained TIs may be used for building the structure–property models. In the case of an unsatisfactory result the obtained set of TIs may be changed using the described generator of TIs. A number of examples of application of the suggested approach for the building QSAR/QSPR models is given.     

Di-isatin heteronuclear compounds and their antibacterial activity

Twenty propylene and butylene tethered di-isatin heteronuclear compounds 5a-t were synthesized, and their antibacterial activities were evaluated. Most of the synthesized di-isatin heteronuclear derivatives were active against both Gram-positive and Gram-negative strains, and some of them exhibited considerable activities against drug-resistant organisms. In particular, di-isatin 5a (MIC: 32-512 μg/mL) was more active than the reference vancomycin against Gram-negative pathogens, demonstrating the antibacterial potential of di-isatin heteronuclear compounds. The inhibitory activity of di-isatin 5a was higher than mono-isatin against Escherichia coli DNA gyrase, suggesting the dimers could improve the inhibitory activity against DNA gyrase when compared with the isatin. The structure-activity relationship was discussed to provide an insight for rational designs of more efficient antibacterial candidates.     

Designing organometallic compounds for catalysis and therapy

Bioorganometallic chemistry is a rapidly developing area of research. In recent years organometallic compounds have provided a rich platform for the design of effective catalysts, e.g. for olefin metathesis and transfer hydrogenation. Electronic and steric effects are used to control both the thermodynamics and kinetics of ligand substitution and redox reactions of metal ions, especially Ru(II). Can similar features be incorporated into the design of targeted organometallic drugs? Such complexes offer potential for novel mechanisms of drug action through incorporation of outer-sphere recognition of targets and controlled activation features based on ligand substitution as well as metal- and ligand-based redox processes. We focus here on η(6)-arene, η(5)-cyclopentadienyl sandwich and half-sandwich complexes of Fe(II), Ru(II), Os(II) and Ir(III) with promising activity towards cancer, malaria, and other conditions.     

Bridged isocytosine-adenosine compounds: Synthesis and antibacterial evaluation

In an approach to novel antibacterial agents, we synthesized a series of 5-nitrosoisocytosines in which a 6-alkylamino substituent is bridged, through an amide linkage at the terminus of the alkyl chain, to the 5′-position of a 5′-deoxyadenosine moiety. A corresponding series of 5-nitro analogues were also prepared. None of the bridged compounds showed significant antibacterial activity.     

Peptoids as source of compounds eliciting antibacterial activity

N-Alkylglycine oligomers (peptoids) constitute a family of non-natural peptidomimetics attractive for the early drug discovery process because of their physicochemical features, easy of adaptation to combinatorial chemistry approaches and their proteolytic stability. Consequently, peptoid libraries have found application for discovering hits against a wide diversity of pharmaceutical targets, among which different examples of antibacterials are found. In the present work, research efforts addressed towards the identification of peptoids as antibacterial agents are discussed.     

Designing of precise vaccine construct against visceral leishmaniasis through predicted epitope ensemble: A contemporary approach

Visceral leishmaniasis (VL) caused by Leishmania donovani is a fatal parasitic disease affecting primarily the poor population in endemic countries. Increasing number of deaths as well as resistant to existing drugs necessitates the development of an effective vaccine for successful treatment of VL. The present study employed a combinatorial approach for designing monomer vaccine construct against L. donovani by applying forecasted B- and T- cell epitopes from 4 genome derived antigenic proteins having secretory signal peptides and glycophosphatidylinositol (GPI) anchors with ≤ 1 transmembrane helix. The forecasted population coverage of chosen T cell epitope ensemble (combined HLA class I and II) cover 99.14 % of world-wide human population. The predicted 3D structure of vaccine constructs (VC1/VC2) were modeled using homology modeling approach and docked to innate immune receptors TLR-2 and TLR-4 with respective docking energies −1231.4/−910.3 and −1119.4/−1476 kcal/mol. Overall, the aforementioned designed vaccine constructs were found appropriate for including in self-assembly protein nanoparticles (SAPN) for further study in developing cutting-edge precision vaccine against VL in short duration with cost-effective manner.     

Active methylene compounds in a very effective approach to 3-substituted isobenzofuranones through tandem aldol/lactonization reactions

In this article we describe a new accessible methodology for the synthesis of isobenzofuran-1(3H)-ones. In this process we exploited an effective, economic, useful and environmentally benign K₂CO₃ catalyzed, solvent-free one-pot tandem aldol-lactonization reaction between active methylene compounds and methyl 2-carboxy benzaldehyde. A particularly simple work-up and purification procedure are additional advantages addressed to a general green chemistry approach to this important class of heterocyclic compounds.     

Novel naphthalene-based bis-pyridinium compounds with pronounced antibacterial activity

Novel para-substituted bis-pyridinium compounds containing 2,7-dioxynaphthalene spacer were synthesized in two simple steps from the corresponding dihydroxy-naphthalene. The microbiological study on five reference (E. coli ATCC 25922, K. pneumoniae ATCC 70060, S. aureus ATCC 43300, P. aeruginosa ATCC27853, and A. baumannii ATCC 15308) and five clinical (E. coli B-3421/19,K. pneumoniae B-2523/18, S. aureus B-8648, P. aeruginosa B-2099/18 and A. baumannii B-2926/18) bacterial strains showed promising range of antibacterial properties for these biocides, compared to modern sanitizers.