Studies on rationally designed, allosteric, coagulation inhibitors

Heparin is a natural allosteric modulator, with numerous structural and conformational variations leading to many reports of bleeding complications and variations in anticoagulant effects. A flurry of research has been directed towards understanding this puzzle. This work entails the utilization of three unique strategies to further our understanding of this complex issue. Traditional synthetic, biosynthetic and biophysical approaches have failed to conquer the GAG-protein complexity. Computational analysis however could serve as a powerful approach to decipher this dilemma. A dual filter algorithm was incorporated to identify unique hexasaccharide sequences for HCII and AT. Our experimental studies exhibit a good correlation with our computational findings in addition, to the discovery of the first reported heparin based hexasaccharide sequence (HX1) as a potent activator of HCII and AT. In contrast to the enormity of GAG sequences, there appears to be a pattern where rare sequences have been identified to modulate characteristic functions in proteins. Our search led us to a biosynthetically rare GAG residue 2-O-sulfated glucuronic acid (GlcAp2S). Our computational studies indicated elements of selective recognition with coagulation enzymes propelling us towards synthesizing a polymer, HS2S2S enriched in GlcAp2S and GlcNp2S saccharides. Our biological studies indicate its potential in activating AT and HCII in addition to a previously unobserved inhibition of thrombin but not FXa, which is corroborated by our computational studies. These studies therefore showcase the importance of studying rare sequences to further our understanding of differential recognition of proteins of the coagulation cascade. An alternate anticoagulant strategy involves utilization of upstream enzymes like FXIa. Consequently, we devised a rational strategy, which targets the differential hydrophobic domain near the heparin binding sites of proteins through the design of molecules termed as sulfated allosteric modulators. Our endeavor led to the discovery of a library of quinazolin4-(3H)ones) dimers as selective inhibitors of FXIa. We recognized the linker length and geometry to be an important element affecting potency and selectivity. We therefore synthesized a library of 18 dimers using simple reaction schemes. Our inhibition studies do highlight a 9-fold improvement in potency

The Origin and Early Evolution of Life

What is life? How, where, and when did life arise? These questions have remained most fascinating over the last hundred years. Systems chemistry is the way to go to better understand this problem and to try and answer the unsolved question regarding the origin of Life. Self-organization, thanks to the role of lipid boundaries, made possible the rise of protocells. The role of these boundaries is to separate and co-locate micro-environments, and make them spatially distinct; to protect and keep them at defined concentrations; and to enable a multitude of often competing and interfering biochemical reactions to occur simultaneously. The aim of this Special Issue is to summarize the latest discoveries in the field of the prebiotic chemistry of biomolecules, self-organization, protocells and the origin of life. In recent years, thousands of excellent reviews and articles have appeared in the literature and some breakthroughs have already been achieved. However, a great deal of work remains to be carried out. Beyond the borders of the traditional domains of scientific activity, the multidisciplinary character of the present Special Issue leaves space for anyone to creatively contribute to any aspect of these and related relevant topics. We hope that the presented works will be stimulating for a new generation of scientists that are taking their first steps in this fascinating field

Glycosylated nanomaterials : neutralisation and detection of bacteria and toxins

The identification and treatment of bacterial infections remains a major healthcare challenge, especially to ensure appropriate application of a limited spectrum of antibiotics. Therefore the development of alternatives to antibiotics and new analytical tools to probe pathogenic infection processes and as point-of-care biosensors is crucial to combat the spread of infectious diseases. Glycopolymers offer many opportunities for interfacing synthetic materials with biological systems. However, the nature of the interactions between glycopolymers and their biological targets, lectins, and the structural features necessary to obtain high-affinity materials are not fully understood. The application of synthetic glycopolymers to anti-adhesive therapies has so far been limited by their lack of lectin specificity. Herein a number of tandem post-polymerisation modification methods are utilised to probe the multivalent inhibition of a bacterial toxin as a function of linker length, carbohydrate density, and glycopolymer chain length. Guided by structural-biology information, the binding-pocket depth of the toxin was probed and used as a means to specifically improve inhibition of the toxin by the glycopolymer. Glycosylated gold nanoparticles that change colour due to lectin-mediated aggregation may find use as biosensors to aid in the detection of infectious diseases and biological warfare agents such as ricin. Here, carbohydrate-functionalised, gold nanoparticles have been used to discriminate between lectins and bacterial phenotypes. Optimisation of the particle coating is required to ensure stability in complex media, but still allow for rapid detection readouts

Bacterial carbohydrates trigger Candida albicans virulence

Grimes, Catherine LeimkuhlerThe human body is home to a diverse ecosystem containing trillions of microorganisms collectively referred to as the microbiome. Interactions between bacterial and fungal species have been correlated to the progression of cancer and Crohn’s disease. Despite the implications for human health, there is a lack of molecular understanding of how fungi recognize and respond to bacteria. It has been demonstrated that normally benign Candida albicans turns pathogenic when exposed to fragments of the bacterial cell wall. However, the molecular mechanism of this interaction is not well characterized. The work descried in this dissertation improves the molecular understanding of how Candida albicans is capable of recognizing molecules of bacterial origin and demonstrates for the first time that the Cyr1 can bind diverse bacterial carbohydrates to initiate hyphae growth. Importantly, the work described is the first to determine the strength of the interaction between Cyr1 and the peptidoglycan fragment, MTP, and the first report of Cyr1 binding the anthracycline, doxorubicin, and its carbohydrate moiety, daunosamine. ☐ In the larger biological landscape; this dissertation adds another level of molecular understanding used by the LRR domain. Purification of the LRR domain of Cyr1 allowed the successful development of a surface plasmon resonance assay to characterize the binding of bacterial derived carbohydrates. The mid-nanomolar binding affinities for MTP and daunosamine offer unique examples of strong protein-monosaccharide interactions. By comparing these molecular details, insight can be gained into how one domain can respond to a variety of ligands. Overall, this dissertation provides new tools to study the LRR domain and molecular level insight for carbohydrate – protein interactionsUniversity of Delaware, Department of Chemistry and BiochemistryPh.D