AI is a viable alternative to high throughput screening: a 318-target study

High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.

Development and evaluation of a novel educational program for providers on the use of polygenic risk scores

PURPOSE

This study aimed to develop an online educational program for using PRS for breast and ovarian cancer risk-assessments and evaluate the impact on genetic healthcare providers' (GHP) attitudes, confidence, knowledge, and preparedness.

METHODS

The educational program comprised of an online module covering theoretical aspects of PRS, and a facilitated virtual workshop with pre-recorded roleplays and case discussions. Data were collected in pre-and post-education surveys. Eligible participants were GHPs working in Australian familial cancer clinics registered to recruit patients for a breast and ovarian cancer PRS clinical trial (n=12).

RESULTS

124 GHPs completed the PRS education, of whom 80 (64%) and 67 (41%) completed the pre-and post-education surveys, respectively. Pre-education, GHPs reported limited experience, confidence and preparedness using PRS, but recognized its potential benefits. Post-education GHPs indicated improved attitudes (p=<0.001), confidence (p=<0.001), knowledge (p=<0.001), and preparedness (p=<0.001) to use PRS. Most GHPs felt the program entirely met their learning needs (73%) and was completely relevant to their clinical practice (88%). GHPs identified PRS implementation barriers, including limited funding models, diversity issues, and need for clinical guidelines.

CONCLUSIONS

Our education program improved GHP attitudes, confidence, knowledge, and preparedness for using PRS/personalized risk and provides a framework for development of future programs.

Poleward Shifts and Altered Periodicity in Boreal Bird Irruptions Over Six Decades

Range boundaries are long-term biogeographic features of species distributions and abundance. However, many species demonstrate dynamic range boundaries, reflecting strong seasonal and annual variability in migratory behavior. As a form of facultative migration, irruptions involve the movement of many individuals outside of their resident range in response to climate variability, resource availability, and demographic processes. Many species have experienced range shifts and altered phenology in response to modern climate change, but spatiotemporal changes in irruption dynamics are less well known. We quantified changes in the geography and periodicity of boreal bird irruptions across eastern North America from 1960-2021. Using data from Audubon's Christmas Bird Count for nine finch species, including several exhibiting recent population declines, we evaluated latitudinal trends in southern range and irruption boundaries and characterized irruption periodicity using spectral wavelet analysis. Six boreal birds exhibited significant northward shifts in their southern range boundaries and three species displayed shifts in their southern irruption boundaries. Irruption periodicity across multiple species was consistent across the 1960s and 1970s, culminating in frequent and synchronized irruptions of multiple species (superflights) during earlier decades. Coherence between species dampened beginning in the early 1980s as superflight periodicity became increasingly unstructured, finally reforming in recent decades, after 2000. Boreal birds are considered important sentinels of the boreal forests, and northward shifts and altered periodicity of irruptions may indicate broad-scale changes in climate- and resource-associated drivers operating across the boreal forests.

Use of the ACTH challenge test to identify the predominant glucocorticoid in the southern sea otter (Enhydra lutris nereis)

After nearly being hunted to extinction during the fur trade of the late 20th Century, sea otter (Enhydra lutris) populations have recovered to varying degrees of their historical range. While overall population numbers and range have increased, there are regions in which expansion has occurred at a slower rate and/or animal numbers have decreased, which may be a result of chronic stress from a variety of sources. Some have employed glucocorticoid analysis in their attempts to validate these explanations. Our goal was to conduct a controlled study using sea otters managed under human care to validate the use of serum glucocorticoid analysis to monitor stress physiology in the sea otter. We used a standard ACTH challenge test to compare cortisol and corticosterone responses, thereby identifying the primary glucocorticoid in the sea otter. Fourteen sea otters of both sexes (five males, nine females), including juveniles, sub-adults and adults, participated in the study. The results of the testing supported cortisol as the primary glucocorticoid in the sea otter. Sex and age did not affect how the individual responded to the ACTH or saline injection. Interestingly, the saline injection not only confirmed the effects of the ACTH on glucocorticoid release from the adrenal glands but also provided information on how long it takes the sea otter's glucocorticoid levels to return to baseline after capture and sedation. The insight gained from this study will aid in future efforts to better understand the role of stress in free-ranging sea otter populations. Recognition of the primary glucocorticoid will facilitate evaluation of more stable biological material, such as fur or whiskers, which tend to be less affected by the diurnal cycling of glucocorticoids.

Evaluating the association of single-nucleotide polymorphisms with tenofovir exposure in a diverse prospective cohort of women living with HIV

Higher exposure to tenofovir (TFV) increases the risk for kidney function decline, but the impact of genetic factors on TFV exposure is largely unknown. We investigated whether single-nucleotide polymorphisms (SNPs, n=211) in 12 genes are potentially involved in TFV exposure. Participants (n=91) from the Women's Interagency HIV Study, underwent a 24 h intensive pharmacokinetic sampling of TFV after witnessed dose and TFV area under the time-concentration curves (AUCs) were calculated for each participant. SNPs were assayed using a combination of array genotyping and Sanger sequencing. Linear regression models were applied to logarithmically transformed AUC. Those SNPs that met an a priori threshold of P<0.001 were considered statistically associated with TFV AUC. ABCG2 SNP rs2231142 was associated with TFV AUC with rare allele carriers displaying 1.51-fold increase in TFV AUC (95% confidence interval: 1.26, 1.81; P=1.7 × 10^-5). We present evidence of a moderately strong effect of the rs2231142 SNP in ABCG2 on a 24 h TFV AUC.

