The Biochemical Mechanisms of Antimicrobial Photodynamic Therapy†

The unbridled dissemination of multidrug-resistant pathogens is a major threat to global health and urgently demands novel therapeutic alternatives. Antimicrobial photodynamic therapy (aPDT) has been developed as a promising approach to treat localized infections regardless of drug resistance profile or taxonomy. Even though this technique has been known for more than a century, discussions and speculations regarding the biochemical mechanisms of microbial inactivation have never reached a consensus on what is the primary cause of cell death. Since photochemically generated oxidants promote ubiquitous reactions with various biomolecules, researchers simply assumed that all cellular structures are equally damaged. In this study, biochemical, molecular, biological and advanced microscopy techniques were employed to investigate whether protein, membrane or DNA damage correlates better with dose-dependent microbial inactivation kinetics. We showed that although mild membrane permeabilization and late DNA damage occur, no correlation with inactivation kinetics was found. On the other hand, protein degradation was analyzed by three different methods and showed a dose-dependent trend that matches microbial inactivation kinetics. Our results provide a deeper mechanistic understanding of aPDT that can guide the scientific community toward the development of optimized photosensitizing drugs and also rationally propose synergistic combinations with antimicrobial chemotherapy.     

Random matrix theory for transition strength densities in finite quantum systems: Results from embedded unitary ensembles

Embedded random matrix ensembles are generic models for describing statistical properties of finite isolated interacting quantum many-particle systems. For the simplest spinless fermion (or boson) systems, with say m$m$ fermions (or bosons) in N$N$ single particle states and interacting via k$k$-body interactions, we have EGUE(k$k$) [embedded GUE of k$k$-body interactions] with GUE embedding and the embedding algebra is U(N)$U\left(N\right)$. A finite quantum system, induced by a transition operator, makes transitions from its states to the states of the same system or to those of another system. Examples are electromagnetic transitions (then the initial and final systems are same), nuclear beta and double beta decay (then the initial and final systems are different), particle addition to or removal from a given system and so on. Towards developing a complete statistical theory for transition strength densities (transition strengths multiplied by the density of states at the initial and final energies), we have derived formulas for the lower order bivariate moments of the strength densities generated by a variety of transition operators. Firstly, for a spinless fermion system, using EGUE(k$k$) representation for a Hamiltonian that is k$k$-body and an independent EGUE(t$t$) representation for a transition operator that is t$t$-body and employing the embedding U(N)$U\left(N\right)$ algebra, finite-N$N$ formulas for moments up to order four are derived, for the first time, for the transition strength densities. Secondly, formulas for the moments up to order four are also derived for systems with two types of spinless fermions and a transition operator similar to beta decay and neutrinoless beta decay operators. In addition, moments formulas are also derived for a transition operator that removes k₀$k_0$ number of particles from a system of m$m$ spinless fermions. In the dilute limit, these formulas are shown to reduce to those for the EGOE version derived using the asymptotic limit theory of Mon and French (1975). Numerical results obtained using the exact formulas for two-body (k=2$k=2$) Hamiltonians (in some examples for k=3$k=3$ and 4$4$) and the asymptotic formulas clearly establish that in general the smoothed (with respect to energy) form of the bivariate transition strength densities take bivariate Gaussian form for isolated finite quantum systems. Extensions of these results to bosonic systems and EGUE ensembles with further symmetries are discussed.     

An efficient coarse-grained approach for the electron transport through large molecular systems under dephasing environment

Dephasing effects in electron transport in molecular systems connected between contacts average out the quantum characteristics of the system, forming a bridge to the classical behavior as the size of the system increases. For the evaluation of the conductance of the molecular systems which have sizes within this boundary domain, it is necessary to include these dephasing effects. These effects can be calculated by using the D’Amato-Pastawski model. However, this method is computationally demanding for large molecular systems since transmission functions for all pairs of atomic orbitals need to be calculated. To overcome this difficulty, we develop an efficient coarse-grained model for the calculation of conductance of molecular junctions including decoherence. By analyzing the relationship between chemical potential and inter-molecular coupling, we find that the chemical potential drops stepwise in the systems with weaker inter-unit coupling. Using this property, an efficient coarse-grained algorithm which can reduce computational costs considerably without losing the accuracy is derived and applied to one-dimensional organic systems as a demonstration. This model can be used for the study of the orientation dependence of conductivity in various phases (amorphous, crystals, and polymers) of large molecular systems such as organic semiconducting materials.     

