In-silico guided chemical exploration of KDM4A fragments hits

BACKGROUND

Lysine demethylase enzymes (KDMs) are an emerging class of therapeutic targets, that catalyse the removal of methyl marks from histone lysine residues regulating chromatin structure and gene expression. KDM4A isoform plays an important role in the epigenetic dysregulation in various cancers and is linked to aggressive disease and poor clinical outcomes. Despite several efforts, the KDM4 family lacks successful specific molecular inhibitors.

RESULTS

Herein, starting from a structure-based fragments virtual screening campaign we developed a synergic framework as a guide to rationally design efficient KDM4A inhibitors. Commercial libraries were used to create a fragments collection and perform a virtual screening campaign combining docking and pharmacophore approaches. The most promising compounds were tested in-vitro by a Homogeneous Time-Resolved Fluorescence-based assay developed for identifying selective substrate-competitive inhibitors by means of inhibition of H3K9me3 peptide demethylation. 2-(methylcarbamoyl)isonicotinic acid was identified as a preliminary active fragment, displaying inhibition of KDM4A enzymatic activity. Its chemical exploration was deeply investigated by computational and experimental approaches which allowed a rational fragment growing process. The in-silico studies guided the development of derivatives designed as expansion of the primary fragment hit and provided further knowledge on the structure-activity relationship.

CONCLUSIONS

Our study describes useful insights into key ligand-KDM4A protein interaction and provides structural features for the development of successful selective KDM4A inhibitors.

Surface ruptures database related to the 26 December 2018, MW 4.9 Mt. Etna earthquake, southern Italy

We provide a database of the surface ruptures produced by the 26 December 2018 Mw 4.9 earthquake that struck the eastern flank of Mt. Etna volcano in Sicily (southern Italy). Despite its relatively small magnitude, this shallow earthquake caused about 8 km of surface faulting, along the trace of the NNW-trending active Fiandaca Fault. Detailed field surveys have been performed in the epicentral area to map the ruptures and to characterize their kinematics. The surface ruptures show a dominant right-oblique sense of displacement with an average slip of about 0.09 m and a maximum value of 0.35 m. We have parsed and organized all observations in a concise database, with 932 homogeneous georeferenced records. The Fiandaca Fault is part of the complex active Timpe faults system affecting the eastern flank of Etna, and its seismic history indicates a prominent surface-faulting potential. Therefore, this database is essential for unravelling the seismotectonics of shallow earthquakes in volcanic areas, and contributes updating empirical scaling regressions that relate magnitude and extent of surface faulting.

Oligomeric state, hydrodynamic properties and target recognition of human Calcium and Integrin Binding protein 2 (CIB2)

Calcium- and Integrin-Binding protein 2 (CIB2) is a small and ubiquitously expressed protein with largely unknown biological function but ascertained role in hearing physiology and disease. Recent studies found that CIB2 binds Ca2+ with moderate affinity and dimerizes under conditions mimicking the physiological ones. Here we provided new lines of evidence on CIB2 oligomeric state and the mechanism of interaction with the α7B integrin target. Based on a combination of native mass spectrometry, chemical cross-linking/mass spectrometry, analytical gel filtration, dynamic light scattering and molecular dynamics simulations we conclude that CIB2 is monomeric under all tested conditions and presents uncommon hydrodynamic properties, most likely due to the high content of hydrophobic solvent accessible surface. Surface plasmon resonance shows that the interaction with α7B occurs with relatively low affinity and is limited to the cytosolic region proximal to the membrane, being kinetically favored in the presence of physiological Mg2+ and in the absence of Ca2+. Although CIB2 binds to an α7B peptide in a 1:1 stoichiometry, the formation of the complex might induce binding of another CIB2 molecule.