Effects of obeticholic acid on lipoprotein metabolism in healthy volunteers

The bile acid analogue obeticholic acid (OCA) is a selective farnesoid X receptor (FXR) agonist in development for treatment of several chronic liver diseases. FXR activation regulates lipoprotein homeostasis. The effects of OCA on cholesterol and lipoprotein metabolism in healthy individuals were assessed. Two phase I studies were conducted to evaluate the effects of repeated oral doses of 5, 10 or 25 mg OCA on lipid variables after 14 or 20 days of consecutive administration in 68 healthy adults. Changes in HDL and LDL cholesterol levels were examined, in addition to nuclear magnetic resonance analysis of particle sizes and sub-fraction concentrations. OCA elicited changes in circulating cholesterol and particle size of LDL and HDL. OCA decreased HDL cholesterol and increased LDL cholesterol, independently of dose. HDL particle concentrations declined as a result of a reduction in medium and small HDL. Total LDL particle concentrations increased because of an increase in large LDL particles. Changes in lipoprotein metabolism attributable to OCA in healthy individuals were found to be consistent with previously reported changes in patients receiving OCA with non-alcoholic fatty liver disease or non-alcoholic steatohepatitis.

A Systems Model for Ursodeoxycholic Acid Metabolism in Healthy and Patients With Primary Biliary Cirrhosis

A systems model was developed to describe the metabolism and disposition of ursodeoxycholic acid (UDCA) and its conjugates in healthy subjects based on pharmacokinetic (PK) data from published studies in order to study the distribution of oral UDCA and potential interactions influencing therapeutic effects upon interruption of its enterohepatic recirculation. The base model was empirically adapted to patients with primary biliary cirrhosis (PBC) based on current understanding of disease pathophysiology and clinical measurements. Simulations were performed for patients with PBC under two competing hypotheses: one for inhibition of ileal absorption of both UDCA and conjugates and the other only of conjugates. The simulations predicted distinctly different bile acid distribution patterns in plasma and bile. The UDCA model adapted to patients with PBC provides a platform to investigate a complex therapeutic drug interaction among UDCA, UDCA conjugates, and inhibition of ileal bile acid transport in this rare disease population.

Epigenomic analysis of the HOX gene loci reveals mechanisms that may control canonical expression patterns in AML and normal hematopoietic cells

HOX genes are highly expressed in many acute myeloid leukemia (AML) samples, but the patterns of expression and associated regulatory mechanisms are not clearly understood. We analyzed RNA sequencing data from 179 primary AML samples and normal hematopoietic cells to understand the range of expression patterns in normal versus leukemic cells. HOX expression in AML was restricted to specific genes in the HOXA or HOXB loci, and was highly correlated with recurrent cytogenetic abnormalities. However, the majority of samples expressed a canonical set of HOXA and HOXB genes that was nearly identical to the expression signature of normal hematopoietic stem/progenitor cells. Transcriptional profiles at the HOX loci were similar between normal cells and AML samples, and involved bidirectional transcription at the center of each gene cluster. Epigenetic analysis of a subset of AML samples also identified common regions of chromatin accessibility in AML samples and normal CD34(+) cells that displayed differences in methylation depending on HOX expression patterns. These data provide an integrated epigenetic view of the HOX gene loci in primary AML samples, and suggest that HOX expression in most AML samples represents a normal stem cell program that is controlled by epigenetic mechanisms at specific regulatory elements.

Apc and p53 interaction in DNA damage and genomic instability in hepatocytes

Disruption of Apc within hepatocytes activates Wnt signaling, perturb differentiation and ultimately lead to neoplasia. Apc negatively regulates Wnt signaling but is also involved in organizing the cytoskeleton and may play a role in chromosome segregation. In vitro studies have implicated Apc in the control of genomic stability. However, the relevance of this data has been questioned in vivo as Apc is lost earlier than the onset of genomic instability. Here, we analyse the relationship between immediate loss of Apc and the acquisition of genomic instability in hepatocytes. We used Cre-lox technology to inactivate Apc and in combination with p53 in vivo, to define the consequences of gene loss upon cell-cycle regulation, proliferation, death and aneuploidy. We show that whilst Apc loss leads to increased proliferation, it also leads to increased apoptosis, the accumulation of p53, p21 and markers of DSBs and DNA repair. Flow cytometry revealed an increased 4N DNA content, consistent with a G2 arrest. Levels of anaphase bridges were also elevated, implicating failed chromosome segregation. This was accompanied by an increase in centrosome number which demonstrates a role for Apc in maintaining euploidy.

To address the role of p53 in these processes, we analyzed combined loss of Apc and p53, which led to a further increase in proliferation, cell death, DNA damages and repair and a bypass of G2 arrest than was observed with Apc loss. However we observed only a marginal effect on anaphase bridges and centrosome number which could be due to increased cell death. Our data therefore establishes, in an in vivo setting, that APC loss leads to a DNA damage signature and genomic instability in the liver and that additional loss of p53 leads to an increase in the DNA damage signal but not to an immediate increase in the genomic instability phenotype.

Emerging potential of therapeutic targeting of ubiquitin-specific proteases in the treatment of cancer

The ubiquitin-proteasome system (UPS) has emerged as a therapeutic focus and target for the treatment of cancer. The most clinically successful UPS-active agents (bortezomib and lenalidomide) are limited in application to hematologic malignancies, with only marginal efficacy in solid tumors. Inhibition of specific ubiquitin E3 ligases has also emerged as a valid therapeutic strategy, and many targets are currently being investigated. Another emerging and promising approach in regulation of the UPS involves targeting deubiquitinases (DUB). The DUBs comprise a relatively small group of proteins, most with cysteine protease activity that target several key proteins involved in regulation of tumorigenesis, apoptosis, senescence, and autophagy. Through their multiple contacts with ubiquitinated protein substrates involved in these pathways, DUBs provide an untapped means of modulating many important regulatory proteins that support oncogenic transformation and progression. Ubiquitin-specific proteases (USP) are one class of DUBs that have drawn special attention as cancer targets, as many are differentially expressed or activated in tumors or their microenvironment, making them ideal candidates for drug development. This review attempts to summarize the USPs implicated in different cancers, the current status of USP inhibitor-mediated pharmacologic intervention, and future prospects for USP inhibitors to treat diverse cancers.

