Enhancing the Small-Scale Screenable Biological Space beyond Known Chemogenomics Libraries with Gray Chemical Matter─Compounds with Novel Mechanisms from High-Throughput Screening Profiles

Phenotypic assays have become an established approach to drug discovery. Greater disease relevance is often achieved through cellular models with increased complexity and more detailed readouts, such as gene expression or advanced imaging. However, the intricate nature and cost of these assays impose limitations on their screening capacity, often restricting screens to well-characterized small compound sets such as chemogenomics libraries. Here, we outline a cheminformatics approach to identify a small set of compounds with likely novel mechanisms of action (MoAs), expanding the MoA search space for throughput limited phenotypic assays. Our approach is based on mining existing large-scale, phenotypic high-throughput screening (HTS) data. It enables the identification of chemotypes that exhibit selectivity across multiple cell-based assays, which are characterized by persistent and broad structure activity relationships (SAR). We validate the effectiveness of our approach in broad cellular profiling assays (Cell Painting, DRUG-seq, and Promotor Signature Profiling) and chemical proteomics experiments. These experiments revealed that the compounds behave similarly to known chemogenetic libraries, but with a notable bias toward novel protein targets. To foster collaboration and advance research in this area, we have curated a public set of such compounds based on the PubChem BioAssay dataset and made it available for use by the scientific community.

TROPHY-U-01, a phase II open-label study of sacituzumab govitecan in patients with metastatic urothelial carcinoma progressing after platinum-based chemotherapy and checkpoint inhibitors: updated safety and efficacy outcomes

BACKGROUND

Sacituzumab govitecan (SG) is a Trop-2-directed antibody-drug conjugate containing cytotoxic SN-38, the active metabolite of irinotecan. SG received accelerated US Food and Drug Administration approval for locally advanced (LA) or metastatic urothelial carcinoma (mUC) previously treated with platinum-based chemotherapy and a checkpoint inhibitor, based on cohort 1 of the TROPHY-U-01 study. Mutations in the uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) gene are associated with increased adverse events (AEs) with irinotecan-based therapies. Whether UGT1A1 status could impact SG toxicity and efficacy remains unclear.

PATIENTS AND METHODS

TROPHY-U-01 (NCT03547973) is a multicohort, open-label, phase II registrational study. Cohort 1 includes patients with LA or mUC who progressed after platinum- and checkpoint inhibitor-based therapies. SG was administered at 10 mg/kg intravenously on days 1 and 8 of 21-day cycles. The primary endpoint was objective response rate (ORR) per central review; secondary endpoints included progression-free survival, overall survival, and safety. Post hoc safety analyses were exploratory with descriptive statistics. Updated analyses include longer follow-up.

RESULTS

Cohort 1 included 113 patients. At a median follow-up of 10.5 months, ORR was 28% (95% CI 20.2% to 37.6%). Median progression-free survival and overall survival were 5.4 months (95% CI 3.5-6.9 months) and 10.9 months (95% CI 8.9-13.8 months), respectively. Occurrence of grade ≥3 treatment-related AEs and treatment-related discontinuation were consistent with prior reports. UGT1A1 status was wildtype (∗1|∗1) in 40%, heterozygous (∗1|∗28) in 42%, homozygous (∗28|∗28) in 12%, and missing in 6% of patients. In patients with ∗1|∗1, ∗1|∗28, and ∗28|∗28 genotypes, any grade treatment-related AEs occurred in 93%, 94%, and 100% of patients, respectively, and were managed similarly regardless of UGT1A1 status.

CONCLUSIONS

With longer follow-up, the ORR remains high in patients with heavily pretreated LA or mUC. Safety data were consistent with the known SG toxicity profile. AE incidence varied across UGT1A1 subgroups; however, discontinuation rates remained relatively low for all groups.

Activation of human STING by a molecular glue-like compound

Stimulator of interferon genes (STING) is a dimeric transmembrane adapter protein that plays a key role in the human innate immune response to infection and has been therapeutically exploited for its antitumor activity. The activation of STING requires its high-order oligomerization, which could be induced by binding of the endogenous ligand, cGAMP, to the cytosolic ligand-binding domain. Here we report the discovery through functional screens of a class of compounds, named NVS-STGs, that activate human STING. Our cryo-EM structures show that NVS-STG2 induces the high-order oligomerization of human STING by binding to a pocket between the transmembrane domains of the neighboring STING dimers, effectively acting as a molecular glue. Our functional assays showed that NVS-STG2 could elicit potent STING-mediated immune responses in cells and antitumor activities in animal models.

