Comparative Docking Assessment of Glucokinase Interactions with its Allosteric Activators

Glucokinase (GK) is expressed in multiple organs and plays a key role in hepatic glucose metabolism and pancreatic insulin secretion. GK could indeed serve as pacemaker of glycolysis and could be an attractive target for type 2 diabetes (T2D). The recent preclinical data of first GK activator RO-28-1675 has opened up a new field of GK activation as a powerful tool in T2D therapies. The GK allosteric site is located ~20Å away from glucose binding site. Chemical structure of Glucokinase activators (GKA) includes three chemical arms; all consisting of cyclic moiety and joined in a shape resembling the letter Y. In this study, comparative docking assessment using Autodock4 revealed that the three arms bind to three aromatic/hydrophobic subpockets at the allosteric site. Our dockings have overall consistency with experimental data in both docking modes and simulated binding free energies, and offer insights on understanding GK/GKA interactions and further GKA design. Specifically, for the first pocket, involvement of Arg63 as key residue in two specific hydrogen-bond formations with all allosteric activators defines the binding feature; for the second pocket, it has the most diverse binding interactions, mostly aromatic, hydrophobic and multiple hydrogen bonds. The site has the best potential for further GKA optimization by utilizing aromatic heterocycles and hydrogen bond forming linkers to build the GKA 2nd arm

Exploration of fragment-derived modulators of glycoside hydrolases

Previous work at York demonstrated that fragment molecules can increase the activity of the glycoside hydrolase, BtGH84. The initial aim of this project was to use fragment-based discovery methods to identify activators of several enzymes used in cellulose degradation where low activity is one of the limiting steps in the industrial process. This was successful for one enzyme, the fungal glycoside hydrolase, TrBgl2. The characterisation of the mechanism of activation for this enzyme is the main focus of this thesis. A fragment screen of a library of 560 commercially available fragments using a kinetic assay identified a small molecule activator of TrBgl2. An analogue by catalogue approach and detailed kinetic analysis identified compounds that behaved as nonessential activators with up to a 2-fold increase in maximum activation. The compounds did not activate the related bacterial glycoside hydrolase CcBglA demonstrating specificity. Interestingly, an analogue of the initial fragment inhibits both TrBgl2 and CcBglA, apparently through a mixed-model mechanism. Although it was not possible to determine crystal structures of activator binding to 55 kDa TrBgl2, solution NMR experiments demonstrated a specific binding site for the activator. A partial assignment of the NMR spectrum gave the identity of the amino acids at this site, allowing a model for TrBgl2 activation to be built. The activator binds at the entrance of the substrate binding site, stabilizing the enzyme-substrate complex

A Molecular Modelling Approach for Designing a Novel Semisynthetic Metalloenzyme Based on Thermolysin

Current computational chemistry tools were used to solve the problem of screening for the best conformation of potential protein-ligand-metal complex in designing a novel semisynthetic metalloenzyme. The computational tools used were Computational Atlas Topography of Protein (CASTp), a sophisticated molecular modeling environment InsightII, a conventional drug-docking algorithm Autodock 3.05 and a schematic diagram for protein-ligand interactions for a given PDB file LIGPLOT. Overall 48 protein pockets on the thermolysin structure were measured using CASTp and the four biggest pockets based on their number of residues and surface area were identified to be suitables site for the modification. Ten different sizes and multifunctional groups of chemical ligands were studied for their thermodynamic valuation using the AutoDock 3.05 program. For further modification, phosphoethanolamaine (PSE), phenylalanine (PHE), phenylacetic acid (PAC) and phenanthroline (PHN) were chosen as they possessed the lowest docking energy of -8.49, -8.34, -7.33 and -7.06 kcal/mol, respectively. Non-covalent interactions included hydrogen bonding and hydrophobic interaction between the ligands and the thermolysin were determined using CASTp. The result showed that larger ligands with multifunctional groups such as PSE and PHE showed higher number interactions compared to the smaller ligands. In terms of specific pockets for the modification, different protein-ligand complexes showed different suitable pockets; complex of thermolysin and PSE ligand at pocket 45, complex of thermolysin and PAC ligand at pocket 48 and both complexes of thermolysin with PHE and PHN ligands at pocket 45, respectively. To verify the final metal ion orientation, three procedures were conducted to narrow down the number of possible conformations for the modification. From four tested metal ions (Ca2+, Mg2+, Fe2+ and Zn2+ ), Ca2+ was identified to be the most favorable metal ion for the modification. It had orientated within an allowed geometry in all tested protein ligand complexes. Meanwhile, both Mg2+ and Fe2+ were identified as favorable metal ions in KEI-PSE and KEI-PAC complexes, respectively. Zn2+ however, showed non favorable docking in all tested complexes due to improper parameterized file for zinc ion in AutoDock