Improved performance of SPECT-CT In-111 capromab pendetide by correlation with diffusion-weighted magnetic resonance imaging for identifying metastatic pelvic lymphadenopathy in prostate cancer

PURPOSE

To preliminarily evaluate the potential for an improvement in diagnostic performance by a combined interpretation of In-111 capromab pendetide single photon emission computed tomography (SPECT) including computed tomography (CT) image fusion with magnetic resonance diffusion-weighted imaging (MR-DWI) for identifying prostate cancer in pelvic lymph nodes thru correlation with histopathology.

MATERIALS AND METHODS

This institutional approved, retrospective study identified patients with available histopathology of lymph nodes removed at the time of radical prostatectomy and who had undergone staging with In-111 capromab pendetide SPECT-CT and/or pelvic MRI (including DWI). The performance of In-111 capromab pendetide SPECT for identifying malignant lymph nodes was assessed. Subsequently, a combined reading of In-111 capromab pendetide SPECT and prostate MRI with DWI was performed and the performance assessed.

RESULTS

18 patients underwent In-111 capromab pendetide SPECT-CT. Of these, 12 patients had also undergone imaging with MR-DWI. In-111 capromab pendetide SPECT-CT had a sensitivity of 40.0% and specificity of 96.7% for identification of malignant lymph nodes. However, In-111 capromab pendetide SPECT-CT combined with MRI with DWI had a sensitivity of 88.9% and specificity of 98.5%.

CONCLUSIONS

The addition of MR-DWI to the interpretation of In-111 capromab pendetide SPECT-CT may increase the sensitivity for detecting malignant lymph nodes in prostate cancer. Future prospective evaluation of combined In-111 capromab pendetide SPECT-CT and MR-DWI is indicated and may improve clinical evaluation of nodal disease in prostate cancer.

Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase

Incorporation of divalent metal ions into an active site is a fundamental catalytic tool used by diverse enzymes. Divalent cations are used by protein kinases to both stabilize ATP binding and accelerate chemistry. Kinetic analysis establishes that Cyclin-dependent kinase 2 (CDK2) requires simultaneous binding of two Mg(2+) ions for catalysis of phosphoryl transfer. This tool, however, comes with a price: the rate-acceleration effects are opposed by an unavoidable rate-limiting consequence of the use of two Mg(2+) ions by CDK2. The essential metal ions stabilize ADP product binding and limit the overall rate of the reaction. We demonstrate that product release is rate limiting for activated CDK2 and evaluate the effects of the two catalytically essential Mg(2+) ions on the stability of the ADP product within the active site. We present two new crystal structures of CDK2 bound to ADP showing how the phosphate groups can be coordinated by either one or two Mg(2+) ions, with the occupancy of one site in a weaker equilibrium. Molecular dynamics simulations indicate that ADP phosphate mobility is more restricted when ADP is coordinated by two Mg(2+) ions compared to one. The structural similarity between the rigid ADP·2Mg product and the cooperatively assembled transition state provides a mechanistic rational for the rate-limiting ADP release that is observed. We demonstrate that although the simultaneous binding of two Mg(2+) ions is essential for efficient phosphoryl transfer, the presence of both Mg(2+) ions in the active site also cooperatively increases ADP affinity and opposes its release. Evolution of protein kinases must have involved careful tuning of the affinity for the second Mg(2+) ion in order to balance the needs to stabilize the chemical transition state and allow timely product release. The link between Mg(2+) site affinity and activity presents a chemical handle that may be used by regulatory factors as well as explain some mutational effects.

Briefly bound to activate: transient binding of a second catalytic magnesium activates the structure and dynamics of CDK2 kinase for catalysis

We have determined high-resolution crystal structures of a CDK2/Cyclin A transition state complex bound to ADP, substrate peptide, and MgF(3)(-). Compared to previous structures of active CDK2, the catalytic subunit of the kinase adopts a more closed conformation around the active site and now allows observation of a second Mg(2+) ion in the active site. Coupled with a strong [Mg(2+)] effect on in vitro kinase activity, the structures suggest that the transient binding of the second Mg(2+) ion is necessary to achieve maximum rate enhancement of the chemical reaction, and Mg(2+) concentration could represent an important regulator of CDK2 activity in vivo. Molecular dynamics simulations illustrate how the simultaneous binding of substrate peptide, ATP, and two Mg(2+) ions is able to induce a more rigid and closed organization of the active site that functions to orient the phosphates, stabilize the buildup of negative charge, and shield the subsequently activated γ-phosphate from solvent.

Structure of a thyroid hormone receptor DNA-binding domain homodimer bound to an inverted palindrome DNA response element

Thyroid hormone receptor (TR), as a member of the nuclear hormone receptor family, can recognize and bind different classes of DNA response element targets as either a monomer, a homooligomer, or a heterooligomer. We report here the first crystal structure of a homodimer TR DNA-binding domain (DBD) in complex with an inverted repeat class of thyroid response element (TRE). The structure shows a nearly symmetric structure of the TR DBD assembled on the F2 TRE where the base recognition contacts in the homodimer DNA complex are conserved relative to the previously published structure of a TR-9-cis-retinoic acid receptor heterodimer DNA complex. The new structure also reveals that the T-box region of the DBD can function as a structural hinge that enables a large degree of flexibility in the position of the C-terminal extension helix that connects the DBD to the ligand-binding domain. Although the isolated TR DBDs exist as monomers in solution, we have measured highly cooperative binding of the two TR DBD subunits onto the inverted repeat DNA sequence. This suggests that elements of the DBD can influence the specific TR oligomerization at target genes, and it is not just interactions between the ligand-binding domains that are responsible for TR oligomerization at target genes. Mutational analysis shows that intersubunit contacts at the DBD C terminus account for some, but not all, of the cooperative homodimer TR binding to the inverted repeat class TRE.