Preferential Binding of Mg2+ Over Ca2+ to CIB2 Triggers an Allosteric Switch Impaired in Usher Syndrome Type 1J

Calcium and integrin binding protein 2 (CIB2) shares with the other members of the CIB family the ability to bind Ca²⁺ and Mg²⁺ via two functional EF-hand motifs, namely EF3 and EF4. As a cation sensor, CIB2 is able to switch to a conformation likely associated with specific biological functions yet to be clarified. Recent findings demonstrate the involvement of CIB2 in hearing physiology and a single, conservative point mutation (p.E64D) has been related to Usher Syndrome type 1J (USH1J) and non-syndromic hearing loss. We present an exhaustive biochemical and biophysical characterization of human wild type (WT) and E64D CIB2. We found that CIB2 does not possibly work as a calcium sensor under physiological conditions, its affinity for Ca²⁺ (K_d^app = 0.5 mM) being too low for detecting normal intracellular levels. Instead, CIB2 displays a significantly high affinity for Mg²⁺ (K_d^app = 290 μM), and it is probably Mg²⁺ -bound under physiological conditions. At odds with the homologous protein CIB1, CIB2 forms a non-covalent dimer under conditions that mimic the physiological ones, and as such it interacts with its physiological target α7B integrin. NMR spectroscopy revealed a long-range allosteric communication between the residue E64, located at the N-terminal domain, and the metal cation binding site EF3, located at the C-terminal domain. The conservative E64D mutation breaks up such inter-domain communication resulting in the impaired ability of CIB2 to switch to its Mg²⁺-bound form. The ability to bind the target integrin peptide was substantially conserved for E64D CIB2, thus suggesting that the molecular defect associated with USH1J resides in its inability to sense Mg²⁺ and adopt the required conformation.

Arabidopsis calmodulin-like protein CML36 is a calcium (Ca2+) sensor that interacts with the plasma membrane Ca2+-ATPase isoform ACA8 and stimulates its activity

Calmodulin-like (CML) proteins are major EF-hand-containing, calcium (Ca2+)-binding proteins with crucial roles in plant development and in coordinating plant stress tolerance. Given their abundance in plants, the properties of Ca2+ sensors and identification of novel target proteins of CMLs deserve special attention. To this end, we recombinantly produced and biochemically characterized CML36 from Arabidopsis thaliana We analyzed Ca2+ and Mg2+ binding to the individual EF-hands, observed metal-induced conformational changes, and identified a physiologically relevant target. CML36 possesses two high-affinity Ca2+/Mg2+ mixed binding sites and two low-affinity Ca2+-specific sites. Binding of Ca2+ induced an increase in the α-helical content and a conformational change that lead to the exposure of hydrophobic regions responsible for target protein recognition. Cation binding, either Ca2+ or Mg2+, stabilized the secondary and tertiary structures of CML36, guiding a large structural transition from a molten globule apo-state to a compact holoconformation. Importantly, through in vitro binding and activity assays, we showed that CML36 interacts directly with the regulative N terminus of the Arabidopsis plasma membrane Ca2+-ATPase isoform 8 (ACA8) and that this interaction stimulates ACA8 activity. Gene expression analysis revealed that CML36 and ACA8 are co-expressed mainly in inflorescences. Collectively, our results support a role for CML36 as a Ca2+ sensor that binds to and modulates ACA8, uncovering a possible involvement of the CML protein family in the modulation of plant-autoinhibited Ca2+ pumps.

High progesterone levels during the luteal phase related to the use of an aromatase inhibitor in breast cancer patients

OBJECTIVE

To evaluate the hormonal profile in three breast cancer patients who underwent controlled ovarian stimulation in the presence of the aromatase inhibitor letrozole.

PATIENTS AND METHODS

In IVF University referral center, a case series of three breast cancer patients who underwent controlled ovarian stimulation (COS) with recombinant FSH and letrozole were investigated. Ovulation was induced with hCG (case No. 1) or with GnRH agonist (case No. 2-3). The primary outcome of our study was the detection of progesterone levels in the luteal phase.

RESULTS

Very high progesterone values (mean 186.6 ± 43.6 ng/mL) during the luteal phase were recorded in all three cases.

CONCLUSIONS

High progesterone levels can be related to the use of letrozole independently of the most commonly used trigger regimen. Although progesterone has long been considered a protective factor against breast cancer, several studies have demonstrated that progesterone could expand a transformation-sensitive stem cell population in the mammary glands. The estrogen negative feedback effect on the hypothalamus-pituitary axis and the disruption of steroid biosynthesis and could represent an intriguing reason behind this phenomenon. Our results highlight the need to evaluate further the increase in progesterone levels in the luteal phase in women with breast cancer undergoing COS with letrozole.

