Leif A. Eriksson

Structure and dynamics of monomer-template complexation: an explanation for molecularly imprinted polymer recognition site heterogeneity.

We here present the first simulation of a complete molecularly imprinted polymer prepolymerization system. Molecular dynamics studies were performed for a system comprising a total of 1199 discrete molecules, replicating the components and concentrations employed in the corresponding polymer synthesis. The observed interactions correlate well with results obtained from (1)H NMR spectroscopic studies. Comparison with simulations performed in the absence of cross-linking agent (ethylene dimethacrylate) demonstrated its significance in the formation of ligand recognition sites. Moreover, the influence of events such as template-template (bupivacaine) and monomer-monomer (methacrylic acid) self-association, porogen-template interactions, and template conformational variability was revealed. The template recognition capacity of the modeled polymer system was verified by synthesis of imprinted and reference polymers and subsequent radioligand binding analysis. Collectively, through a series of statistical analyses of molecular trajectories in conjunction with spectroscopic data it was demonstrated that an ensemble of complex structures is present in the prepolymerization mixture and that this diversity is the basis for the binding site heterogeneity observed in molecularly imprinted polymers (MIPs) prepared using the noncovalent strategy.

Evidence of High •OH Radical Quenching Efficiency by Vitamin B6

Molecules acting as antioxidants capable of scavenging reactive oxygen species (ROS) are of the utmost importance in the living cell. The antioxidative properties of pyridoxine (vitamin B6) have recently been discovered. Previous theoretical calculations have shown a high reactivity of pyridoxine toward hydroxyl radicals, where the latter preferably abstract H from either carbon of the two methanol substituents (C8 or C9). In this study, we have explored the reactivity of pyridoxine toward further hydroxyl radicals, considering as the first step the H abstraction from either C8 or C9, also including addition reactions and cyclization. Many of the reactions display similar DeltaG, and hence, the quenching of hydroxyl radicals by pyridoxine may undergo different pathways leading to a mix of products. In addition, we observe that pyridoxine, under high hydroxyl radical concentrations, may scavenge up to eight radicals, supporting its observed high antioxidant activity.

Effects of Ionizing Radiation on Crystalline Cytosine Monohydrate.

Possible radical reaction products observed when subjecting monohydrate crystals of the DNA base cytosineto ionizing radiation are characterized and analyzed by means of density functional theory. Comparison ismade with data from a recently published detailed ESR and ENDOR study by Sagstuen et al. (Sagstuen, E.;Hole, E. O.; Nelson, W. H.; Close, D. M. J. Phys. Chem. 1992, 96, 8269), as well as earlier studies onmethylcytosine and cytidine monophosphates. For cytosine monohydrate it is found, when comparing computedand measured radical hyperfine coupling constants, that products other than those initially assumed are possiblybeing formed. Instead of the original model that irradiation leads to the net reaction of dehydrogenation atthe N1 position of one cytosine molecule and hydrogenation at the N3 position of a second cytosine, wepresent an alternative mechanism where water is involved in the process. This alternative mechanism leadsto the formation of N3 hydrogenation and C5 hydroxylation net products, as the main reactions. Not only dothe hyperfine couplings provide a better match for the latter but they are also energetically favored over thefirst mechanism.

Rational design and validation of a Tip60 histone acetyltransferase inhibitor

Histone acetylation is required for many aspects of gene regulation, genome maintenance and metabolism and dysfunctional acetylation is implicated in numerous diseases, including cancer. Acetylation is regulated by histone acetyltransferases (HATs) and histone deacetylases and currently, few general HAT inhibitors have been described. We identified the HAT Tip60 as an excellent candidate for targeted drug development, as Tip60 is a key mediator of the DNA damage response and transcriptional co-activator. Our modeling of Tip60 indicated that the active binding pocket possesses opposite charges at each end, with the positive charges attributed to two specific side chains. We used structure based drug design to develop a novel Tip60 inhibitor, TH1834, to fit this specific pocket. We demonstrate that TH1834 significantly inhibits Tip60 activity in vitro and treating cells with TH1834 results in apoptosis and increased unrepaired DNA damage (following ionizing radiation treatment) in breast cancer but not control cell lines. Furthermore, TH1834 did not affect the activity of related HAT MOF, as indicated by H4K16Ac, demonstrating specificity. The modeling and validation of the small molecule inhibitor TH1834 represents a first step towards developing additional specific, targeted inhibitors of Tip60 that may lead to further improvements in the treatment of breast cancer.

The Influence of Cholesterol on the Properties and Permeability of Hypericin Derivatives in Lipid Membranes.

The promising photosensitizing properties of hypericin, a natural quinine substituted with hydroxyl and alkyl groups, have led to the proposal that it can be utilized in photodynamic therapy. Neither the detailed mechanism behind the powerful action of hypericin, arising as a result of light excitation, nor the intracellular localization and transportation of the molecule is yet fully understood. The behavior of hypericin derivatives in a pure dipalmitoylphosphatidylcholine (DPPC) lipid membrane has recently been studied theoretically by means of molecular dynamics simulations. Natural membranes however contain many important constituents-cholesterol being one of the most essential-that influence the function and structure of the membrane, and thereby also the behavior of drug molecules therein. In the present study, we investigated hypericin and its brominated derivatives in membranes containing 9 and 25 mol % cholesterol. The results show that the presence of cholesterol in the membrane affects the permeability of the hypericin molecules and does so differently for the various molecules in the two membranes. Hypericin containing one bromine was found to exhibit the lowest free energy profile for the transport process into the lipids, and also the highest permeability coefficients, indicating that this molecule displays the fastest and easiest diffusion in the membranes. All three molecules were found to accumulate most preferably close to the polar headgroup region in both membranes.

