Energy-entropy prediction of octanol–water logP of SAMPL7 N-acyl sulfonamide bioisosters

From Springer Nature via Jisc Publications RouterHistory: received 2021-03-04, accepted 2021-06-17, registration 2021-06-18, pub-print 2021-07, pub-electronic 2021-07-10, online 2021-07-10Publication status: PublishedFunder: Engineering and Physical Sciences Research Council; doi: http://dx.doi.org/10.13039/501100000266; Grant(s): EP/L015218/1, EP/N025105/1Abstract: Partition coefficients quantify a molecule’s distribution between two immiscible liquid phases. While there are many methods to compute them, there is not yet a method based on the free energy of each system in terms of energy and entropy, where entropy depends on the probability distribution of all quantum states of the system. Here we test a method in this class called Energy Entropy Multiscale Cell Correlation (EE-MCC) for the calculation of octanol–water logP values for 22 N-acyl sulfonamides in the SAMPL7 Physical Properties Challenge (Statistical Assessment of the Modelling of Proteins and Ligands). EE-MCC logP values have a mean error of 1.8 logP units versus experiment and a standard error of the mean of 1.0 logP units for three separate calculations. These errors are primarily due to getting sufficiently converged energies to give accurate differences of large numbers, particularly for the large-molecule solvent octanol. However, this is also an issue for entropy, and approximations in the force field and MCC theory also contribute to the error. Unique to MCC is that it explains the entropy contributions over all the degrees of freedom of all molecules in the system. A gain in orientational entropy of water is the main favourable entropic contribution, supported by small gains in solute vibrational and orientational entropy but offset by unfavourable changes in the orientational entropy of octanol, the vibrational entropy of both solvents, and the positional and conformational entropy of the solute

Oral bioavailability of carbohydrate mimetics : an "in vitro" and "in vivo" evaluation

Carbohydrates play a crucial role in metabolism, cell recognition, cell differentiation, and adhesion processes. Therefore, these molecules represent a potent source for the development of new treatments against many different diseases with an unmet medical need. However, compounds of this class have major inherent drawbacks related to their chemical structure. Carbohydrates are complex and hydrophilic structures with a large polar surface area, which commonly results in poor pharmacokinetic (PK) properties including low oral bioavailability and short plasma half-life due to fast renal clearance. To overcome the poor PK properties of the natural ligands, specific structural modifications have to be implemented in the drug development process from the beginning. Improvements of newly synthesized compounds have to be constantly monitored with in vitro and in vivo PK measurements, allowing a direct feedback for further structural modifications. To this purpose, a PADMET platform (Physicochemical properties, Absorption, Distribution, Metabolism, Elimination, Toxicity) of in vitro assays, addressing different aspects that influence the PK properties of a molecule was developed and optimized. The intestinal absorption is a major hurdle to achieve sufficient oral bioavailability of carbohydrate mimetics and therefore,the focus of this work is set on the permeability of carbohydrate mimetic by passive permeation or active transport. In this thesis, three different targets for the development of potent lead structures starting from natural carbohydrates are discussed: • E-selectin is a lectin expressed on endothelial cells upon an inflammatory stimulus and is crucial for the recruitment of leukocytes to the side of inflammation. Therefore, E- selectin has been recognized as a potent target for the treatment of various diseases with an inflammatory component. The carbohydrate epitope recognized by E-selectin is the tetrasaccharide sialyl Lewisx (sLex). For the treatment of chronic inflammatory diseases, an oral administration is of interest. However, the development of an orally bioavailable E-selectin antagonist from sLex is challenging due to its chemical properties. To overcome the hurdle of insufficient intestinal absorption, an ester prodrug strategy and a bioisosteric replacement were followed and further evaluated by in vivo PK studies in mice. The ester prodrug approach resulted in insufficient oral bioavailability but improvement of the apparent plasma half-life, whereas the bioisosteric approach lead to the first orally bioavailable E-selectin antagonist. • Uropathogenic Eschericha coli (UPEC) are the main cause of urinary tract infections(UTI). UPEC are expressing the virulence factor FimH on the distal tip of type 1 fimbriae, which binds to mannosides on the luminal surface of the bladder to prevent bacteria from being washed out by urine flow. FimH is therefore a promising target for an antiadhesive treatment of UTIs in order to replace current antibiotic treatment strategies. In this work, known biphenyl-α-D-manno-pyranosides were further developed in terms of affinity and in vitro PK properties. • Sialic acids bound or in free circulation are regulated by sialyltransferases and neuraminidases (NEU). Selective inhibitors for the human neuraminidase NEU3 is of interest to study the physiological and pathophysiological role of neuraminidases and further evaluate the potential to develop therapeutics. Here, the development of specific NEU3 inhibitors, as well as the attempt to optimize their PK properties is reported

Development of glycosylation based cancer therapies using metabolic oligosaccharide engineering

Abnormal glycosylation is a universal feature of cancer; however, in the past these changes have been viewed as passive by products of abnormal metabolism with efforts largely being directed at using these characteristic abnormalities as biomarkers for cancer detection. More recently glycosylation has been shown to play a number of crucial roles in the activity and localization of proteins and in the overall behavior of cells. While cancer related glycosylation abnormalities may have a metabolic origin, they likely play a much larger role in the maturation of the disease phenotype and in its eventual progression. In order to study changes in glycosylation, alterations in the glycan patterns need to be made this can either be done by genetic manipulation of the glycosylation machinery or by altering fluxes through the pathway via metabolic oligosaccharide engineering. One of the major advantages of using a flux based approach is that it can make use of pharmacologically relevant small molecules that are easier to use than genetic means. However a significant roadblock to use to metabolic oligosaccharide engineering is the low uptake efficiency of sugar molecules, this is overcome by the use of short chain acid (SCFA) linked sugar molecules. The addition of these SCFA groups converts these molecules into a unique form of prodrug in that they need to resist esterase processing outside the cell and require intracellular esterase processing to release the core sugar. The first part of this thesis characterizes the esterase processing of these sugar analog prodrugs. The analogs were found to be fairly resistant to extracellular inactivation surviving for between 2 and 4 h in 100% fetal bovine serum. In comparison intracellular processing was shown to be much faster, interestingly there appeared to be an activation of the intracellular esterases by analog treatments. Investigation of this iii crosstalk revealed that increased sialylation of carboxyl esterases led to a stabilization of more active trimeric and hexameric forms of this enzyme. The next portion of the study used metabolic oligosaccharide engineering as a tool to alter glycosylation and the epidermal growth factor receptor’s sialylation is observed to increase. The effect of increased sialylation on the epidermal growth factor receptor (EGFR) is investigated and shown to lead to an inhibition of EGFR signaling. This understanding of the functional significance of altered glycosylation is then translated towards clinical end points with 1,3,4-O-Bu3ManNAc shown to have remarkable synergy when used in conjunction with EGFR targeting drugs Erlotinib and Gefitinib. Finally, the underlying molecular mechanism by which this analog induced change in glycosylation affects receptor signaling is characterized. Increased sialylation caused by analog treatment was found to disrupt the galectin lattice which led to an increase in non clathrin mediated endocytosis wherein the resulting endosomes are fated primarily for degradation, this leads to a decrease in EGFR surface localization and increased signal attenuation