@phdthesis{Merget2015,
  author    = {Merget, Benjamin},
  title     = {Computational methods for assessing drug-target residence times in bacterial enoyl-ACP reductases and predicting small-molecule permeability for the \(Mycobacterium\) \(tuberculosis\) cell wall},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-127386},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2015},
  abstract  = {\textbf{Molecular Determinants of Drug-Target Residence Times of Bacterial Enoyl-ACP Reductases.} Whereas optimization processes of early drug discovery campaigns are often affinity-driven, the drug-target residence time \$t_R\$ should also be considered due to an often strong correlation with \textit{in vivo} efficacy of compounds. However, rational optimization of \$t_R\$ is not straightforward and generally hampered by the lack of structural information about the transition states of ligand association and dissociation. The enoyl-ACP reductase FabI of the fatty acid synthesis (FAS) type II is an important drug-target in antibiotic research. InhA is the FabI enzyme of \textit{Mycobacterium tuberculosis}, which is known to be inhibited by various compound classes. Slow-onset inhibition of InhA is assumed to be associated with the ordering of the most flexible protein region, the substrate binding loop (SBL). Diphenylethers are one class of InhA inhibitors that can promote such SBL ordering, resulting in long drug-target residence times. Although these inhibitors are energetically and kinetically well characterized, it is still unclear how the structural features of a ligand affect \$t_R\$. Using classical molecular dynamics (MD) simulations, recurring conformational families of InhA protein-ligand complexes were detected and structural determinants of drug-target residence time of diphenyl\-ethers with different kinetic profiles were described. This information was used to deduce guidelines for efficacy improvement of InhA inhibitors, including 5'-substitution on the diphenylether B-ring. The validity of this suggestion was then analyzed by means of MD simulations. Moreover, Steered MD (SMD) simulations were employed to analyze ligand dissociation of diphenylethers from the FabI enzyme of \textit{Staphylococcus aureus}. This approach resulted in a very accurate and quantitative linear regression model of the experimental \$ln(t_R)\$ of these inhibitors as a function of the calculated maximum free energy change of induced ligand extraction. This model can be used to predict the residence times of new potential inhibitors from crystal structures or valid docking poses. Since correct structural characterization of the intermediate enzyme-inhibitor state (EI) and the final state (EI*) of two-step slow-onset inhibition is crucial for rational residence time optimization, the current view of the EI and EI* states of InhA was revisited by means of crystal structure analysis, MD and SMD simulations. Overall, the analyses affirmed that the EI* state is a conformation resembling the 2X23 crystal structure (with slow-onset inhibitor \textbf{PT70}), whereas a twist of residues Ile202 and Val203 with a further opened helix \$\alpha 6\$ corresponds to the EI state. Furthermore, MD simulations emphasized the influence of close contacts to symmetry mates in the SBL region on SBL stability, underlined by the observation that an MD simulation of \textbf{PT155} chain A with chain B' of a symmetry mate in close proximity of the SBL region showed significantly more stable loops, than a simulation of the tetrameric assembly. Closing Part I, SMD simulations were employed which allow the delimitation of slow-onset InhA inhibitors from rapid reversible ligands. \textbf{Prediction of \textit{Mycobacterium tuberculosis} Cell Wall Permeability.} The cell wall of \textit{M. tuberculosis} hampers antimycobacterial drug design due to its unique composition, providing intrinsic antibiotic resistance against lipophilic and hydrophilic compounds. To assess the druggability space of this pathogen, a large-scale data mining endeavor was conducted, based on multivariate statistical analysis of differences in the physico-chemical composition of a normally distributed drug-like chemical space and a database of antimycobacterial--and thus very likely permeable--compounds. The approach resulted in the logistic regression model MycPermCheck, which is able to predict the permeability probability of small organic molecules based on their physico-chemical properties. Evaluation of MycPermCheck suggests a high predictive power. The model was implemented as a freely accessible online service and as a local stand-alone command-line version. Methodologies and findings from both parts of this thesis were combined to conduct a virtual screening for antimycobacterial substances. MycPermCheck was employed to screen the chemical permeability space of \textit{M. tuberculosis} from the entire ZINC12 drug-like database. After subsequent filtering steps regarding ADMET properties, InhA was chosen as an exemplary target. Docking to InhA led to a principal hit compound, which was further optimized. The quality of the interaction of selected derivatives with InhA was subsequently evaluated using MD and SMD simulations in terms of protein and ligand stability, as well as maximum free energy change of induced ligand egress. The results of the presented computational experiments suggest that compounds with an indole-3-acethydrazide scaffold might constitute a novel class of InhA inhibitors, worthwhile of further investigation.},
  subject      = {Computational chemistry},
