Design, virtual screening and structural studies of new molecules with potential antitumor and antiinflammatory activity

2010 - 2011Computational methodologies in combination with experimental techniques as Nuclear Magnetic Resonance (NMR) have become a crucial component in drug discovery process, from hit identification to lead optimization. The study of ligand-macromolecule interactions, in fact, has a crucial role for the design and the development of new and more powerful drugs. In this project, different aspects of interaction and recognition processes between ligand and macromolecule, and streostructure assignment has been studied through this kind of combined approach with the aim to identify novel potential antitumor and/or antiinflammatory molecules. In particular, because the strong interconnection between the tumoral and inflammatory pathology has led to the identification of new target utilizable for the therapy, in this project will be described proteins (Histone deacetilase, HDAC; Nicotinamide Phosphoribosyltransferase, NMPRTase or Nampt; microsomal prostaglandin E2 synthase, mPGES-1; human synovial Phospholipases A2, hsPLA2; human Farnesoid-X-Receptor, FXR; human Pregnane-X-Receptor, PXR; Bile Acid Receptor GPBAR-1, TGR5) involved in essential cellular processes and acting at diverse levels and phases of the tumor and inflammation diseases. The results obtained can be summarized in three main areas of activity, whose relative weight was varied according to the development of the overall project: a) Support in the design of original scaffolds for the generation of libraries potentially utilizable in therapy. This work was exclusively conducted in silico by a molecular docking technique in order to direct the design of the new molecules basing on the analysis of ligand-target interactions and the synthetic possibilities. This kind of approach was successfully applied leading to the identification of new potential inhibitors for HDAC enzymes with ciclic (mono and bis amides, paragraph 2.2; conformationally locked calixarenes, paragraph 2.4), and linear (hydroxamic tertiary amines, paragraph 2.3) structures, and isoform selective (paragraph 2.6), and of ligands for microsomal prostaglandin E2 synthase (mPGES)-1 (two series of triazole-based compounds; paragraphs 4.2 and 4.3). For each of this described studied, the good qualitative accordance between the calculated and experimental data has made possible the identifications of new lead compounds, rationalizing in this way the key features to the target inhibition. b) Rationalization of the biological activity of compounds by the study of the drug-receptor interactions. Molecular docking was used for the detailed study of antiinflammatory and antitumoral compounds whose activities are known a priori. In fact, thanks to this procedure, in this thesis several rationalizations of binding modes were reported related to Ugi products derivatives of CHAP 1 (HDAC inhibitors, paragraph 2.5), new and potent inhibitor of NMPRTAse analogs of FK866 and CHS 828 (chapter 3), marine natural products as inhibitors of hsPLA2 (BLQ and CLDA, chapter 5), 4-methylen sterols extracted from Theonella swinhoei as ligands of FXR and PXR (chapter 6), and known compounds as taurolitholic acid and ciprofloxacin (chapter 7), agonists of TGR5. Through the in silico methodology the putative binding modes for the reported molecules was described offering a complete rationalization of docking results, evaluating the influence of the ligand target interactions (e.g. hydrophobic, hydrophilic, electrostatic contacts) on the biological activity. c) Determination of relative configuration of natural products. The complete comprehension of the three dimensional structure of synthetic or isolated molecules is fundamental to design and characterize new platform potentially utilizable in therapy. On this basis, the combined approach between the quantum mechanical (QM) calculation of NMR parameters and NMR spectroscopy was revealed a very useful mean to lead the total synthesis of natural product toward the right isomer avoiding waste of time and resources (paragraph 8.1). Moreover, the stereostructure assignment of marine natural products conicasterol F and its analog thonellasterol I was reported in the paragraph 8.2. by a novel combined approach between the quantitative interproton distance determinations by ROE and quantum mechanical calculations of chemical shifts. (edited by author)X n.s

On the Modeling of the Donor/Acceptor Compensation Ratio in Carbon‐Doped GaN to Univocally Reproduce Breakdown Voltage and Current Collapse in Lateral GaN Power HEMTs

The intentional doping of lateral GaN power high electron mobility transistors (HEMTs) with carbon (C) impurities is a common technique to reduce buffer conductivity and increase breakdown voltage. Due to the introduction of trap levels in the GaN bandgap, it is well known that these impurities give rise to dispersion, leading to the so‐called “current collapse” as a collateral effect. Moreover, first‐principles calculations and experimental evidence point out that C introduces trap levels of both acceptor and donor types. Here, we report on the modeling of the donor/acceptor compensation ratio (CR), that is, the ratio between the density of donors and acceptors associated with C doping, to consistently and univocally reproduce experimental breakdown voltage (VBD) and current‐collapse magnitude (ΔICC). By means of calibrated numerical device simulations, we confirm that ΔICC is controlled by the effective trap concentration (i.e., the difference between the acceptor and donor densities), but we show that it is the total trap concentration (i.e., the sum of acceptor and donor densities) that determines VBD, such that a significant CR of at least 50% (depending on the technology) must be assumed to explain both phenomena quantitatively. The results presented in this work contribute to clarifying several previous reports, and are helpful to device engineers interested in modeling C‐doped lateral GaN power HEMTs

The effects of carbon on the bidirectional threshold voltage instabilities induced by negative gate bias stress in GaN MIS-HEMTs