CO-MP4, a polyethylene glycol-conjugated haemoglobin derivative and carbon monoxide carrier that reduces myocardial infarct size in rats

BACKGROUND AND PURPOSE

MP4 (Hemospan) is a Hb-based oxygen therapeutic agent, based on polyethylene-glycol (PEG) conjugation to Hb, undergoing clinical trials as an oxygen carrier. This study describes the functional interaction between MP4 and carbon monoxide (CO), as a CO delivery agent, and the effects of CO-MP4 on myocardial infarct size following ischaemia and reperfusion in rats.

EXPERIMENTAL APPROACH

Kinetic measurements of CO-MP4 binding were used to evaluate the effects of PEG modification on Hb subunit structure/function and to calculate CO-MP4 equilibrium constants. CO transport by CO-MP4 was shown by ligand (O2/CO) partitioning between MP4 and red blood cell (RBC)-Hb. Pharmacological effects of CO-MP4 were studied on myocardial infarction in rats.

KEY RESULTS

CO binding kinetics show primary structural/functional effects on beta chains in MP4, with alpha chains maintaining the ability to undergo tertiary conformational transition. CO confers long-term, room-temperature stability and is able to rapidly re-equilibrate between MP4 and RBCs. In a rat model of myocardial infarct, in contrast to oxy-MP4, CO-MP4 reduced infarct size when administered prior to the induction of ischaemia.

CONCLUSIONS AND IMPLICATIONS

MP4 PEGylation chemistry modifies the individual function of Hb subunits, but results in an overall CO equilibrium constant similar to that for unmodified Hb. CO-MP4 is able to deliver CO to the circulation and reduces ischaemia/reperfusion injury in rats, providing the first evidence for this drug as a CO therapeutic agent.

Regulation of luteinizing hormone receptor mRNA expression by mevalonate kinase--role of the catalytic center in mRNA recognition

We have shown that hormone-induced downregulation of luteinizing hormone receptor (LHR) in the ovary is post-transcriptionally regulated by an mRNA binding protein. This protein, later identified as mevalonate kinase (MVK), binds to the coding region of LHR mRNA, suppresses its translation, and the resulting ribonucleoprotein complex is targeted for degradation. Mutagenesis and crystallographic studies of rat MVK have established Ser146, Glu193, Asp204 and Lys13 as being crucial for its catalytic function. The present study examined the structural aspects of MVK required for LHR mRNA recognition and translational suppression. Single MVK mutants (S146A, E193Q, D204N and K13A) were overexpressed in 293T cells. Cytosolic fractions were examined for LHR mRNA binding activities by RNA electrophoretic mobility shift analysis. All the single MVK mutants showed decreased LHR mRNA binding activity compared with the wild-type MVK. Double mutants (S146A & E193Q, E193Q & D204N and E193Q & K13A) of MVK also showed a significant decrease in binding to LHR mRNA, suggesting that the residues required for catalytic function are also involved in LHR mRNA recognition. Mutation of the residues outside the catalytic site (D316A and S314A) did not cause any change in LHR mRNA binding activity of MVK when compared with wild-type MVK. To examine the biological effects of these mutants on LHR mRNA expression, a full-length capped rat LHR mRNA was synthesized and translated using a rabbit reticulocyte lysate system in the presence or absence of the MVK mutant proteins. The results showed that mutations of the active site residues of MVK abrogated the inhibitory effect on LHR mRNA translation. Therefore, these data indicate that an intact active site of MVK is required for its binding to rat LHR mRNA and for its translational suppressor function.

Heterogeneous interactions of calcite aerosol with sulfur dioxide and sulfur dioxide–nitric acid mixtures

The heterogeneous chemistry of sulfur dioxide with CaCO(3) (calcite) aerosol as a function of relative humidity (RH) has been studied under isolated particle conditions in an atmospheric reaction chamber using infrared absorption spectroscopy. The reaction of SO(2) with calcite produced gas phase CO(2) as a product in addition to the conversion of the particulate carbonate to sulfite. The reaction extent was found to increase with elevated RH, as has been observed for the similar reaction with HNO(3), but much higher relative humidities were needed to significantly enhance the reaction. Mixed experiments in which calcite aerosol was exposed to both HNO(3) and SO(2) were also performed. The overall reaction extent at a given relative humidity did not appear to be increased by having both reactant gases present. The role of carbonate aerosol as an atmospheric sink for sulfur dioxide and particulate nitrogen and sulfur correlations are discussed.

Heterogeneous conversion of calcite aerosol by nitric acid

The reaction of nitric acid with calcite aerosol at varying relative humidities has been studied under suspended particle conditions in an atmospheric reaction chamber using infrared absorption spectroscopy. The reactant concentration in the chamber, as well as the appearance of gas phase products and surface adsorbed species, was spectroscopically monitored before and after mixing with CaCO(3) (calcite) particles. The interaction with HNO(3) was found to lead to gas phase CO(2) evolution and increased water uptake due to heterogeneous conversion of the carbonate to particulate nitrate. The reaction was enhanced as the relative humidity of the system was increased, especially at relative humidities above the reported deliquescence point of particulate Ca(NO(3))(2). The measured reaction extent demonstrates that the total calcite particulate mass is available for reaction with HNO(3) and the conversion process is not limited to the particle surface. The spectroscopy of the surface formed nitrate suggests a highly concentrated solution environment with a significant degree of ion pairing. The implications of the HNO(3) loss and the formation of the particulate nitrate product for atmospheric chemistry are discussed.