  language  = {en}
}
@phdthesis{Schuster2016,
  author    = {Schuster, Ann-Christin},
  title     = {Chemical and functional analyses of the plant cuticle as leaf transpiration barrier},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-133475},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2016},
  abstract  = {Cuticles cover all above-ground primary plant organs and are lipoid in nature consisting of a cutin matrix with cuticular waxes embedded within or deposited on its surface. The foremost function of the plant cuticle is the limitation of transpirational water loss into the surrounding atmosphere. Transpiration of water vapour from plants differs between stomatal and cuticular transpiration. Stomatal closure minimises the stomatal water loss and the remaining, much lower water transpiration occurs through the plant cuticle. Temperature influence on the transpiration barrier properties of intact leaves is not yet known, despite the importance of the cuticular transpiration especially under drought and heat conditions. The present study focuses on the temperature-dependent minimum water permeability of whole leaves, in comparison to the temperature effect on the cuticular permeance of isolated, astomatous cuticles (Chapter I - III). The minimum water permeability was determined gravimetrically from leaf drying curves and represents the cuticular water permeability of intact, stomatous leaves under conditions of complete stomatal closure. The temperature effect on the transpiration barrier of the desert plant Rhazya stricta and the Mediterranean sclerophyll Nerium oleander exposed a continuous increase of minimum water permeabilities with an increase in temperature. In contrast to other published studies, no abrupt and steep increase of the water permeability at high temperatures was detected. This steep increase indicates structural changes of the barrier properties of isolated cuticular membranes with a drastic decrease of efficiency. A stabilising impact of the cell wall on the plant cuticle of intact leaves was proposed. This steadying effect was confirmed with different experimental approaches measuring the cuticular water permeability of Prunus laurocerasus intact leaves. Physiological analysis of water transport on isolated, astomatous leaf cuticles indicated a drastic decline of the barrier properties at elevated temperatures for Prunus laurocerasus but not for Nerium oleander. Cuticular components were quantitatively and qualitatively analysed by gas chromatography with a flame ionisation detector and a mass spectrometric detector, respectively. A high accumulation of pentacyclic triterpenoids as cuticular wax components in relation to the cutin monomer coverage was detected for Nerium oleander and for Rhazya stricta leaves, too. Accordingly, reinforcing of the cutin matrix by triterpenoids was proposed to improve the mechanical strength and to reduce the extensibility of plant cuticles. Thus, structural changes of the cuticular barrier properties were potentially suppressed at elevated temperatures. The function of the cuticular wax amount and/or wax composition and its relation with the cuticular water permeability remains to be elucidated. In the second part of this work the cuticular wax quantity and quality as well as its impact on the transpiration barrier properties was analysed in order to deduce a potential relation between chemistry and function of plant cuticles (Chapter IV - V). Chemical analyses of the cuticular wax components of a wide range of plant species, including one tropical (Vanilla planifolia), temperate (Juglans regia, Plantago lanceolata), Mediterranean (Nerium oleander, Olea europaea) and one desert (Rhazya stricta) plant species, were conducted. The cuticular wax compositions of nine characteristic plant species from xeric limestone sites naturally located in Franconia (Southern Germany) were determined for the first time. The corresponding minimum or cuticular water permeabilities of both stomatous and astomatous leaf surfaces were measured to detect a potential relationship between the cuticular wax amount, wax composition and the cuticular barrier properties. It was demonstrated that abundant cuticular wax amounts did not constitute more efficient transpiration barriers. However, 55\% of the cuticular barrier function can be attributed to the very-long-chain aliphatic wax coverages. These new findings provide evidence that the acyclic wax constituents play a pivotal role establishing efficient transpiration barriers. Additionally, these findings strengthen the hypothesis that cyclic components, such as pentacyclic triterpenoids, do not hinder the water diffusion through plant cuticles as effectively as acyclic constituents. For the first time a relationship between the cuticular wax composition and the transpiration barrier properties of a wide range of plant species proved insights into the potential relation between chemistry and function of plant cuticles.},
  subject      = {Kutikula},
  language  = {en}
}
@phdthesis{SchuesslergebHecht2018,
  author    = {Sch{\"u}ßler [geb. Hecht], Nina Kristin Petra},