Glycolytic Inhibitors as Leads for Drug Discovery in the Pathogenic Free-Living Amoebae

The free-living amoeba, Naegleria fowleri, can cause a rare yet usually lethal infection of the brain called primary amebic meningoencephalitis. Because of poor diagnostics and limited treatment options, the mortality rate associated with the disease is \u3e97%. Due to our finding that glucose is critical for trophozoite growth in culture, we have been interested in exploiting amoebae glucose metabolism to identify new potential drug targets. We have characterized the first enzyme of the glycolytic pathway, glucokinase (Glck), from N. fowleri and two other pathogenic free-living amoeba, Acanthamoeba castellanii and Balamuthia mandrillaris. We have assessed their biochemical properties and tested potential inhibitors on the recombinant Glcks, which revealed that these enzymes are sufficiently different from one another that developing pan-amoeba inhibitors may be challenging. However, their individual differences from the human host enzyme suggests that species-specific Glck inhibitors could be identified. We have also explored targeting the glucose metabolizing enzyme enolase in N. fowleri using a series of phosphonate human enolase 2 (ENO-2) specific inhibitors that were developed to treat human cancer. These compounds are curative for ENO-1 deleted glioblastoma in a rodent model, can cross the blood-brain barrier, and are of limited toxicity to non-human primates. The phosphonate inhibitors were toxic to N. fowleri in vitro with (1-hydroxy-2-oxopiperidin-3-yl) phosphonic acid (HEX) being the most potent, with an EC50 value of 0.21 ± 0.02 µM, almost 1500-fold lower than the concentration required to impact human cells. Unbiased metabolomics indicates that glycolytic intermediates upstream of NfENO accumulate in HEX treated amoebae. In an effort to genetically validate new targets for therapeutic intervention, we have initiated efforts to develop molecular tools for use in N. fowleri. We have designed a vector for transient transfection of the amoebae that harbors portions of the 5’UTR of actin 1 (NF0111190) upstream of both eYFP and a hygromycin resistance gene, termed pJMJM1. We have tested a variety of approaches used in other parasite systems for plasmid delivery including the transfection reagent SuperFect, Amaxa Nucleofector technologies, and various electroporation settings. Transfection of N. fowleri flagellates with 5 µg pJMJM1 by electroporation (100 V, 500 µF, 400 Ω) yielded a population of fluorescent cells seven days after being treated with 300 µg/mL hygromycin, but this expression of eYFP was lost over time. More recently, we have used CRISPR/Cas9- mediated gene editing to successfully introduce an eYFP repair template into a predicted protein locus. While fluorescent cells were not noted in the culture, editing was confirmed by PCR analysis. Development of these molecular techniques will provide an important tool for uncovering potential target genes and allow for a better understanding of amoeba biology

Computational Studies of Liver Receptor Homolog 1 in the Presence of Small Molecule Agonists: Allosteric Communication and Virtual Screening for New Potential Drug Candidates

Liver Receptor Homolog 1 (LRH-1) is a nuclear receptor whose dysfunction is affiliated with diseases such as diabetes and cancer. Recent investigations demonstrate that higher levels of activation and modulation of its activity can be achieved through its interaction with phospholipids (PLs) and synthetic small molecules. We employed molecular dynamics (MD) simulations to understand more about the structural basis of LRH-1’s activity when bound to small molecule agonist RJW100 as well as the RJW100 derivative 65endo. We find that RJW100 and derivative 65endo can trigger allosteric communication in LRH-1 despite the RJW100 scaffold inducing motions that differ from those induced by PLs. We also provide supporting evidence that a key threonine residue and a water network may be important in RJW100’s ability to activate LRH-1. Finally, in a campaign to identify new LRH-1 lead compounds, virtual screening was performed against RJW100, 65endo, and a second RJW100 derivative, 8AC