Surface-enhanced hyper-Raman scattering (SEHRS) on Ag film over Nanosphere (FON) electrodes: surface symmetry of centrosymmetric adsorbates

Electrochemical surface-enhanced hyper-Raman scattering (SEHRS) and surface-enhanced Raman scattering (SERS) of centrosymmetric molecules on Ag film over nanosphere (AgFON) electrodes are presented. The SEHR spectra of trans-1,2-bis(4-pyridyl)ethylene (BPE) at different potentials (vs Ag/AgCl) are presented for the first time, and a reversible potential tuning of the SEHR spectra of BPE is demonstrated. The SEHRS and SERS techniques were used to determine to what extent either site symmetry reduction or field gradient effects dictate the origin of the observed vibrational spectra. It is found that the SEHR and SER spectra for the molecules studied were distinctly different at all frequency regions at a fixed voltage, suggesting that centrosymmetry is largely retained upon adsorption to the AgFON surface and that field gradient effects are negligible. This work also shows that the SEHR spectra clearly depend on potential, whereas the SER spectra are essentially independent of potenial. It is determined that the combination of changes in deltaGads and the presence of coadsorbed counterions are responsible for altering the local symmetry of the adsorbate and only SEHRS has the sensitivity to detect these changes in the surface environment. Thus, SEHRS is a uniquely useful spectroscopic tool that is much more sensitive to the local adsorption environment than is SERS.

A Src-like inactive conformation in the abl tyrosine kinase domain

The improper activation of the Abl tyrosine kinase results in chronic myeloid leukemia (CML). The recognition of an inactive conformation of Abl, in which a catalytically important Asp-Phe-Gly (DFG) motif is flipped by approximately 180 degrees with respect to the active conformation, underlies the specificity of the cancer drug imatinib, which is used to treat CML. The DFG motif is not flipped in crystal structures of inactive forms of the closely related Src kinases, and imatinib does not inhibit c-Src. We present a structure of the kinase domain of Abl, determined in complex with an ATP-peptide conjugate, in which the protein adopts an inactive conformation that resembles closely that of the Src kinases. An interesting aspect of the Src-like inactive structure, suggested by molecular dynamics simulations and additional crystal structures, is the presence of features that might facilitate the flip of the DFG motif by providing room for the phenylalanine to move and by coordinating the aspartate side chain as it leaves the active site. One class of mutations in BCR-Abl that confers resistance to imatinib appears more likely to destabilize the inactive Src-like conformation than the active or imatinib-bound conformations. Our results suggest that interconversion between distinctly different inactive conformations is a characteristic feature of the Abl kinase domain.

Surface-enhanced Raman spectroscopy biosensors: excitation spectroscopy for optimisation of substrates fabricated by nanosphere lithography

In the 28 years since its discovery, surface-enhanced Raman scattering (SERS) has progressed from model system studies of pyridine on a roughened silver electrode to state-of-the-art surface science studies and real-world sensing applications. Each year, the number of SERS publications increases as nanoscale material design techniques advance and the importance of trace analyte detection increases. To achieve the lowest limits of detection, both the relationship between surface nanostructure and laser excitation wavelength and the analyte-surface binding chemistry must be carefully optimised. This work exploits the highly tunable nature of nanoparticle optical properties to establish the optimisation conditions. Two methods are used to study the optimised conditions of the SERS substrate: plasmon-sampled and wavelength-scanned surfaced Raman excitation spectroscopy (SERES). The SERS enhancement condition is optimised when the energy of the localised surface plasmon resonance of the nanostructures lies between the energy of the excitation wavelength and the energy of the vibration band of interest. These optimised conditions enabled the development of SERS-based sensors for the detection of a Bacillus anthracis biomarker and glucose in a serum-protein matrix.

Structure of the kinase domain of an imatinib-resistant Abl mutant in complex with the Aurora kinase inhibitor VX-680

We present a high-resolution (2.0 A) crystal structure of the catalytic domain of a mutant form of the Abl tyrosine kinase (H396P; Abl-1a numbering) that is resistant to the Abl inhibitor imatinib. The structure is determined in complex with the small-molecule inhibitor VX-680 (Vertex Pharmaceuticals, Cambridge, MA), which blocks the activity of various imatinib-resistant mutant forms of Abl, including one (T315I) that is resistant to both imatinib and BMS-354825 (dasatinib), a dual Src/Abl inhibitor that seems to be clinically effective against all other imatinib-resistant forms of BCR-Abl. VX-680 is shown to have significant inhibitory activity against BCR-Abl bearing the T315I mutation in patient-derived samples. The Abl kinase domain bound to VX-680 is not phosphorylated on the activation loop in the crystal structure but is nevertheless in an active conformation, previously unobserved for Abl and inconsistent with the binding of imatinib. The adoption of an active conformation is most likely the result of synergy between the His(396)Pro mutation, which destabilizes the inactive conformation required for imatinib binding, and the binding of VX-680, which favors the active conformation through hydrogen bonding and steric effects. VX-680 is bound to Abl in a mode that accommodates the substitution of isoleucine for threonine at residue 315 (the "gatekeeper" position). The avoidance of the innermost cavity of the Abl kinase domain by VX-680 and the specific recognition of the active conformation explain the effectiveness of this compound against mutant forms of BCR-Abl, including those with mutations at the gatekeeper position.