Novel Capsular Aggregates from Flexible Tripodal Triureas with Cs Symmetry

Tris(2‐ and 3‐ureidobenzyl)amines with C_s symmetry self‐assemble in solution forming mixtures of regioisomeric capsular aggregates, one of which is chiral and the other centrosymmetric. Under certain conditions, a predominance of the centrosymmetric regioisomer is found before equilibrium, that is, a mixture close to the statistical ratio of the two species is reached. In the solid state, there is a preference for the centrosymmetric capsules. Molecular models of both regioisomeric aggregates have been built and analyzed for comparison. Guests inside capsules formed by self‐assembly of desymmetrized tris(3‐ureidobenzyl)amines feel different magnetic environments, depending on whether they are inside a chiral or an achiral regioisomeric container. Of special significance are the experiments with a more flexible triurea endowed with an ureidopropylic arm, which self‐assembles with the same efficiency as the more rigid tris(ureidobenzyl)amines.     

Electron spin resonance in pyrolyzed lignin

An investigation has been made into electron spin resonance (ESR) occurring in the ranges of carbons prepared from periodate lignin by vacuum pyrolysis. Line shape, line width, g-factors, saturation effects, and free spin concentration have been measured and the effect of oxygen on these parameters has been examined. A g-shift and lines with inhomogeneous broadening have been observed. In the presence of oxygen the lower-temperature carbons showed an unexpected increase in the detectable free spin concentration. The discussion includes factors affecting the nature of the free spins in the pyrolyzed material.     

Dual Nucleophilic Substitution Reactions of O,O‐Diethyl 2,4‐dinitrophenyl Phosphate and Thionophosphate Triesters

The reactions of the title compounds with phenoxides, secondary alicyclic (SA) amines, and pyridines, in 44 wt% ethanol–water, at 25°C and an ionic strength of 0.2 M, were subjected to kinetic and product studies. From analytical techniques (HPLC and NMR), two pathways were detected (nucleophilic attack at the phosphoryl center and at the C‐1 aromatic carbon) for the reactions of all the nucleophiles with the phosphate ( 2 ) and for the pyridinolysis of the thionophosphate ( 1 ). Only aromatic nucleophilic substitution was found for the reactions of 1 with phenoxides and SA amines. For the dual reactions, the nucleophilic rate constants (k_N) were separated in two terms: $k_{\rm N}^{\rm P}$ and $k_{\rm N}^{{\rm Ar}}$, which are the rate constants for the corresponding electrophilic centers. The absence of a break in the Brønsted‐type plots for the attack at P is consistent with concerted mechanisms. The Brønsted slopes, β_Ar 0.32–0.71, for the attack at the aromatic C‐1, are in agreement with stepwise mechanisms where formation of a Meisenheimer complex is the rate‐determining step. © 2013 Wiley Periodicals, Inc. Int J Chem Kinet 45: 202–211, 2013     

Glutamine: fructose-6-phosphate amidotransferase (GFAT): homology modelling and designing of new inhibitors using pharmacophore and docking based hierarchical virtual screening protocol

Glutamine: fructose-6-phosphate amidotransferase (GFAT), also termed GFPT1 and GFAT1, catalyzes the first committed step of the hexosamine biosynthesis pathway in mammals and consequently plays an important role in type 2 diabetes. In the present study, a combination of pharmacophore modelling, homology modelling, and molecular docking analysis was performed to design new glutamine competitive inhibitors of human GFAT, and to investigate important interaction details of inhibitor molecules. A pharmacophore model of GFAT inhibitors was developed, subsequently validated, and utilized for the screening by the PHASE database to identify new molecules. Afterwards, homology modelling was performed to construct the glutamine-binding site of the GFAT protein. The modelled active site was utilized to dock the studied molecules to investigate important receptor-ligand interactions and to scrutinize database-screened molecules on the basis of essential interactions. This systematic in silico protocol helped us to identify new molecules that would be explored for the treatment of type 2 diabetes and its complications.