Discovery and Characterization of Clinical Candidate LXE408 as a Kinetoplastid-Selective Proteasome Inhibitor for the Treatment of Leishmaniases

Visceral leishmaniasis is responsible for up to 30,000 deaths every year. Current treatments have shortcomings that include toxicity and variable efficacy across endemic regions. Previously, we reported the discovery of GNF6702, a selective inhibitor of the kinetoplastid proteasome, which cleared parasites in murine models of leishmaniasis, Chagas disease, and human African trypanosomiasis. Here, we describe the discovery and characterization of LXE408, a structurally related kinetoplastid-selective proteasome inhibitor currently in Phase 1 human clinical trials. Furthermore, we present high-resolution cryo-EM structures of the Leishmania tarentolae proteasome in complex with LXE408, which provides a compelling explanation for the noncompetitive mode of binding of this novel class of inhibitors of the kinetoplastid proteasome.

Optimization of Platelet-Derived Growth Factor Receptor (PDGFR) Inhibitors for Duration of Action, as an Inhaled Therapy for Lung Remodeling in Pulmonary Arterial Hypertension

A series of potent PDGFR inhibitors has been identified. The series was optimized for duration of action in the lung. A novel kinase occupancy assay was used to directly measure target occupancy after i.t. dosing. Compound 25 shows 24 h occupancy of the PDGFR kinase domain, after a single i.t. dose and has efficacy at 0.03 mg/kg, in the rat moncrotaline model of pulmonary arterial hypertension. Examination of PK/PD data from the optimization effort has revealed in vitro:in vivo correlations which link duration of action in vivo with low permeability and high basicity and demonstrate that nonspecific binding to lung tissue increases with lipophilicity.

Utilizing Chemical Genomics to Identify Cytochrome b as a Novel Drug Target for Chagas Disease

Unbiased phenotypic screens enable identification of small molecules that inhibit pathogen growth by unanticipated mechanisms. These small molecules can be used as starting points for drug discovery programs that target such mechanisms. A major challenge of the approach is the identification of the cellular targets. Here we report GNF7686, a small molecule inhibitor of Trypanosoma cruzi, the causative agent of Chagas disease, and identification of cytochrome b as its target. Following discovery of GNF7686 in a parasite growth inhibition high throughput screen, we were able to evolve a GNF7686-resistant culture of T. cruzi epimastigotes. Clones from this culture bore a mutation coding for a substitution of leucine by phenylalanine at amino acid position 197 in cytochrome b. Cytochrome b is a component of complex III (cytochrome bc₁) in the mitochondrial electron transport chain and catalyzes the transfer of electrons from ubiquinol to cytochrome c by a mechanism that utilizes two distinct catalytic sites, Q_N and Q_P. The L197F mutation is located in the Q_N site and confers resistance to GNF7686 in both parasite cell growth and biochemical cytochrome b assays. Additionally, the mutant cytochrome b confers resistance to antimycin A, another Q_N site inhibitor, but not to strobilurin or myxothiazol, which target the Q_P site. GNF7686 represents a promising starting point for Chagas disease drug discovery as it potently inhibits growth of intracellular T. cruzi amastigotes with a half maximal effective concentration (EC₅₀) of 0.15 µM, and is highly specific for T. cruzi cytochrome b. No effect on the mammalian respiratory chain or mammalian cell proliferation was observed with up to 25 µM of GNF7686. Our approach, which combines T. cruzi chemical genetics with biochemical target validation, can be broadly applied to the discovery of additional novel drug targets and drug leads for Chagas disease.

Chagas Disease, or American trypanosomiasis, is caused by the kinetoplastid protozoan Trypanosoma cruzi and is primarily transmitted to a mammalian host via a triatomine insect vector (the “kissing bug”) infected with T. cruzi parasites. Although discovered in 1909 by the physician Dr. Carlos Chagas, the disease gained recognition by the public health community only following a major outbreak in Brazil during the 1960s. Approximately eight million people (primarily in Central and South America) are infected with T. cruzi and cases are becoming more widespread due to migration out of the endemic regions. Current treatment options have severe problems with toxicity, limited efficacy, and long administration. Hence, discovery of new drugs for treatment of Chagas disease has become of prime interest to the biomedical research community. In this study, we report identification of a potent inhibitor of T. cruzi growth and use a chemical genetics-based approach to elucidate the associated mechanism of action. We found that this compound, GNF7686, targets cytochrome b, a component of the mitochondrial electron transport chain crucial for ATP generation. Our study provides new insights into the use of phenotypic screening to identify novel targets for kinetoplastid drug discovery.

