The molecular modelling of calixarene inclusion complexes

Chapter 1: This consists of a literature review and an introduction into the variety of computational techniques and methodologies available. Chapter 2: The molecular modelling of alkali metal complexes with calixarenes. We have published three papers in this area1. The HyperChem molecular modelling software package has been demonstrated to be a straightforward and computationally undemanding technique that is surprisingly good at reproducing the structures of a range of metallocalixarenes. Chapter 3: The molecular modelling of the enantioselective complexation of chiral amines by chiral calix[4]arenes. With reference to the enantioselective complexation studies we have shown that by using molecular modelling software, an insight can be gained into the interactions that occur on complexation of chiral amines by chiral calixarenes. By observing the hydrogen bonding patterns formed between the host and guest we can postulate why one enantiomer interacts more strongly than the other and, hence, provide a plausible explanation for the observed enantiomeric selectivity observed in the fluorescence quenching experiments. Chapter 4: The catalysis of the Diels Alder reaction by ionic liquids. The first example of the usage of dialkylimidazolium salts (R2 lm+X‘) as heterogeneous and homogeneous Lewis acids catalysts in the Diels-Alder reaction is detailed in a published paper

Novel Microtubule targetting agents, pyrrolo-1,5,benzoxazepines induce apoptosis in multi-drug-resistant cancer cells

PURPOSE: The development of multi-drug resistance (MDR) due to the expression of members of the ATPase binding cassette (ABC) transporter family is a major obstacle in cancer treatment. The broad range of substrate specificities associated with these transporters leads to the efflux of many anti-cancer drugs from tumour cells. Therefore, the development of new chemotherapeutic agents that are not substrates of these transporters is important. We have recently demonstrated that some members of a novel series of pyrrolo-1,5-benzoxazepine (PBOX) compounds are microtubule-depolymerising agents that potently induce apoptosis in several cancer cell lines and impair growth of mouse breast tumours. The aim of this current study was to establish if PBOXs were capable of inducing apoptosis in cancer cells expressing either P-glycoprotein or breast cancer resistance protein (BCRP), two of the main ABC transporters associated with MDR. METHODS: We performed in vitro studies to assess the effects of PBOXs on cell proliferation, cell cycle and apoptosis in human cancer cell lines and their drug-resistant substrains expressing either P-glycoprotein or BCRP. In addition, we performed a preliminary molecular docking study to examine interactions between PBOXs and P-glycoprotein

DataPype: A Fully Automated Unified Software Platform for Computer-Aided Drug Design

With the advent of computer-aided drug design (CADD), traditional physical testing of thousands of molecules has now been replaced by target-focused drug discovery, where potentially bioactive molecules are predicted by computer software before their physical synthesis. However, despite being a significant breakthrough, CADD still faces various limitations and challenges. The increasing availability of data on small molecules has created a need to streamline the sourcing of data from different databases and automate the processing and cleaning of data into a form that can be used by multiple CADD software applications. Several standalone software packages are available to aid the drug designer, each with its own specific application, requiring specialized knowledge and expertise for optimal use. These applications require their own input and output files, making it a challenge for nonexpert users or multidisciplinary discovery teams. Here, we have developed a new software platform called DataPype, which wraps around these different software packages. It provides a unified automated workflow to search for hit compounds using specialist software. Additionally, multiple virtual screening packages can be used in the one workflow, and if different ways of looking at potential hit compounds all predict the same set of molecules, we have higher confidence that we should make or purchase and test the molecules. Importantly, DataPype can run on computer servers, speeding up the virtual screening for new compounds. Combining access to multiple CADD tools within one interface will enhance the early stage of drug discovery, increase usability, and enable the use of parallel computing

Single point mutations reveal amino acid residues important for Chromobacterium violaceum transaminase activity in the production of unnatural amino acids

Unnatural amino acids (UAAs) are chiral amines with high application potential in drug discovery and synthesis of other valuable chemicals. Biocatalysis offers the possibility to synthesise novel optically pure UAAs with different physical and chemical properties. While the biocatalytic potential of transaminases in the synthesis of UAAs has been demonstrated, there is still a need to improve the activity with non-native substrates and to understand which amino acids residues are important for activity with these UAAs. Using a rational design approach, six variants of Chromobacterium violaceum DSM30191 transaminase (CV_TA) carrying a single and one variant carrying two substitutions were generated. Among the variants with a single substitution, CV_Y168F showed a 2 to 2.6-fold increased affinity for 2-oxooctanoic acid (2-OOA) and 3-oxobutyric acid (3-OBA) methyl ester used to synthesise an ?- and ?-UAA. Analysis of the first half of the transaminase reaction showed no change in the activity with the donor (S)-1-phenylethylamine. The combination of W60C and Y168F substitutions improved the CV_TA affinity for 2-OOA 10-fold compared to the wild type. Other substitutions showed no change, or reduced activity with the tested substrates. Our findings provide structural information on CV_TA and demonstrate the potential of rational design for biosynthesis of UAA

