Diss. (sammanfattning) Göteborg : Göteborgs universitet, 2010.

Accurate prediction of protein-ligand binding affinity is essential to computational drug discovery. Current approaches are limited by the accuracy of the underlying potential energy model that describes atomic interactions. A more rigorous physical model is critical for evaluating molecular interactions to chemical accuracy. The objective of this thesis research is to develop a polarizable force field with an accurate representation of electrostatic interactions, and apply this model to protein-ligand recognition and to ultimately solve practical problems in computer aided drug discovery. By calculating the hydration free energies of a series of organic small molecules, an optimal protocol is established to develop the electrostatic parameters from quantum mechanics calculations. Next, the systematical development and parameterization procedure of AMOEBA protein force field is presented. The derived force field has gone through extensive validations in both gas phase and condensed phase. The last part of the thesis involves the application of AMOEBA to study protein-ligand interactions. The binding free energies of benzamidine analogs to trypsin using molecular dynamics alchemical perturbation are calculated with encouraging accuracy. AMOEBA is also used to study the thermodynamic effect of constraining and hydrophobicity on binding energetics between phosphotyrosine(pY)-containing tripeptides and the SH2 domain of growth receptor binding protein 2 (Grb2). The underlying mechanism of an "entropic paradox" associated with ligand preorganization is explored. / text

Advances in genome and proteome research have led to a dramatic increase in the number of macromolecular targets of interest to the life sciences. A solution-phase method to simultaneously reveal all ligand-target binding pairs from a single solution containing libraries of ligands and targets could significantly increase the efficiency and effectiveness of target-oriented screening efforts. Here, we describe interaction-dependent PCR (IDPCR), a solution-phase method to identify binding partners from combined libraries of small-molecule ligands and targets in a single experiment. Binding between DNA-linked targets and DNA-linked ligands induces formation of an extendable duplex. Extension links codes identifying the ligand and target into one selectively amplifiable DNA molecule. In a model selection, IDPCR resulted in the enrichment of DNA encoding all five known protein-ligand pairs out of 67,599 possible sequences.

The research described in this dissertation is focused on the knowledge-based, often in silico assisted design, targeted synthesis, and biological evaluation of small molecules of interest for two translational medicinal chemistry projects. The first project (Part 1) is aimed at the identification of blood brain barrier (BBB) penetrable dual specificity tyrosine phosphorylation regulated kinase-1A (DYRK1A) inhibitors as a potential disease modifying approach to mitigate cognitive deficits associated with Alzheimer's neurodegeneration. Two major series with potent activity against DYRK1A were identified in addition to a number of other chemotype sub-series that also exhibit somewhat promising activity. Extensive profiling of active analogs revealed interesting biological activity and selectivity, which led to the identification of two analogs for in vivo studies and revealed new opportunities for further investigation into other kinase targets implicated in neurodegeneration and polypharmacological approaches. The second project (Part 2) is focused on the development of compounds that inhibit PGE₂ production, while not affecting cyclooxygenase (COX) activity, as a novel approach to treat cancer. Compounds were designed with the intention of inhibiting microsomal prostaglandin E₂ synthase-1 (mPGES-1); however, biological evaluation revealed phenotypically active compounds in a cell based assay with an unknown mechanism of action. Further profiling revealed promising anticancer activity in xenograft mouse models. In addition, PGE₂ has been implicated in an immune evasion mechanism of F. tularensis, a strain of bacteria that remains an exploitable threat in biowarfare, thus a small number of analogs were evaluated in a cell model of F. tularensis infection stimulated PGE₂ production.