Lead Identification to Clinical Candidate Selection

Chagas disease affects 8 million people worldwide and remains a main cause of death due to heart failure in Latin America. The number of cases in the United States is now estimated to be 300,000, but there are currently no Food and Drug Administration (FDA)–approved drugs available for patients with Chagas disease. To fill this gap, we have established a public-private partnership between the University of California, San Francisco and the Genomics Institute of the Novartis Research Foundation (GNF) with the goal of delivering clinical candidates to treat Chagas disease. The discovery phase, based on the screening of more than 160,000 compounds from the GNF Academic Collaboration Library, led to the identification of new anti-Chagas scaffolds. Part of the screening campaign used and compared two screening methods, including a colorimetric-based assay using Trypanosoma cruzi expressing β-galactosidase and an image-based, high-content screening (HCS) assay using the CA-I/72 strain of T. cruzi. Comparing molecules tested in both assays, we found that ergosterol biosynthesis inhibitors had greater potency in the colorimetric assay than in the HCS assay. Both assays were used to inform structure-activity relationships for antiparasitic efficacy and pharmacokinetics. A new anti– T. cruzi scaffold derived from xanthine was identified, and we describe its development as lead series.

Electronic versus lattice match for metal-semiconductor epitaxial growth: Pb on Ge(111)

Lattice match is important for epitaxial growth. We show that a competing mechanism, electronic match, can dominate at small film thicknesses for metal-semiconductor systems, where quantum confinement and symmetry requirements may favor a different growth pattern. For Pb(111) on Ge(111), an accidental lattice match leads to a √3 × √3 configuration involving a 30° in-plane rotation at large film thicknesses, but it gives way to an incommensurate (1 × 1) configuration at small film thickness. The transformation follows an approximately inverse-film-thickness dependence with superimposed bilayer oscillations.

Raman scattering and growth disorders in single as-grown TiO2 nanowires

An oxidation procedure has been developed to grow single-crystalline TiO(2) nanowires of the pure rutile phase, allowing subsequent characterizations of SEM, XRD, Raman, and TEM without any post-growth preparations. TEM observations support that the 1D anisotropic growth is dominated by oriented attachment processes, leading to typical growth-induced defects in the nanowires. Spatial variations of the rutile E(g) and A(1g) Raman modes were unambiguously revealed on single nanowires while scanned along the growth direction parallel to the rutile [110]. Symmetry-sensitive deviations were identified by comparing the Raman data with the spatial correlation model calculations based on realistic dispersion relations of the rutile, reflecting morphology-correlated defect distributions along single nanowires. This work provides an efficient, non-destructive in situ characterization approach for guiding growth design in future nanotechnology.

Electronic structures of an epitaxial graphene monolayer on SiC(0001) after gold intercalation: a first-principles study

The atomic and electronic structures of an Au-intercalated graphene monolayer on the SiC(0001) surface were investigated using first-principles calculations. The unique Dirac cone of graphene near the K point reappeared as the monolayer was intercalated by Au atoms. Coherent interfaces were used to study the mismatch and the strain at the boundaries. Our calculations showed that the strain at the graphene/Au and Au/SiC(0001) interfaces also played a key role in the electronic structures. Furthermore, we found that at an Au coverage of 3/8 ML, Au intercalation leads to a strong n-type doping of graphene. At 9/8 ML, it exhibited a weak p-type doping, indicative that graphene was not fully decoupled from the substrate. The shift in the Dirac point resulting from the electronic doping was not only due to the different electronegativities but also due to the strain at the interfaces. Our calculated positions of the Dirac points are consistent with those observed in the ARPES experiment (Gierz et al 2010 Phys. Rev. B 81 235408).

Liver X receptor modulators: a review of recently patented compounds (2007 - 2009)

IMPORTANCE OF THE FIELD

Liver X receptors (LXRs) are ligand activated transcription factors involved in cholesterol metabolism, glucose homeostasis, inflammation and lipogenesis. With the important physiological role of LXRs in reverse cholesterol transport (RCT), atherosclerosis is the best investigated therapeutic indication. While atherosclerosis is not yet clinically validated, Wyeth's LXRalpha/beta agonist LXR-623 indicated the key LXR target genes involved in RCT (ABCA1 and ABCG1) are upregulated in peripheral blood cells in a dose-dependent manner. While discontinued for CNS safety concerns, investigation of LXR-623 supports atherosclerosis as a clinical indication, and the possibility of identifying LXR agonists with profiles that avoid the strong lipogenic effects of full LXRalpha/beta agonists.

AREAS COVERED IN THIS REVIEW

Patents for LXR agonists from late 2006 up to August 2009 with emphasis on chemical matters and relationship to earlier disclosures, the biological data associated with selected analogues and therapeutic indications.

WHAT THE READER WILL GAIN

An overview of the majority of LXR scaffolds with representative structure activity relationships as well as the companies that are the chief players in the field.

TAKE HOME MESSAGE

The future application of LXR agonists depends upon the discovery of LXR agents without lipogenic effects. Limiting activation of LXRalpha is a popular strategy.