Discovery and Structure-Based Design of Inhibitors of the WD Repeat-Containing Protein 5 (WDR5)-MYC Interaction

WDR5 is a critical chromatin cofactor of MYC. WDR5 interacts with MYC through the WBM pocket and is hypothesized to anchor MYC to chromatin through its WIN site. Blocking the interaction of WDR5 and MYC impairs the recruitment of MYC to its target genes and disrupts the oncogenic function of MYC in cancer development, thus providing a promising strategy for the treatment of MYC-dysregulated cancers. Here, we describe the discovery of novel WDR5 WBM pocket antagonists containing a 1-phenyl dihydropyridazinone 3-carboxamide core that was identified from high-throughput screening and subsequent structure-based design. The leading compounds showed sub-micromolar inhibition in the biochemical assay. Among them, compound 12 can disrupt WDR5-MYC interaction in cells and reduce MYC target gene expression. Our work provides useful probes to study WDR5-MYC interaction and its function in cancers, which can also be used as the starting point for further optimization toward drug-like small molecules.

Mechanism of Resistance to the WDR5 Inhibitor in MLL-Rearranged Leukemia

Drug resistance is a major problem often limiting the long-term effectiveness of targeted cancer therapeutics. Resistance can be acquired through mutations or amplification of the primary drug targets or activation of bypass signaling pathways. Considering the multifaceted function of WDR5 in human malignancies, WDR5 has emerged as an attractive drug target for the discovery of small-molecule inhibitors. In this study, we investigated if cancer cells might develop resistance to a highly potent WDR5 inhibitor. We established a drug-adapted cancer cell line and discovered that WDR5^P173L mutation occurs in the resistant cells, which confers resistance by preventing target engagement of the inhibitor. This work elucidated the WDR5 inhibitor's potential resistance mechanism in a preclinical study as a reference for future study in the clinical stage.

Discovery and characterization of a selective IKZF2 glue degrader for cancer immunotherapy

Malignant tumors can evade destruction by the immune system by attracting immune-suppressive regulatory T cells (Treg) cells. The IKZF2 (Helios) transcription factor plays a crucial role in maintaining function and stability of Treg cells, and IKZF2 deficiency reduces tumor growth in mice. Here we report the discovery of NVP-DKY709, a selective molecular glue degrader of IKZF2 that spares IKZF1/3. We describe the recruitment-guided medicinal chemistry campaign leading to NVP-DKY709 that redirected the degradation selectivity of cereblon (CRBN) binders from IKZF1 toward IKZF2. Selectivity of NVP-DKY709 for IKZF2 was rationalized by analyzing the DDB1:CRBN:NVP-DKY709:IKZF2(ZF2 or ZF2-3) ternary complex X-ray structures. Exposure to NVP-DKY709 reduced the suppressive activity of human Treg cells and rescued cytokine production in exhausted T-effector cells. In vivo, treatment with NVP-DKY709 delayed tumor growth in mice with a humanized immune system and enhanced immunization responses in cynomolgus monkeys. NVP-DKY709 is being investigated in the clinic as an immune-enhancing agent for cancer immunotherapy.

Discovery of Potent Small-Molecule Inhibitors of WDR5-MYC Interaction

WD repeat domain 5 (WDR5) is a member of the WD40-repeat protein family that plays a critical role in multiple processes. It is also a prominent target for pharmacological inhibition in diseases such as cancer, aging, and neurodegenerative disorders. Interactions between WDR5 and various partners are essential for sustaining its function. Most drug discovery efforts center on the WIN (WDR5 interaction motif) site of WDR5 that is responsible for the recruitment of WDR5 to chromatin. Here, we describe the discovery of novel WDR5 inhibitors for the other WBM (WDR5 binding motif) pocket on this scaffold protein, to disrupt WDR5 interaction with its binding partner MYC by high-throughput biochemical screening, subsequent molecule optimization, and biological assessment. These new WDR5 inhibitors provide useful probes for future investigations of WDR5 and an avenue for targeting WDR5 as a therapeutic strategy.

1022 Early Cholecystectomy in the Ageing Population

Background

The age group of patients presenting acutely with biliary pathology is rising and gallstone disease can no longer be said to be a disease of the young. The World Health Organisation classifies those aged 65 and over as elderly. Early cholecystectomy is accepted as a safe and effective method of managing acute biliary pathology, reducing further admissions, and reducing in-hospital stays. Our unit does not use age as barrier but uses performance status and co-morbidity to identify potential candidates for cholecystectomy.