Although some progress has been made in the treatment of cancer over the last sixty years, the majority of chemotherapeutics has fallen short. Because general chemotherapies that target DNA replication have only a limited efficacy and significant non-target side-effects, a new paradigm for cancer drug development has been adopted. Using a molecular targeted approach, new gene and protein targets have been identified and the development of chemotherapies that are specific to these targets has already begun. In this study, compounds that interact with two key cancer targets, the G-quadruplex of the c-Myc promoter and p-glycoprotein, have been investigated. By developing such compounds, improvements in treatment efficacy is anticipated with an aspiration for decreased mortality attributable to cancer.Formation of DNA secondary structures, such as the G-quadruplex, in the NHE III1 region of the c-Myc promoter has been shown to repress c-Myc transcription. Because c-Myc is an oncogene that is overexpressed in a variety of cancers, stabilization of the G-quadruplex by small molecules would be advantageous in cancer treatment. Using Fluorescence Resonance Energy Transfer, with Taq Polymerase Stop assays for confirmation, a group of compounds were identified that stabilize the c-Myc G-quadruplex structure. Using a colon cancer model, two compounds were shown to decrease c-Myc gene and protein expression. Also, exposure to the compounds for 48 hours results in an induction of caspase-3, indicative of apoptosis. Furthermore, surface plasmon resonance suggests that compound-induced stabilization of the c-Myc G-quadruplex can prevent sustained binding of the regulatory protein NM23-H2 by increasing its dissociation from the G-quadruplex. This may subsequently prevent unraveling of the G-quadruplex.Because resistance to chemotherapy reduces its effectiveness, development of multidrug resistance (MDR) modulators was also studied. Psorospermin is a topoisomerase II-directed DNA alkylating agent active against MDR cell lines. In a study examining the mechanism of psorospermin's P-glycoprotein modulation, Flow Cytometry demonstrated that doxorubicin-resistant multiple myeloma cells pre-treated with psorospermin enhanced intracellular retention of doxorubicin. Because neither transcription of mdr1 nor translation of P-glycoprotein was downregulated by psorospermin, resistance reversal is most likely due to a direct interaction between the side chain of psorospermin and P-glycoprotein, inhibiting drug efflux.

Viral proteases are often considered to be attractive drug targets because of their crucial function in the viral replication machinery. In order to increase our knowledge of these important targets and to contribute to the discovery and development of new antiviral drugs, the proteases from hepatitis C virus (HCV) and human cytomegalovirus (HCMV) have been produced and their interactions with inhibitors and fragments have been characterized, using enzyme inhibition and SPR biosensor based interaction assay. The structure activity relationships and the resistance profiles of a series of HCV NS3 protease inhibitors based on either P2 proline or phenylglycine residues were analyzed using wild type genotype 1a and the major resistant variants A156T and D168V. The observed susceptibility to substitutions associated with these resistance variants was concluded to depend on the P2 and the P1 residue, and not only on the P2 residue as previously had been suggested. In order to be able to evaluate how the potency of inhibitors is affected by genetic variation, their effect was evaluated on wild type NS3 from genotype 1a, 1b and 3a as well as on the resistant variant R155K from genotype 1a. To enable a comparison of the inhibitory effect on the enzyme variants, the compounds were analyzed under conditions optimized for each variant. VX-950 was found to be the least susceptible compound to resistance and genetic variation. A more detailed analysis showed that the kinetic and mechanistic features of the inhibitors were significantly different for the different genotypes. The reversible non covalent macrocyclic inhibitor ITMN 191 was revealed to have favorable kinetics for all three genotypes. This is an advantage for the design of broad spectrum drugs. A fragment based procedure for identifying and validating novel scaffolds for inhibitors of HCMV protease was established. It identified fragments that may serve as starting points for the discovery of effective inhibitors against this challenging target.   The procedures developed for the evaluation and identification of novel HCV NS3 and HCMV protease inhibitors have contributed to a deeper understanding of protease-inhibitor interactions that is expected to have an impact on the design of novel antiviral drugs.

<p>Dengue viruses (DENV) are mosquito&#8208;borne flaviviruses that pose a continued and growing threat to global health. There are estimated to be 390 million DENV infections each year, and because there is no vaccine or approved therapeutic treatment, developing a small&#8208;molecule treatment is imperative. Possible small&#8208;molecule drug therapies for DENV could be immune system modulators, inhibitors of DENV&#8208;required host factor, or inhibitors of a viral gene product. In this study, we chose to take the latter approach and focused our drug discovery efforts on the most highly conserved flaviviral protein, non&#8208;structural protein 5 (NS5). NS5 contains two major domains, each with different enzymatic activities. The N&#8208;terminus has methyltransferase activity, and the C terminus, an RNA&#8208;dependent RNA polymerase (RdRp). The activities of both domains are purine&#8208;dependent, and therefore both domains contribute to the purine&#8208;binding properties of NS5. Inhibition of either of these domains in NS5 results in inadequate propagation of DENV, and the purine&#8208;binding domains present ideal drug targets for disrupting these activities. These factors make NS5 protein an ideal candidate target for our small&#8208;molecule library screen.</p><p>A high&#8208;throughput fluorescence&#8208;based screen was employed to identify anti&#8208;DENV compounds based on their ability to competitively bind NS5. The screen was performed by binding green fluorescent protein NS5 fusion protein (GFP&#8208;NS5) to immobilized ATP resin, and then performing parallel elutions using over 3,000 distinct compounds. One compound in particular, HS&#8208;205020, was able to competitively elute GFP&#8208;NS5 from the ATP resin and also exhibited antiviral activity in both the U937+DCSIGN human monocyte cell line and BHK&#8208;21 cells. Additionally, HS&#8208;205020 was able to inhibit DENV NS5 RNA polymerase activity in vitro. HS&#8208;205020 is chemically distinct from the majority of previously reported NS5 inhibitors, which are nucleoside analogs that can cause severe toxicity in animal studies. In contrast, over the concentration range that produced anti&#8208;DENV effects, HS&#8208;205020 showed comparable viabilities to ribavirin, an FDA approved hepatitis C virus (HCV) therapeutic. These findings support HS&#8208;205020 as a potential dengue antiviral candidate, and its chemical scaffold represents as an ideal starting compound for future structure&#8208;activity relationship studies.</p> / Dissertation