  title     = {Novel formulation principles for bioavailability enhancement of poorly water-soluble and poorly permeable drugs},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-162766},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Since four decades, high-throughput screenings have been conducted in drug discovery, fuelling the identification of potential new drug candidates. This approach, however, often promotes the detection of compounds with undesired physico-chemical properties like poor aqueous solubility or low membrane permeability. Indeed, dissolution and absorption of a drug are prerequisites for systemic exposure and therapeutic effects. Therefore, innovative strategies to optimize unfavourable performance of new drug candidates are in great demand in order to increase drug concentrations at the site of action whilst simultaneously reducing drug variability. In chapter I of this research work, hydrophobic ion pairing (HIP) is discussed as a promising strategy to improve the bioavailability of BCS class III compounds, which have high aqueous solubility and low permeability. The review points out the limitations of poorly absorbable drugs and details the approach of pairing these APIs with hydrophobic counterions. Apart from the motivation to tailor physico-chemical, biopharmaceutical and toxicological properties of BCS class III compounds, the hydrophobic ion pairing facilitates their formulation into drug delivery systems. Besides advantageous effects, disadvantages of the ion pair formation, such as the decreased aqueous solubility of the ions pair, are critically outlined. Finally, the review covers an overview of non-invasive administration routes permitted after ion pair formation, including oral/enteral, buccal, nasal, ocular and transdermal drug administration. Overall, the HIP approach offers substantial benefits regarding the bioavailability enhancement of BCS class III compounds. Chapter II concerns GHQ168 developed by Holzgrabe et al., a BCS class II compound characterized by low aqueous solubility and high permeability. GHQ168 was developed for the treatment of human African trypanosomiasis (HAT), a tropical disease for which novel active compounds are urgently needed. This lead compound was found to be very active against trypanosoma brucei brucei and trypanosoma brucei rhodesiense in cell culture assays, however, the low aqueous solubility prevented further preclinical development. To target this drawback, two different approaches were selected, including (I) the chemical modification and (II) the spray drying of GHQ168. The newly synthesized set of derivatives as well as the spray dried GHQ168 were subjected to a physico-chemical and microbiological characterization. It turned out that both approaches successfully improved aqueous solubility, however, for the derivatives of GHQ168 at the expense of activity. Furthermore, the pharmacokinetic parameters of GHQ168 and of the most active derivatives, GHQ242 and GHQ243, were evaluated. Elimination half-lives between 1.5 to 3.5 h after intraperitoneal administration and modest to strong serum albumin binding for GHQ243 (45\%) and GHQ168 (80\%) and very high binding (> 99\%) for GHQ242 were detected. The spray dried formulation of GHQ168, as well as GHQ242 and GHQ243 were investigated in two in vivo studies in mice infected with t. b. rhodesiense (STIB900), referred to as (I) stringent model and (II) early-treatment model. In the stringent model (2 applications/day on day 3-6 after infection) the mean survival duration (MSD) of mice treated with spray dried GHQ168 exceeded the MSD of the untreated control group (17 days versus 9 days), a difference that was statistically significant. In contrast, no statistical difference was observed for GHQ242 (14 days) and GHQ243 (12 days). GHQ168 was further assessed in the early-treatment model (2 applications/day on day 1-4 after infection) and again a statistically significant improvement of MSD (32 days (end of observation period) versus 7 days) was observed. Finally, exciting antitrypanosomal efficacy for the spray dried formulation of GHQ168 was demonstrated. NADPH oxidases (NOX) were found to be the main source of endothelial reactive oxygen species (ROS) formation. Chapter III reports on the formulation studies on triazolopyrimidine derivatives from the VAS library, a set of NADPH oxidase inhibitors. These were developed for the treatment of elevated ROS levels, which contribute to the development of cardiovascular diseases. Although in vitro results from numerous studies indicated promising efficacy and selectivity for the VAS-compounds, the low water solubility impeded the in vivo translation and further preclinical development. For this reason, three derivatives, VAS2870, VAS3947, and VAS4024 were physico-chemically characterized and VAS3947, the most soluble compound, was selected for further formulation studies. These approaches included (I) spray drying, (II) microemulsification and (III) complexation with cyclodextrins in order to develop formulations for oral and parenteral application. Solubility improvement of VAS3947 was successfully demonstrated for all preparations as expressed by supersaturation ratios in comparison to the solubility of the unformulated compound. For seven spray dried formulations, the ratio ranged from 3-9, and the ratio for four microemulsions was 8-19 after 120 min, respectively. The six cyclodextrin formulations achieved the highest supersaturation ratio between 3 and 174 after 20 hours. NMR measurements elucidated the inclusion of VAS3947 within the CD's cavity as well as the interaction with its outer surface. Ultimately, NOX inhibitors were opened for oral and parenteral administration for the first time. After successful solubility improvement of VAS3947, further investigations towards in vivo studies were conducted including stability studies with a focus on stability in solution and in plasma as presented in chapter IV. Furthermore, permeability and