Method

Patients over the age of 65 who underwent acute cholecystectomy (AC) via the emergency cholecystectomy lists, were audited from 31st December 2019 to 31st June 2021. Patient demographics, co-morbidities and surgical factors were recorded. The primary outcome measures were in-hospital stay and re-admission, secondary outcomes were complications and perioperative mortality.

Results

41 elderly patients underwent AC during the audit period, (Female 56%, Male 44%). 30 patients had acute cholecystitis (73%). The median inpatient stay following surgery was 2 days (range 2–5 days) and the median admission to surgery time was 6 days (range 5–12 days). Three patients had a subtotal cholecystectomy. There were 3 complications from surgery which were all between a Clavien-Dindo score of 2 and 3. There were 3 immediate post-operative readmissions, with one 30-day mortality from ERCP pancreatitis and not from the operation.

Conclusion

Early cholecystectomy appears to be a safe and effective treatment for this group of patients and based on this evidence we should continue to offer this treatment to patients irrespective of age.

Phenotypic screen identifies calcineurin-sparing FK506 analogs as BMP potentiators for treatment of acute kidney injury

Acute kidney injury (AKI) is a life-threatening disease with no known curative or preventive therapies. Data from multiple animal models and human studies have linked dysregulation of bone morphogenetic protein (BMP) signaling to AKI. Small molecules that potentiate endogenous BMP signaling should have a beneficial effect in AKI. We performed a high-throughput phenotypic screen and identified a series of FK506 analogs that act as potent BMP potentiators by sequestering FKBP12 from BMP type I receptors. We further showed that calcineurin inhibition was not required for this activity. We identified a calcineurin-sparing FK506 analog oxtFK through late-stage functionalization and structure-guided design. OxtFK demonstrated an improved safety profile in vivo relative to FK506. OxtFK stimulated BMP signaling in vitro and in vivo and protected the kidneys in an AKI mouse model, making it a promising candidate for future development as a first-in-class therapeutic for diseases with dysregulated BMP signaling.

Using opportunistic screening with abdominal CT to identify osteoporosis and osteopenia in patients with diabetes

Opportunistic osteoporosis screening involves measuring the attenuation of L1 vertebrae on abdominal computed tomography (CT), which correlates with DXA T-score. We found that this approach is useful for detecting low bone mass in patients with diabetes and propose L1 attenuation ≤ 135 Hounsfield units (HU) as a threshold for which DXA should be strongly considered.

INTRODUCTION

Attenuation of the L1 vertebrae on computer tomography (CT) images done for other reasons ("Opportunistic Osteoporosis Screening") has been found to correlate well with DXA-derived T-score. However, the method and the thresholds have never been tested specifically in those with diabetes mellitus (DM), in whom the fracture risk is greater than explained by BMD.

METHODS

In a retrospective study of subjects with DM who had both abdominal CT and DXA within 6 months of each other, we compared L1 attenuation and DXA T-score to define the sensitivity and specificity of thresholds previously established in the general population.

RESULTS

There were 313 subjects among whom 18 (5.8%) had prior major osteoporotic fracture (MOF). Subjects with MOF had lower T-scores (- 2.3 ± 1.4 vs. - 0.9 ± 1.4, p < 0.001) and L1 attenuation (104 HU ± 46 vs. 149 HU ± 47, p < 0.001) than non-fracture subjects. L1 attenuation ≤ 160 HU was 91% sensitive for osteoporosis, while ≤ 110 HU was 80% specific. For a higher T-score of ≤ - 1.5, L1 attenuation ≤ 135 HU showed balanced sensitivity and specificity (65% and 69%, respectively).

CONCLUSION

Opportunistic osteoporosis screening with abdominal CT is useful in determining the need for DXA screening in subjects with diabetes. We propose L1 attenuation ≤ 135 HU as a reasonable threshold for detecting the T-score of ≤ - 1.5, which is likely associated with increased fragility in DM.

Fiber-based sources of coherent MIR radiation: key advances and future prospects (invited)

The mid-infrared (MIR) represents a large portion of the electromagnetic spectrum that is progressively being exploited for an enormous number of applications. Thermal imaging cameras, dental and skin resurfacing lasers, and narcotics detectors at airports are all mainstream examples involving the MIR, but potential applications of MIR technologies are much larger. Accessing the unique opportunities afforded by the MIR is critically dependent on the specific characteristics of MIR emitting sources that become available. In this review, we survey an important enabling technology to the opening up of MIR science and applications, namely that driven by fiber-based sources of coherent MIR radiation. In this review paper, we describe many of the key advances in the innovation and development of such sources over the past few decades and discuss many of the underlying science and technology issues that have resulted in specific recent source achievements, especially in light of new applications enabled by these new source capabilities. We also discuss a few specific anticipated future needs and some potentially disruptive approaches to future MIR fiber source development.