Introductory Lecture : Surface enhanced Raman spectroscopy: new materials, concepts, characterization tools, and applications

Surface-enhanced Raman spectroscopy (SERS) is currently experiencing a renaissance in its development driven by the remarkable discovery of single molecule SERS (SMSERS) and the explosion of interest in nanophotonics and plasmonics. Because excitation of the localized surface plasmon resonance (LSPR) of a nanostructured surface or nanoparticle lies at the heart of SERS, it is important to control all of the factors influencing the LSPR in order to maximize signal strength and ensure reproducibility. These factors include material, size, shape, interparticle spacing, and dielectric environment. All of these factors must be carefully controlled to ensure that the incident laser light maximally excites the LSPR in a reproducible manner. This article describes the use of nanosphere lithography for the fabrication of highly reproducible and robust SERS substrates for both fundamental studies and applications. Atomic layer deposition (ALD) is introduced as a novel fabrication method for dielectric spacers to study the SERS distance dependence and control the nanoscale dielectric environment. Wavelength scanned SER excitation spectroscopy (WS SERES) measurements show that enhancement factors approximately 10(8) are obtainable from NSL-fabricated surfaces and provide new insight into the electromagneticfield enhancement mechanism. Tip-enhanced Raman spectroscopy (TERS) is an extremely promising new development to improve the generality and information content of SERS. A 2D correlation analysis is applied to SMSERS data. Finally, the first in vivo SERS glucose sensing study is presented.

Wavelength-Scanned Surface-Enhanced Raman Excitation Spectroscopy

A detailed wavelength-scanned surface-enhanced Raman excitation spectroscopy (WS SERES) study of benzenethiol adsorbed on Ag nanoparticle arrays, fabricated by nanosphere lithography (NSL), is presented. These NSL-derived Ag nanoparticle array surfaces are both structurally well-characterized and extremely uniform in size. The WS SERES spectra are correlated, both spatially and spectrally, with the corresponding localized surface plasmon resonance (LSPR) spectra of the nanoparticle arrays. The surface-enhanced Raman scattering (SERS) spectra were measured in two excitation wavelength ranges: (1) 425-505 nm, and (2) 610-800 nm, as well as with the 532-nm line from a solid-state diode-pumped laser. The WS SERES spectra have line shapes similar to those of the LSPR spectra. The maximum SERS enhancement factor is shown to occur for excitation wavelengths that are blue-shifted with respect to the LSPR lambda(max) of adsorbate-covered nanoparticle arrays. Three vibrational modes of benzenethiol (1575, 1081, and 1009 cm(-1)) are studied simultaneously on one substrate, and it is demonstrated that the smaller Raman shifted peak shows a maximum enhancement closer to the LSPR lambda(max) than that of a larger Raman shifted peak. This is in agreement with the predictions of the electromagnetic (EM) enhancement mechanism of SERS. Enhancement factors of up to approximately 10(8) are achieved, which is also in good agreement with our previous SERES studies.

Rapid detection of an anthrax biomarker by surface-enhanced Raman spectroscopy

A rapid detection protocol suitable for use by first-responders to detect anthrax spores using a low-cost, battery-powered, portable Raman spectrometer has been developed. Bacillus subtilis spores, harmless simulants for Bacillus anthracis, were studied using surface-enhanced Raman spectroscopy (SERS) on silver film over nanosphere (AgFON) substrates. Calcium dipicolinate (CaDPA), a biomarker for bacillus spores, was efficiently extracted by sonication in nitric acid and rapidly detected by SERS. AgFON surfaces optimized for 750 nm laser excitation have been fabricated and characterized by UV-vis diffuse reflectance spectroscopy and SERS. The SERS signal from extracted CaDPA was measured over the spore concentration range of 10(-14)-10(-12) M to determine the saturation binding capacity of the AgFON surface and to calculate the adsorption constant (Kspore=1.7 x 10(13) M(-1)). At present, an 11 min procedure is capable of achieving a limit of detection (LOD) of approximately 2.6 x 10(3) spores, below the anthrax infectious dose of 10(4) spores. The data presented herein also demonstrate that the shelf life of prefabricated AgFON substrates can be as long as 40 days prior to use. Finally, these sensing capabilities have been successfully transitioned from a laboratory spectrometer to a field-portable instrument. Using this technology, 10(4) bacillus spores were detected with a 5 s data acquisition period on a 1 month old AgFON substrate. The speed and sensitivity of this SERS sensor indicate that this technology can be used as a viable option for the field analysis of potentially harmful environmental samples.

Eccentric decline squat protocol offers superior results at 12 months compared with traditional eccentric protocol for patellar tendinopathy in volleyball players

BACKGROUND

Conservative treatment of patellar tendinopathy has been minimally investigated. Effective validated treatment protocols are required.

OBJECTIVES

To investigate the immediate (12 weeks) and long term (12 months) efficacy of two eccentric exercise programmes for the treatment of patellar tendinopathy.

METHODS

This was a prospective randomised controlled trial of 17 elite volleyball players with clinically diagnosed and imaging confirmed patellar tendinopathy. Participants were randomly assigned to one of two treatment groups: a decline group and a step group. The decline group were required to perform single leg squats on a 25 degrees decline board, exercising into tendon pain and progressing their exercises with load. The step group performed single leg squats on a 10 cm step, exercising without tendon pain and progressing their exercises with speed then load. All participants completed a 12 week intervention programme during their preseason. Outcome measures used were the Victorian Institute of Sport Assessment (VISA) score for knee function and 100 mm visual analogue scale (VAS) for tendon pain with activity. Measures were taken throughout the intervention period and at 12 months.

RESULTS

Both groups had improved significantly from baseline at 12 weeks and 12 months. Analysis of the likelihood of a 20 point improvement in VISA score at 12 months revealed a greater likelihood of clinical improvements in the decline group than the step group. VAS scores at 12 months did not differ between the groups.