In this paper, numerical device simulations are used to point out the possible contributions of carbon doping to the threshold voltage instabilities induced by negative gate bias stress in AlGaN/GaN metal–insulator–semiconductor high-electron mobility transistors. It is suggested that carbon can have a role in both negative and positive threshold voltage shifts, as a result of (1) the changes in the total negative charge stored in the carbon-related acceptor traps in the GaN buffer, and (2) the attraction of carbon-related free holes to the device surface and their capture into interface traps or recombination with gate-injected electrons. For a proper device optimization of carbon-doped MIS-HEMTs, it is therefore important to take these mechanisms into account, in addition to those related to defects in the gate dielectric volume and interface which are conventionally held responsible for threshold voltage instabilities

Estimation of the Direct Cost of HIV-Infected Patients in Greece on an Annual Basis

AbstractObjectiveHIV infection is currently regarded as a global chronic disease. The purpose of this study was to assess the direct cost of illness per patient per year in Greece.MethodsA retrospective study for the estimation of the direct cost of HIV infection was performed from the third-party payer perspective. Data from 447 patients monitored in a general hospital of Athens were collected from their medical records. The survey involved all services and treatments that patients (stratified into three health states according to the number of CD4 cells/ml as defined by the Centers for Disease Control and Prevention classification system for HIV infection) received in 1 year, as well as demographic data.ResultsThe annual direct cost per patient was calculated at €6859 ± €4699. Antiretroviral therapy cost was estimated at €5741, while the annual cost of providing health care services regardless of health state was computed at €1118, with laboratory investigation and imaging studies representing €924 (13.5%), outpatient visits €34 (0.5%), and hospitalization €160 (2.3%) of total cost, respectively. Overall, direct cost per patient was found to increase as the CD4 T lymphocytes decreased, leading to prolonged hospitalization and an increase in the number of laboratory tests. Direct cost for patients with more than 500 CD4 cells/μl was estimated at €6067, whereas for those with 200 to 499 cells/μl and less than 200 cells/μl, it was assessed at €6857 and €7654, respectively.ConclusionsThe direct cost of HIV infection per patient increased as CD4 T lymphocytes decreased. The largest part of expenses was attributed to antiretroviral therapy, followed by laboratory tests/imaging studies, hospitalization, and finally outpatient visits

Altered behavioral and metabolic circadian rhythms in mice with disrupted NAD+ oscillation

The Intracellular levels of nicotinamide adenine dinucleotide (NAD+) are rhythmic and controlled by the circadian clock. However, whether NAD+ oscillation in turn contributes to circadian physiology is not fully understood. To address this question we analyzed mice mutated for the NAD+ hydrolase CD38. We found that rhythmicity of NAD+ was altered in the CD38-deficient mice. The high, chronic levels of NAD+ results in several anomalies in circadian behavior and metabolism. CD38-null mice display a shortened period length of locomotor activity and alteration in the rest-activity rhythm. Several clock genes and, interestingly, genes involved in amino acid metabolism were deregulated in CD38-null livers. Metabolomic analysis identified alterations in the circadian levels of several amino acids, specifically tryptophan levels were reduced in the CD38-null mice at a circadian time paralleling with elevated NAD+ levels. Thus, CD38 contributes to behavioral and metabolic circadian rhythms and altered NAD+ levels influence the circadian clock

Gate-Bias Induced RON Instability in p-GaN Power HEMTs

In this letter, we investigate the on-resistance ( RON ) instability in p-GaN power HEMTs induced by a positive or negative gate bias ( VGB ), following the application of a quasi-static initialization voltage ( VGP ) of opposite sign. The transient behavior of this instability was characterized at different temperatures in the 90–135 °C range. By monitoring the resulting drain current transients, the activation energy as well as time constants of the processes are characterized. Not trivially, both RON increase/decrease were found to be thermally activated and with same activation energy. We attribute the thermal activation of both RON increase/decrease to the charging/discharging of hole traps present in the AlGaN barrier in the region below the gate

Novel artful applications of vaccines at the horizon

Some live vaccines, particularly Bacillus Calmette-Guerin (BCG), oral polio vaccine (OPV), and measles vaccine, can reduce the incidence of all-cause mortality by outreaching the mere control of specific infections and exerting off-target effects. Asides from the prevention of viral infection, some other vaccines, such as those against flu or rotavirus, could reduce the risk of developing autoimmunity. The nonspecific effects of vaccines are mediated by the innate immune system, mainly through the so-called trained innate immunity. These observations paved the way for developing tolerogenic and trained immunity-based vaccines with substantial implications for more effective use of vaccines and combat vaccine hesitancy

A Chemical-Biological Study Reveals C-9-type Iridoids as Novel Heat Shock Protein 90 (Hsp90) Inhibitors

The potential of heat shock protein 90 (Hsp90) as a therapeutic target for numerous diseases has made the identification and optimization of novel Hsp90 inhibitors an emerging therapeutic strategy. A surface plasmon resonance (SPR) approach was adopted to screen some iridoids for their Hsp90 alpha binding capability. Twenty-four iridoid derivatives, including 13 new natural compounds, were isolated from the leaves of Tabebuia argentea and petioles of Catalpa bignonioides. Their structures were elucidated by NMR, electrospray ionization mass spectrometry, and chemical methods. By means of a panel of chemical and biological approaches, four iridoids were demonstrated to bind Hsp90 alpha. In particular, the dimeric iridoid argenteoside A was shown to efficiently inhibit the chaperone in biochemical and cellular assays. Our results disclose C-9-type iridoids as a novel class of Hsp90 inhibitors