Spectral trimming technique: a new approach for suppressing motion artefacts in stress electrocardiography

Motion artefacts in electrocardiographic (ECG) signal are suppressed mainly by adaptive noise cancellation and wavelet denoising. While the former requires a motion sensor in addition to ECG electrodes, the latter removes some of the desired low-frequency components in the signal. In this paper spectral trimming technique is being introduced for suppressing the motion artefacts in stress electrocardiography. In this method, Fourier spectral coefficients up to 1.221 Hz of noisy signal are trimmed on the basis of template derived from resting ECG signal in the same subject. The proposed spectral trimming technique has yielded the lowest value of mean ± standard deviation for root mean square error (18.92 ± 8.71) and highest value of the signal to noise ratio (6.439 ± 4.266) as compared to other three methods, namely adaptive noise cancellation, wavelet decomposition and adaptive line enhancement with compatible value of correlation coefficient. Subsequently, spectral trimming technique has been implemented in real-time (deferred by 8.2 s) application for stress electrocardiography. Spectral trimming technique thus offers a method of choice for motion artefact suppression in offline as well as deferred online applications. This method takes care of the limitations of conventional methods such as adaptive noise cancellation or wavelet denoising for suppressing motion artefacts in stress electrocardiography.

Systematic Chemogenetic Library Assembly

Chemogenetic libraries, collections of well-defined chemical probes, provide tremendous value to biomedical research but require substantial effort to ensure diversity as well as quality of the contents. We have assembled a chemogenetic library by data mining and crowdsourcing institutional expertise. We are sharing our approach, lessons learned, and disclosing our current collection of 4,185 compounds with their primary annotated gene targets (https://github.com/Novartis/MoaBox). This physical collection is regularly updated and used broadly both within Novartis and in collaboration with external partners.

Luminescent ion-doped transparent glass ceramics for mid-infrared light sources [invited]

Glass ceramics (GCs), which consist essentially of a homogeneous solid state dispersion of nanocrystals (NCs) embedded in a chemically inert and mechanically robust glass matrix, appear to be an extremely promising class of solid state materials that can be easily tailored into arbitrary shapes, including a new generation of optical fibers, for efficient incoherent and coherent sources of mid-infrared (MIR) light emission. This unique capability not only stems from the fact that one can tailor the underlying glass matrix for optimal macroscopic physical properties and ultrahigh transparency at the wavelengths of interest (resulting in appropriate "transparent glass ceramics" or TGCs), but also stems from the fact that one can embed these matrices with size and structure-tailored NCs, which in turn can be doped with relatively high concentrations of MIR emitting rare-earth or transition metal ions. This potential is tantamount to the localization of these highly efficient MIR ionic emitters into carefully selected and highly favorable "process-engineered" custom crystalline host "nanocages," while insulating the ionic emitters from the emission-quenching glass host matrix, the latter being chosen largely because of its highly favorable macroscopic bulk properties, including its ductility and formability into near-arbitrary shapes (at appropriate temperatures). Such MIR TGCs appear to be very promising for numerous photonics applications, including compact and relatively efficient waveguide sensors, broadband incoherent MIR light sources, superluminescent light sources, advanced fiber-optic devices, and broadly wavelength-tunable and ultrashort pulse mode-locked fiber and bulk solid-state lasers. In this paper, we review past achievements in this field, starting with an overview of TGCs, followed by discussions of currently preferred methods of fabrication, characterization, and optimization of suitably doped oxyfluoride, tellurite, and chalcogenide TGCs and of our projections of anticipated future developments in this field at both the materials and device levels.