Biophysical, biochemical and inhibition studies of hexokinases

Hexokinase is the first enzyme in glycolysis, a major pathway for the generation of energy in all eukaryotes. Mammalian cells have four isoforms (I, II, III, IV) that have different tissue distribution and kinetic properties. Among all isoforms, human hexokinase II (hHKII) has been found to be implicated in many cancers with an increased expression which serves a dual role. First, it maintains the high glycolytic rate of malignant cells (Warburg effect) and second it prevents apoptosis when is bound to mitochondria. Trypanosoma brucei is a parasite that causes Human African Trypanosomiasis (HAT) and has two isoforms with extensive sequence similarity (98%), TbHKI (active form) and TbHK2 (inactive form). The bloodstream-form parasites (BSF) depend exclusively on glycolysis for their survival. The enzyme from both organisms is a validated target for drug-discovery against both cancer and HAT. The aim of the present study is the discovery of novel and specific inhibitors of the enzymes based on their structure. Structure-based drug discovery is commonly used in pharmaceutical companies to aid in the discovery of potent lead compounds. In silico studies were performed in this project using the known crystal structure of human hexokinase I and a model of TbHKI generated by the protein modelling tool Phyre2. The docking programs, AutoDock (AD) and AutoDock Vina (Vina), were chosen to perform the docking of ~3 million compounds to the target molecules and scoring functions calculated the predicted binding affinities of each compound. In total, 28 compounds were purchased to test on the target molecules. In the experimental part of the project, the two enzymes were cloned, expressed and purified. hHKII was successfully purified giving a high yield of active and pure protein. The protein was characterised using many biophysical methods to establish the oligomeric state, the homogeneity and the secondary structure. Crystallisation trials failed and for this reason, N and C domains of the hHKII were purified separately. Unfortunately, the domains also failed to crystallise thus SAXS data were collected and analysed to gain information of their shape at low resolution. A novel inhibition assay was developed and used to identify four weak inhibitors against full length hHKII. TbHKI was difficult to express in a soluble form as most of the protein was expressed in inclusion bodies. The purification resulted in a small amount of active protein that was used entirely for biochemical assays. Four compounds were purchased from the docking of the TbHKI model and one was found to inhibit the enzyme over 65% at 100 μΜ. Because the active site of both enzymes (hHKII, TbHKI) is well conserved the compounds from hHKII docking were also screened against the TbHKI. Four compounds were found to inhibit this enzyme while one of them was also an inhibitor for human isoform. The remaining three were specific for inhibition of TbHKI

Understanding Human Erythrocyte Glucose Transporter (GLUT1) Mediated Glucose Transport Phenomena Through Structural Analysis

GLUT1-mediated, facilitated sugar transport is proposed to be an example of transport by a carrier that alternately presents exofacial (e2) and endofacial (e1) substrate binding sites, commonly referred to as the alternating access carrier model. This hypothesis is incompatible with observations of co-existent exo- and endofacial ligand binding sites, transport allostery, and e1 ligand (e.g. cytochalasin B) induced GLUT1 sugar occlusion. The fixed-site carrier model proposes co-existent, interacting e2 and e1 ligand binding sites but involves sugar translocation by geminate exchange through internal cavities. Demonstrations of membrane-resident dimeric and tetrameric GLUT1 and of e2, e1 and occluded GLUT conformations in GLUT crystals of monodisperse, detergent-solubilized proteins suggest a third model. Here, GLUT1 is an alternating access carrier but the transporter complex is a dimer of GLUT1 dimers, in which subunit interactions produce two e2 and two e1 conformers at any instant. The crystallographic structures in different conformations can be utilized to further understand the transport cycle, ligand binding behavior and complex kinetics observed in GLUT1. Specifically, the GLUT1 crystal structure and homology models based upon related major facilitator superfamily proteins were used in this study, to understand inhibitor binding, ligand binding induced GLUT1 transport allostery and the existence of helix packing/oligomerization motifs and glycine induced flexibility. These studies suggest that GLUT1 functions as an oligomeric allosteric carrier where cis-allostery is an intramolecular behavior and trans-allostery is an intermolecular behavior. Additionally, mutations of a dynamic glycine affect the turnover of the transporter while mutations to helix packing motifs affect affinity

Mechanism of action and binding mode revealed by the crystal structures of key enzymes in plants' sugar metalbolic pathway

Ph.DDOCTOR OF PHILOSOPH

Small molecules as inhibitors of PCSK9: current status and future challenges

Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays an important role in regulating lipoprotein metabolism by binding to low-density lipoprotein receptors (LDLRs), leading to their degradation. LDL cholesterol (LDL-C) lowering drugs that operate through the inhibition of PCSK9 are being pursued for the management of hypercholesterolemia and reducing its associated atherosclerotic cardiovascular disease (CVD) risk. Two PCSK9-blocking monoclonal antibodies (mAbs), alirocumab and evolocumab, were approved in 2015. However, the high costs of PCSK9 antibody drugs impede their prior authorization practices and reduce their long-term adherence. Given the potential of small-molecule drugs, the development of small-molecule PCSK9 inhibitors has attracted considerable attention. This article provides an overview of the recent development of small-molecule PCSK9 inhibitors disclosed in the literature and patent applications, and different approaches that have been pursued to modulate the functional activity of PCSK9 using small molecules are described. Challenges and potential strategies in developing small-molecule PCSK9 inhibitors are also discussed