Hydrolytic deamination of 5-methylcytosine in protic medium--a theoretical study.

The mechanism for the deamination reaction of 5-methylcytosine with H2O in protic medium was investigated using DFT calculations at the B3LYP/6-311G(d,p) level of theory. Two pathways were found. Pathway 5mA is a two-step mechanism where the N3-protonated 5-MeCyt undergoes a nucleophilic attack to carbon C4 by a water dimer before the elimination of an ammonium cation. Pathway 5mB is a three-step mechanism where neutral 5-MeCyt is directly attacked by a water dimer. The resulting intermediate is then protonated to allow the elimination of an ammonium cation. Both pathways lead to the formation of thymine in interaction with an ammonium cation and a water molecule. Pathway 5mA can explain the spontaneous deamination of 5-MeCyt in protic medium at acidic pH, whereas pathway 5mB is more representative of the deamination in protic medium at neutral pH. The nucleophilic addition of the water dimer is rate-determining in both pathways and is associated with an activation free energy in aqueous solution of 137.4 kJ/mol for pathway 5mA and 134.1 kJ/mol for pathway 5mB. This latter value is in agreement with the experimental observation that 5-MeCyt deaminates four- to fivefold faster than Cyt at neutral pH. Both electrostatic and electron-transfer contributions appear to have significant importance. In vacuum, the former one dominates when the substrate is positively charged and the latter one when it is neutral.

Theoretical Investigation of Adenine Radicals Generated in Irradiated DNA Components.

Density functional theory is used to investigate various hydrogenated, dehydrogenated, and hydroxylated radicals formed upon irradiation of adenine. The relative energies, geometries, and hyperfine coupling constants of possible radicals are discussed. Th

Can Range-Separated and Hybrid DFT Functionals Predict Low-Lying Excitations? A Tookad Case Study

The spectral properties of Tookad (Pd-bacteriopheophorbide, Pd-BPheid), an effective photosensitizer that targets mainly prostate tumors, and metal-free BPheid have been studied using time-dependent density functional theory (TD-DFT). The well-established B3LYP functional, which is known to overestimate excitation energies, was included in the study along with recently introduced range-separated and meta hybrid DFT functionals CAM-B3LYP, M06, M06-2X, M06HF, ωB97XD, ωB97X, ωB97, LC-ωPBE, and PBE0 (PBE1PBE). The main focus is the performance of the new functionals in predicting low-lying excitations (>600 nm), to explore their potential roles in drug development for photodynamic therapy. The data suggests that ωB97XD overall performs best for the Qy transition band (the red-most absorption), followed by CAM-B3LYP. LC-ωPBE, ωB97, B3LYP, and PBE1PBE all generated the Qy band far from the experimental position. The error in absorption energy for the Qy band was found to be at most 0.05 eV for ωB97XD, compared to 0.15-0.19 eV for B3LYP. The use of different basis sets used in excited-state calculations was shown to be of less importance as was the use of either B3LYP or M06 in geometry optimizations.

Formation of β-O-4 lignin models – a theoretical study

Summary The formation of two different β-O-4 lignin models is investigated by means of density functional calculations. It is found that the coupling of two coniferyl alcohol radicals forming a quinone methide proceeds by an energy barrier of ~2–5 kcal/mol, and that the associated reaction energy is negative by more than 20 kcal/mol. On the basis of the corresponding results obtained for the coupling of a coniferyl alcohol radical to a coniferyl alcohol, it is argued that the resulting radical, albeit being formed in an energetically less favourable process, might play an important role in lignin polymerisation. Finally, two different reaction mechanisms for the conversion of a quinone methide into a guaiacylglycerol-β-coniferyl ether dilignol through the addition of water are explored.

Properties and Permeability of Hypericin and Brominated Hypericin in Lipid Membranes.

The promising photosensitizing properties of hypericin, a substituted phenanthroperylene quinone naturally found in Saint Johns wort, has led to the proposal that it can be utilized in photodynamic therapy. Structurally modified derivatives are at the present time being investigated to generate a more effective hypericin photosensitizer. Neither the detailed mechanism behind the powerful action of hypericin, arising as a result of light excitation, nor the intracellular localization and transportation is still fully understood. In the present work, molecular dynamics simulations have been performed to study the properties and the permeability of hypericin and modifications thereof, substituted with one or four bromine atoms, in a dipalmitoylphosphatidylcholine lipid membrane. The molecules were found to accumulate in the most dense region of the lipids due to competing interactions with the hydrophobic lipid interior and the polar aqueous environment. This was confirmed by analyzing the radial distribution functions and by the density profiles of the system components. Calculated free energy profiles display large negative changes in free energy for the transport process of the molecules into the lipids, which also support this finding. Permeability coefficients show overall fastest diffusion in the membrane system for hypericin containing one bromine.