Drug discovery is a complicated and expensive process in the billion dollar range. One way of making the drug development process more efficient is better information handling, modelling and visualisation. The majority of todays drugs are small molecules, which interact with drug targets to cause an effect. Since the 1980s large amounts of compounds have been systematically tested by robots in so called high-throughput screening. Ligand-based drug discovery is based on modelling drug molecules. In the field known as Quantitative Structure–Activity Relationship (QSAR) molecules are described by molecular descriptors which are used for building mathematical models. Based on these models molecular properties can be predicted and using the molecular descriptors molecules can be compared for, e.g., similarity. Bioclipse is a workbench for the life sciences which provides ligand-based tools through a point and click interface.  The aims of this thesis were to research, and develop new or improved ligand-based methods and open source software, and to work towards making these tools available for users through the Bioclipse workbench. To this end, a series of molecular signature studies was done and various Bioclipse plugins were developed. An introduction to the field is provided in the thesis summary which is followed by five research papers. Paper I describes the Bioclipse 2 software and the Bioclipse scripting language. In Paper II the laboratory information system Brunn for supporting work with dose-response studies on microtiter plates is described. In Paper III the creation of a molecular fingerprint based on the molecular signature descriptor is presented and the new fingerprints are evaluated for target prediction and found to perform on par with industrial standard commercial molecular fingerprints. In Paper IV the effect of different parameter choices when using the signature fingerprint together with support vector machines (SVM) using the radial basis function (RBF) kernel is explored and reasonable default values are found. In Paper V the performance of SVM based QSAR using large datasets with the molecular signature descriptor is studied, and a QSAR model based on 1.2 million substances is created and made available from the Bioclipse workbench.

Dopamine D3 receptors (DRD3) are implicated in relapse to drugs. The current study investigated the role of DRD3 in cue-induced reinstatement of nicotine-seeking in rats. Rats were trained to lever-press for intravenous infusions of nicotine, associated with the illumination of a cue-light, under a fixed-ratio schedule of reinforcement. Following extinction of the behaviour, where lever pressing had no consequences, reinstatement testing was performed by reintroduction of the cues after systemic or local administration (into discrete brain areas) of the DRD3 selective antagonist SB277011-A. Systemic antagonism of DRD3 significantly attenuated cue-induced reinstatement of nicotine-seeking. The same effect was observed upon infusions of SB277011-A into the basolateral amygdala or the lateral habenula, but not the nucleus accumbens. The current findings implicate DRD3 in cue-induced reinstatement of nicotine, delineate some of the neural substrates underlying this role and support a potential for using selective DRD3 antagonists for the prevention of relapse to smoking.

Dopamine D3 receptors (DRD3) are implicated in relapse to drugs. The current study investigated the role of DRD3 in cue-induced reinstatement of nicotine-seeking in rats. Rats were trained to lever-press for intravenous infusions of nicotine, associated with the illumination of a cue-light, under a fixed-ratio schedule of reinforcement. Following extinction of the behaviour, where lever pressing had no consequences, reinstatement testing was performed by reintroduction of the cues after systemic or local administration (into discrete brain areas) of the DRD3 selective antagonist SB277011-A. Systemic antagonism of DRD3 significantly attenuated cue-induced reinstatement of nicotine-seeking. The same effect was observed upon infusions of SB277011-A into the basolateral amygdala or the lateral habenula, but not the nucleus accumbens. The current findings implicate DRD3 in cue-induced reinstatement of nicotine, delineate some of the neural substrates underlying this role and support a potential for using selective DRD3 antagonists for the prevention of relapse to smoking.