Metal binding affinity and structural properties of calmodulin-like protein 14 from Arabidopsis thaliana

In addition to the well-known Ca(2+) sensor calmodulin, plants possess many calmodulin-like proteins (CMLs) that are predicted to have specific roles in the cell. Herein, we described the biochemical and biophysical characterization of recombinant Arabidopsis thaliana CML14. We applied isothermal titration calorimetry to analyze the energetics of Ca(2+) and Mg(2+) binding to CML14, and nuclear magnetic resonance spectroscopy, together with intrinsic and ANS-based fluorescence, to evaluate the structural effects of metal binding and metal-induced conformational changes. Furthermore, differential scanning calorimetry and limited proteolysis were used to characterize protein thermal and local stability. Our data demonstrate that CML14 binds one Ca(2+) ion with micromolar affinity (Kd ∼ 12 µM) and the presence of 10 mM Mg(2+) decreases the Ca(2+) affinity by ∼5-fold. Although binding of Ca(2+) to CML14 increases protein stability, it does not result in a more hydrophobic protein surface and does not induce the large conformational rearrangement typical of Ca(2+) sensors, but causes only localized structural changes in the unique functional EF-hand. Our data, together with a molecular modelling prediction, provide interesting insights into the biochemical properties of Arabidopsis CML14 and may be useful to direct additional studies aimed at understanding its physiological role.

The treatment of acute psychosis without neuroleptics: six-week psychopathology outcome data from The Soteria Project

BACKGROUND

Today's treatment of acute psychosis usually includes short-term hospitalization and anti-psychotic drug treatment. The Soteria project compared this form of treatment (control) with that of a small, home-like social environment, usually without neuroleptics (experimental).

METHOD

Newly diagnosed, young, unmarried persons with DSM-II schizophrenia were randomly assigned to treatment in two experimental and two control settings. Subjects and families were assessed at admission on 29 independent variables. Treatment environments were studied by means of Moos', COPES or WAS scales. Three dependent six week psychopathology outcome measures were collected.

RESULTS

The groups were comparable on 25 of 29 admission variables. The environments of the two experimental and two control settings were different from each other. The milieus were similar to each other within each condition. At six weeks, psychopathology in both groups had improved significantly, and similarly, and overall change was the same.

CONCLUSION

Specially designed, replicable milieus were able to reduce acute psychotic symptomatology within six weeks, usually without antipsychotic drugs, as effectively as usual hospital ward treatment that included routine neuroleptic drug use.

Screening for frailty: criteria and predictors of outcomes

OBJECTIVE

To determine the reliability of rapid screening by clinically derived geriatric criteria in predicting outcomes of elderly hospitalized patients.

DESIGN

Prospective cohort study of 985 patients screened at the time of hospital admission and followed for 1 year with respect to the outcomes of mortality, hospital readmission, and nursing home utilization.

SETTING

Palo Alto Veterans Affairs Medical Center, a tertiary care teaching hospital.

SUBJECTS

Male patients 65 years of age and older admitted to the Medical and Surgical services during the period from October 1, 1985 through September 30, 1986.

RESULTS

Patients were grouped by specific screening criteria into three groups of increasing frailty: Independent, Frail, and Severely Impaired. Each criterion focused on a geriatric condition and was designed to serve as a marker for frailty. Increasing frailty was significantly correlated with increasing length of hospital stay (P less than 0.0001), nursing home utilization (P less than 0.0001), and mortality (P less than 0.0001). Multivariate analyses revealed that the clinical groups were more predictive of mortality and nursing home utilization than were age or Diagnosis-Related Groups (DRGs). Rehospitalization was unrelated to age, clinical group, or DRG, suggesting that utilization may not be driven by the clinical factors measured in this study.

CONCLUSIONS

Rapid clinical screening using specific geriatric criteria is effective in identifying frail older subjects at risk for mortality and nursing home utilization. Our findings suggest that geriatric syndromes are more predictive of adverse outcomes than diagnosis per se. This well operationalized screening process is inexpensive as well as effective and could easily be introduced into other hospital settings.

[Pneumomediastinum or mediastinal emphysema. Case contribution and classification]

Five cases of pneumomediastinum with different aetiology are reported. The pathogenetic problems are examined and a new classification with physiopathologic criteria proposed.