Identification of Plasmepsin Inhibitors as Selective Antimalarial Agents using Ligand Based Drug Design

We describe the application of Ligand Based Virtual Screening technologies towards the discovery of novel Plasmepsin (PM) inhibitors, a family of malarial parasitic aspartyl proteases. Pharmacophore queries were used to screen vendor libraries in search of active and selective compounds. The virtual hits were biologically assessed for activity and selectivity using whole cell Plasmodium falciparum parasites and on target in PM II, PM IV and the closely related human homologue, Cathepsin D assays. Here we report the virtual screening highlights, structures of the hits and their demonstrated biological activity

Rational ligand-Based Virtual Screening and Structure-Activity Relationship Studies in the Ligand-Binding Domain of the Glucocorticoid Receptor-α.

The interest in developing synthetic glucocorticoids (GCs) arises from the utility of endogenous steroids as potent anti-inflammatory and immunosuppressant agents. The first GCs to be discovered, such as cortisol or dexamethasone, still represent the main treatment for conditions of the inflammatory process, despite the fact that they carry a significant risk of side effects. Hence, there is a continuing need to find drugs that preserve the immune effects of GCs without the side effects, such as those on metabolism (diabetes), bone tissue (osteoporosis), muscles (myopathy), eyes and skin. In this review, we focus on the recent use of ligand-based computational approaches in glucocorticoid receptor (GR) drug design efforts towards the determination of novel G R ligands. We examine a number of ligand­ based (similarity searches, pharmacophore screens, quantitative structure-activity relationships) approaches that have been implemented in recent years. A recent virtual high throughput screening similarity search was successful in developing a novel series of nonsteroidal GR antagonists. Additionally, there has been considerable success in ligand-based structure-analysis relationship generation and lead optimization studies for the GR. Future trends towards integrated GR ligand design incorporating ligand- and structure-based methodologies are inevitable

Integrated virtual screening for the identification of novel and selective peroxisome proliferator-activated receptor (PPAR) scaffolds

We describe a fully customizable and integrated target-specific “tiered” virtual screening approach tailored to identifying and characterizing novel peroxisome proliferator activated receptor γ (PPARγ) scaffolds. Built on structure- and ligand-based computational techniques, a consensus protocol was developed for use in the virtual screening of chemical databases, focused toward retrieval of novel bioactive chemical scaffolds for PPARγ. Consequent from application, three novel PPAR scaffolds displaying distinct chemotypes have been identified, namely, 5-(4-(benzyloxy)-3- chlorobenzylidene)dihydro-2-thioxopyrimidine-4,6(1H,5H)-dione (MDG 548), 3-((4-bromophenoxy)methyl)-N-(4-nitro-1H-pyrazol- 1-yl)benzamide (MDG 559), and ethyl 2-[3-hydroxy-5-(5-methyl-2- furyl)-2-oxo-4-(2-thienylcarbonyl)-2,5-dihydro-1H-pyrrol-1-yl]-4- methyl-1,3-thiazole-5-carboxylate (MDG 582). Fluorescence polarization (FP) and time resolved fluorescence resonance energy transfer (TR-FRET) show that these compounds display high affinity competitive binding to the PPARγ-LBD (EC50 of 215 nM to 5.45 μM). Consequent characterization by a TR-FRET activation reporter assay demonstrated agonism of PPARγ by all three compounds (EC50 of 467−594nM). Additionally, differential PPAR isotype specificity was demonstrated through assay against PPARα and PPARδ subtypes. This work showcases the ability of target specific “tiered screen” protocols to successfully identify novel scaffolds of individual receptor subtypes with greater efficacy than isolated screening methods.

Rational structure-based drug design and optimization in the ligand-binding domain of the glucocorticoid receptor-α

Conclusion : By the end of 2008, there had been limited achievements utilizing docking studies and no published successes in the area of virtual high-throughput screening. However, the availability of novel crystal structures and the use of induced-fit docking protocols are improving docking success rates and promising to aid the future delivery of nonsteroidal ligands.