cytotoxicity assays were performed for the first time. It turned out that VAS3947 was instable in buffer and when exposed to light. Moreover, the compound showed decomposition in the presence of mouse microsomes and in human plasma. The VAS compounds contain an oxazol moiety linked to the triazolopyrimidine skeleton via a thioether. This structural element is responsible for the efficacy of the compound class, however it is susceptible to hydrolysis and to further degradation reactions. Moreover, VAS3947 harmed membrane integrity in the cell permeability assays and cytotoxicity investigations in HEK-293 and HEP-G2 cells revealed IC50 values in the same concentration range as reported for efficacy assays. Summarized, it was demonstrated that substances from the VAS library were no appropriate model compounds for ROS investigations nor suitable candidates for further preclinical development.},
  subject      = {L{\"o}slichkeit},
  language  = {en}
}
@phdthesis{XavierdeSouza2024,
  author    = {Xavier de Souza, Aline},
  title     = {Ecophysiological adaptations of the cuticular water permeability within the Solanaceae family},
  doi       = {10.25972/OPUS-22539},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-225395},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {The cuticle, a complex lipidic layer synthesized by epidermal cells, covers and protects primary organs of all land plants. Its main function is to avoid plant desiccation by limiting non-stomatal water loss. The cuticular properties vary widely among plant species. So far, most of the cuticle-related studies have focused on a limited number of species, and studies addressing phylogenetically related plant species are rare. Moreover, comparative studies among organs from the same plant species are still scarce. Thus, this study focus on organ-specificities of the cuticle within and between plant species of the Solanaceae family. Twenty-seven plant species of ten genera, including cultivated and non- cultivated species, were investigated to identify potential cuticular similarities. Structural, chemical and functional traits of fully expanded leaves, inflated fruiting calyces, and ripe fruits were analyzed. The surface morphology was investigated by scanning electron microscopy. Leaves were mainly amphistomatic and covered by an epicuticular wax film. The diversity and distribution of trichomes varied among species. Only the leaves of S. grandiflora were glabrous. Plant species of the Leptostemonum subgenus had numerous prickles and non-glandular stellate trichomes. Fruits were stomata-free, except for S. muricatum, and a wax film covered their surface. Last, lenticel- like structures and remaining scars of broken trichomes were found on the surface of some Solanum fruits. Cuticular water permeability was used as indicators of the cuticular transpiration barrier efficiency. The water permeability differed among plant species, organs and fruit types with values ranging up to one hundred-fold. The minimum leaf conductance ranged from 0.35 × 10-5 m s-1 in S. grandiflora to 31.54 × 10-5 m s-1 in S. muricatum. Cuticular permeability of fruits ranged from 0.64 × 10-5 m s-1 in S. dulcamara (fleshy berry) to 34.98 × 10-5 m s-1 in N. tabacum (capsule). Generally, the cuticular water loss of dry fruits was about to 5-fold higher than that of fleshy fruits. Interestingly, comparisons between cultivated and non-cultivated species showed that wild species have the most efficient cuticular transpiration barrier in leaves and fruits. The average permeability of leaves and fruits of wild plant species was up to three-fold lower in comparison to the cultivated ones. Moreover, ripe fruits of P. ixocarpa and P. peruviana showed two-times lower cuticular transpiration when enclosed by the inflated fruiting calyx. The cuticular chemical composition was examined using gas chromatography. Very-long-chain aliphatic compounds primarily composed the cuticular waxes, being mostly dominated by n- alkanes (up to 80\% of the total wax load). Primary alkanols, alkanoic acids, alkyl esters and branched iso- and anteiso-alkanes were also frequently found. Although in minor amounts, sterols, pentacyclic triterpenoids, phenylmethyl esters, coumaric acid esters, and tocopherols were identified in the cuticular waxes. Cuticular wax coverages highly varied in solanaceous (62- fold variation). The cuticular wax load of fruits ranged from 0.55 μg cm-2 (Nicandra physalodes) to 33.99 μg cm-2 (S. pennellii), whereas the wax amount of leaves varied from 0.90 μg cm-2 (N. physalodes) to 28.42 μg cm-2 (S. burchellii). Finally, the wax load of inflated fruiting calyces ranged from 0.56 μg cm-2 in P. peruviana to 2.00 μg cm-2 in N. physalodes. For the first time, a comparative study on the efficiency of the cuticular transpiration barrier in different plant organs of closely related plant species was conducted. Altogether, the cuticular chemical variability found in solanaceous species highlight species-, and organ-specific wax biosynthesis. These chemical variabilities might relate to the waterproofing properties of the plant cuticle, thereby influencing leaf and fruit performances. Additionally, the high cuticular water permeabilities of cultivated plant species suggest a potential existence of a trade-off between fruit organoleptic properties and the efficiency of the cuticular transpiration barrier. Last, the high cuticular water loss of the solanaceous dry fruits might be a physiological adaptation favouring seed dispersion.},
  subject      = {Kutikula},
  language  = {en}
}