Thermostable variants constructed via the structure-guided consensus method also show increased stability in salts solutions and homogeneous aqueous-organic media

Enzyme instability is a major factor preventing widespread adoption of enzymes for catalysis. Stability at high temperatures and in the presence of high salt concentrations and organic solvents would allow enzymes to be employed for transformations of compounds not readily soluble in low temperature or in purely aqueous systems. Furthermore, many redox enzymes require costly cofactors for function and consequently a robust cofactor regeneration system. In this work, we demonstrate how thermostable variants developed via an amino acid sequence-based consensus method also showed improved stability in solutions with high concentrations of kosmotropic and chaotropic salts and water-miscible organic solvents. This is invaluable to protein engineers since deactivation in salt solutions and organic solvents is not well understood, rendering a priori design of enzyme stability in these media difficult. Variants of glucose 1-dehydrogenase (GDH) were studied in solutions of different salts along the Hofmeister series and in the presence of varying amounts of miscible organic solvent. Only the most stable variants showed little deactivation dependence on salt-type and salt concentration. Kinetic stability, expressed by the deactivation rate constant k(d,obs), did not always correlate with thermodynamic stability of variants, as measured by melting temperature T(m). However, a strong correlation (R(2) > 0.95) between temperature stability and organic solvent stability was found when plotting T(50)(60) versus C(50)(60) values. All GDH variants retained stability in homogeneous aqueous-organic solvents with >80% v/v of organic solvent.

Role of the Metal/Semiconductor interface in quantum size effects: Pb /Si(111)

Self-organized islands of uniform heights can form at low temperatures on metal/semiconductor systems as a result of quantum size effects, i.e., the occupation of discrete electron energy levels in the film. We compare the growth mode on two different substrates [Si(111)- (7x7) vs Si(111)- Pb(sqrt[3]xsqrt[3] )] with spot profile analysis low-energy electron diffraction. For the same growth conditions (of coverage and temperature) 7-step islands are the most stable islands on the (7x7) phase, while 5-step (but larger islands) are the most stable islands on the (sqrt[3]xsqrt[3] ). A theoretical calculation suggests that the height selection on the two interfaces can be attributed to the amount of charge transfer at the interface.

Herpes simplex chronic laryngitis and vocal cord lesions in a patient with acquired immunodeficiency syndrome

Chronic laryngitis in patients with acquired immunodeficiency syndrome may be due to infections or tumors, such as Kaposi's sarcoma and non-Hodgkin's lymphoma. We present what we believe to be the first proven case of herpes simplex virus chronic laryngitis in a man positive for human immunodeficiency virus. Direct laryngoscopy showed leukoplakic lesions on both vocal cords. Biopsy of the lesions showed squamous epithelial cells with the characteristic features of herpes simplex virus, which was confirmed by immunohistochemical stains. We discuss the differential diagnosis of chronic laryngitis in a human immunodeficiency virus infection. Herpes simplex viral infection of the vocal cords should be considered in patients with acquired immunodeficiency syndrome presenting with chronic hoarseness and leukoplakic lesions on direct laryngoscopy, especially with no evidence of Kaposi's sarcoma, tumor, or cytomegaloviral or fungal infection elsewhere. Treatment should be acyclovir, except in the face of acyclovir resistance.

Clinical experience with atovaquone: a new drug for treating Pneumocystis carinii pneumonia

Atovaquone is a new hydroxynapthoquinone antiprotozoal agent active against Pneumocystis carinii in vitro and in animal models. The authors report an experience using atovaquone to treat 25 patients with mild to moderate P. carinii pneumonia. Eligible patients were treated for 21 days with 750 mg of atovaquone orally three times daily. Prednisone was added when the P(A-a)O2 gradient was between 35-45 mm Hg. Patients were treated under three treatment protocols. Patients in Group 1 participated in one of two randomized comparative drug trials, designed for patients with and without sulfonamide intolerance. Six of seven patients successfully completed treatment, and one patient discontinued treatment because of an adverse reaction (> 5 times baseline increase in transaminase level). Patients in Group 2 were treated with atovaquone for mild to moderate P. carinii pneumonia under a treatment Investigational New Drug protocol because of prior sulfonamide reactions. Fifteen of these 18 patients successfully completed treatment; one died from other complications during treatment and two discontinued treatment for adverse reactions (> 5 times baseline increase in transaminase levels, and a diffuse rash). Serum transaminase levels returned to normal at the end of treatment in all patients with elevated levels. All patients demonstrated clinical resolution of their pneumonia and improvement of pretreatment hypoxemia (Group 1: pretreatment PaO2 = 82 +/- 14 mm Hg, posttreatment PaO2 = 92 +/- 9 mm Hg). Overall, 21 (84%) of 25 patients successfully finished therapy without significant adverse reactions. Atovaquone appears to be an effective and well-tolerated oral treatment for mild to moderate P. carinii pneumonia.(ABSTRACT TRUNCATED AT 250 WORDS)