CONCLUSIONS

Both exercise protocols improved pain and sporting function in volleyball players over 12 months. This study indicates that the decline squat protocol offers greater clinical gains during a rehabilitation programme for patellar tendinopathy in athletes who continue to train and play with pain.

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

We describe herein a computationally intensive project aimed at carrying out molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide base sequences. This initiative was undertaken by an international collaborative effort involving nine research groups, the "Ascona B-DNA Consortium" (ABC). Calculations were carried out on the 136 cases imbedded in 39 DNA oligomers with repeating tetranucleotide sequences, capped on both ends by GC pairs and each having a total length of 15 nucleotide pairs. All MD simulations were carried out using a well-defined protocol, the AMBER suite of programs, and the parm94 force field. Phase I of the ABC project involves a total of approximately 0.6 mus of simulation for systems containing approximately 24,000 atoms. The resulting trajectories involve 600,000 coordinate sets and represent approximately 400 gigabytes of data. In this article, the research design, details of the simulation protocol, informatics issues, and the organization of the results into a web-accessible database are described. Preliminary results from 15-ns MD trajectories are presented for the d(CpG) step in its 10 unique sequence contexts, and issues of stability and convergence, the extent of quasiergodic problems, and the possibility of long-lived conformational substates are discussed.

Surface-enhanced Raman spectroscopy with a laser pointer light source and miniature spectrometer

The initial steps toward a miniature, field portable sensor based on surface-enhanced Raman spectroscopy (SERS) are presented. It is demonstrated that a low-cost miniaturized Raman system can be used in place of a larger, higher-cost conventional Raman system. This system was developed by sequentially replacing components of a laboratory scale Raman spectroscopy system with smaller, lower-cost, commercially available components. For example, a green laser pointer was used as the excitation source, a reflectance probe fiber-optic cable was used for laser delivery and collection, and a compact card-based spectrometer was used for dispersion and detection. Spectra, collected with the laser pointer Raman system, are presented of a resonant (Rhodamine 6G) and a non-resonant (trans-1,2-bis(4-pyridyl)ethylene) molecule as well as a self-assembled monolayer (1-decanethiol). Small, low-cost sensors are in demand for a variety of applications, and SERS is positioned to contribute significantly with its remarkable sensitivity and molecular specificity.Key words: Raman, SERS, fiber-optics, sensor.

Communication and information-giving in high-risk breast cancer consultations: influence on patient outcomes

This longitudinal study aimed to document (i) the information-giving and patient-communication styles of clinical geneticists and genetic counsellors (consultants) in familial breast cancer clinics and (ii) assess the effect of these styles on women's knowledge, whether their expectations were met, satisfaction, risk perception and psychological status. A total of 158 women from high-risk breast cancer families completed self-report questionnaires at 2 weeks preconsultation and 4 weeks postconsultation. The consultations were audiotaped, transcribed and coded. Multivariate logistic regressions showed that discussing prophylactic mastectomy (P=0.00) and oophorectomy (P=0.01) led to women having significantly more expectations met; discussing genetic testing significantly decreased anxiety (P=0.03) and facilitating understanding significantly decreased depression (P=0.05). Receiving a summary letter of the consultation significantly lowered anxiety (P=0.01) and significantly increased the accuracy of perceived risk (P=0.02). Women whose consultant used more supportive communications experienced significantly more anxiety about breast cancer at the 4 weeks follow-up (P=0.00). These women were not significantly more anxious before genetic counselling. In conclusion, this study found that consultants vary in the amount of information they give and the way they communicate; and this variation can result in better or worse psychosocial outcomes. Greater use of supportive and counselling communications appeared to increase anxiety about breast cancer. Identifying methods to assist consultants to address emotional issues effectively may be helpful.

A specific GFP expression assay, penetrance estimate, and histological assessment for a putative splice site mutation in BRCA1

Genetic testing for cancer predisposing mutations in BRCA1 and BRCA2 has been of benefit to many individuals from breast and ovarian cancer-prone kindreds. However, a function has not been assigned to many of the domains that make up these complex proteins and hence, the significance of many sequence variants, including missense mutations, splice-site mutations, and in-frame deletions/insertions, remains unclear. We identified a putative splice site mutation (IVS6-2delA) in BRCA1 in a family attending a Familial Cancer Centre that had a significant history of both breast and ovarian cancer. This sequence variant was not novel but the exact effect on mRNA splicing and hence the biological impact of this sequence variation was unclear and therefore the finding was unable to be used in genetic counseling of the family. Via the construction of novel GFP-based expression fusion constructs, we demonstrated that this sequence variation prevented normal splicing of the BRCA1 transcript. By combining these data with an assessment of the histopathological features of the breast carcinomas in this family and mutation penetrance estimate we were able to conclude that this BRCA1 variant conveyed an increased risk of breast cancer.

Structural basis for the autoinhibition of c-Abl tyrosine kinase

c-Abl is normally regulated by an autoinhibitory mechanism, the disruption of which leads to chronic myelogenous leukemia. The details of this mechanism have been elusive because c-Abl lacks a phosphotyrosine residue that triggers the assembly of the autoinhibited form of the closely related Src kinases by internally engaging the SH2 domain. Crystal structures of c-Abl show that the N-terminal myristoyl modification of c-Abl 1b binds to the kinase domain and induces conformational changes that allow the SH2 and SH3 domains to dock onto it. Autoinhibited c-Abl forms an assembly that is strikingly similar to that of inactive Src kinases but with specific differences that explain the differential ability of the drug STI-571/Gleevec/imatinib (STI-571) to inhibit the catalytic activity of Abl, but not that of c-Src.

Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants

To assess the accuracy of the molecular dynamics (MD) models of nucleic acids, a detailed comparison between MD-calculated and NMR-observed indices of the dynamical structure of DNA in solution has been carried out. The specific focus of our comparison is the oligonucleotide duplex, d(CGCGAATTCGCG)(2), for which considerable structural data have been obtained from crystallography and NMR spectroscopy. An MD model for the structure of d(CGCGAATTCGCG)(2) in solution, based on the AMBER force field, has been extended with a 14 ns trajectory. New NMR data for this sequence have been obtained in order to allow a detailed and critical comparison between the calculated and observed parameters. Observable two-dimensional (2D) nuclear Overhauser effect spectroscopy (NOESY) volumes and scalar coupling constants were back-calculated from the MD trajectory and compared with the corresponding NMR data. The comparison of these results indicate that the MD model is in generally good agreement with the NMR data, and shows closer accord with experiment than back-calculations based on the crystal structure of d(CGCGAATTCGCG)(2) or the canonical A or B forms of the sequence. The NMR parameters are not particularly sensitive to the known deficiency in the AMBER MD model, which is a tendency toward undertwisting of the double helix when the parm.94 force field is used. The MD results are also compared with a new determination of the solution structure of d(CGCGAATTCGCG)(2) using NMR dipolar coupling data.

Tailoring communication in consultations with women from high risk breast cancer families

This multicentre study examined the influence of patient demographic, disease status and psychological variables on clinical geneticists/genetic counsellors (consultants) behaviours in initial consultations with women from high-risk breast cancer families. One hundred and fifty-eight women completed a pre-clinic self-report questionnaire. The consultations were audiotaped, transcribed verbatim and coded. Consultants did not vary their behaviour according to women's expectations. However, significantly more aspects of genetic testing were discussed with women who were affected with breast cancer (P<0.001), screening and management with unaffected women (P=0.01) and breast cancer prevention with younger women (P=0.01). Prophylactic mastectomy was discussed more frequently with women with medical and allied health training (P=0.02), and prophylactic oophorectomy with women affected with breast cancer (P=0.03), those in non-professional occupations (P=0.04) and with a family history of breast and ovarian cancer (P<0.001). Consultants used significantly more behaviours to facilitate understanding with women who were in non-professional occupations (P=0.04); facilitated active patient involvement more with women affected with breast cancer (P<0.001) and used more supportive and counselling behaviours with affected women (P=0.02). This study showed that patient demographics were more likely to predict consultants' communication behaviours than the woman's psychological status. Methods to facilitate assessment of psychological morbidity are needed to allow more tailored communication.

Characterization of potent inhibitors of the Bcr-Abl and the c-kit receptor tyrosine kinases

The early stage of chronic myelogenous leukemia (CML) is caused by the tyrosine kinase Bcr-Abl. Imatinib mesylate (also known as STI-571 and Gleevec), a tyrosine kinase inhibitor, has shown encouraging results in CML clinical trials and has become a paradigm for targeted cancer therapeutics. Recent reports of resistance to imatinib argue for further development of therapies for CML. During studies of signal transduction, we observed that the pyrido[2,3-d]pyrimidine src tyrosine kinase inhibitor PD173955 inhibited Bcr-Abl-dependent cell growth. Subsequently, a related compound, PD180970, was reported as a potent inhibitor of Bcr-Abl. We have compared the potency of these two compounds and four other analogues with imatinib on Bcr-Abl-dependent cell growth, cytokine-dependent cell growth, and tyrosine kinase inhibition. PD173955 inhibited Bcr-Abl-dependent cell growth with an IC(50) of 2-35 nM in different cell lines. Fluorescence-activated cell-sorting analyses of cells treated with PD173955 showed cell cycle arrest in G(1). PD173955 has an IC(50) of 1-2 nM in kinase inhibition assays of Bcr-Abl, and in cellular growth assays it inhibits Bcr-Abl-dependent substrate tyrosine phosphorylation. Of the six pyrido[2,3-d]pyrimidine analogues studied, PD166326 was the most potent inhibitor of Bcr-Abl-dependent cell growth. PD173955 inhibited kit ligand-dependent c-kit autophosphorylation (IC(50) = approximately 25 nM) and kit ligand-dependent proliferation of M07e cells (IC(50) = 40 nM) but had a lesser effect on interleukin 3-dependent (IC(50) = 250 nM) or granulocyte macrophage colony-stimulating factor (IC(50) = 1 microM)-dependent cell growth. These compounds are potent inhibitors of both the Bcr-Abl and c-kit receptor tyrosine kinases and deserve further study as potential treatments for both CML and for diseases in which c-kit has a role.

Molecular dynamics simulation of nucleic acids: successes, limitations, and promise

In the last five years we have witnessed a significant increase in the number publications describing accurate and reliable all-atom molecular dynamics simulations of nucleic acids. This increase has been facilitated by the development of fast and efficient methods for treating the long-range electrostatic interactions, the availability of faster parallel computers, and the development of well-validated empirical molecular mechanical force fields. With these technologies, it has been demonstrated that simulation is not only capable of consistently reproducing experimental observations of sequence specific fine structure of DNA, but also can give detailed insight into prevalent problems in nucleic acid structure, ion association and specific hydration of nucleic acids, polyadenine tract bending, and the subtle environmental dependence of the A-DNA-B-DNA duplex equilibrium. Despite the advances, there are still issues with the methods that need to be resolved through rigorous controlled testing. In general, these relate to deficiencies of the underlying molecular mechanical potentials or applied methods (such as the imposition of true periodicity in Ewald simulations and the need for energy conservation), and significant limits in effective conformational sampling. In this perspective, we provide an overview of our experiences, provide some cautionary notes, and provide recommendations for further study in molecular dynamics simulation of nucleic acids.