Seed transmission of a distinct soybean yellow mottle mosaic virus strain identified from India in natural and experimental hosts

Soybean yellow mottle mosaic virus (SYMMV) is a newly identified member of the genus Gammacarmovirus from grain legumes in India. As the modes of transmission of this virus have not been described, we assessed the possibility of SYMMV to be transmitted through seed collected from field infected mungbean plants and mechanically sap inoculated French bean plants using serological and molecular techniques followed by progeny assays. Direct antigen coated enzyme linked immunosorbent assay (DAC-ELISA) and reverse transcription polymerase chain reaction (RT-PCR) results are inconsistent with field infected mungbean seed tissues to ensure seed transmissibility irrespective of seed number used. Seed from mechanical sap inoculated French bean showed higher absorbance values in DAC-ELISA and amplification corresponding to replicase, movement and coat protein regions of SYMMV genome. The relative accumulation of SYMMV was higher in pod walls, immature seed and stamens and stigma of mechanical sap inoculated French bean. Progeny assays with infected seed revealed the seed transmissibility of SYMMV at the rate of 63.33% in mungbeanand 73.33% in French bean. Mechanical sap inoculation of mungbean progeny seedlings on French bean cv. Pusa Parvati produced characteristic symptoms of SYMMV. The results obtained from this study demonstrate that SYMMV is seed borne in nature and can be transmitted to next generation seedlings. This is the first report of seed transmission of SYMMV in mungbean and French bean.

Previously Uncharacterized Vacuolar-type ATPase Binding Site Discovered from Structurally Similar Compounds with Distinct Mechanisms of Action

Using a comprehensive chemical genetics approach, we identified a member of the lignan natural product family, HTP-013, which exhibited significant cytotoxicity across various cancer cell lines. Correlation of compound activity across a panel of reporter gene assays suggested the vacuolar-type ATPase (v-ATPase) as a potential target for this compound. Additional cellular studies and a yeast haploinsufficiency screen strongly supported this finding. Competitive photoaffinity labeling experiments demonstrated that the ATP6V0A2 subunit of the v-ATPase complex binds directly to HTP-013, and further mutagenesis library screening identified resistance-conferring mutations in ATP6V0A2. The positions of these mutations suggest the molecule binds a novel pocket within the domain of the v-ATPase complex responsible for proton translocation. While other mechanisms of v-ATPase regulation have been described, such as dissociation of the complex or inhibition by natural products including bafilomycin A1 and concanamycin, this work provides detailed insight into a distinct binding pocket within the v-ATPase complex.

Discovery of a ZIP7 inhibitor from a Notch pathway screen

The identification of activating mutations in NOTCH1 in 50% of T cell acute lymphoblastic leukemia has generated interest in elucidating how these mutations contribute to oncogenic transformation and in targeting the pathway. A phenotypic screen identified compounds that interfere with trafficking of Notch and induce apoptosis via an endoplasmic reticulum (ER) stress mechanism. Target identification approaches revealed a role for SLC39A7 (ZIP7), a zinc transport family member, in governing Notch trafficking and signaling. Generation and sequencing of a compound-resistant cell line identified a V430E mutation in ZIP7 that confers transferable resistance to the compound NVS-ZP7-4. NVS-ZP7-4 altered zinc in the ER, and an analog of the compound photoaffinity labeled ZIP7 in cells, suggesting a direct interaction between the compound and ZIP7. NVS-ZP7-4 is the first reported chemical tool to probe the impact of modulating ER zinc levels and investigate ZIP7 as a novel druggable node in the Notch pathway.

Association of trabecular bone score (TBS) and prior fracture differs among minorities in NHANES 2005-2008

The study investigates the association of trabecular bone score (TBS) and fractures among minority populations. In NHANES 2005-2008, TBS was associated with history of fractures in Caucasian subjects but demonstrated somewhat weaker associations in African American and Mexican American women.

INTRODUCTION

Trabecular bone score (TBS), a textural analysis of the lumbar spine DXA image, predicts fractures well in Caucasian (CA) and Asian populations but is less well studied in African American (AA) and Mexican American (MA) subjects. It is not clear whether TBS is associated with or is predictive of fragility in these racial/ethnic groups.

METHODS

We analyzed data from subjects from NHANES 2005-2008 over the age of 40 who had TBS: 1178 CA, 467 AA, and 397 MA women and 1200 CA, 502 AA, and 386 MA men. TBS was categorized into normal, ≥ 1.310, partially degraded < 1.310, and > 1.230, or degraded, ≤ 1.230. History of fracture was assessed by questionnaire.

RESULTS

Among women, there was an increasing prevalence of fracture with worsening TBS category. However, when controlling for age, BMI, and low T-score, the association between TBS category and previous fracture was only significant in CA women (OR 1.49 per worsening category, 95% CI 1.20-1.85). In men, there was also an increase in the prevalence of fracture with worsening TBS category in all races/ethnicities. When controlling for age, BMI, and low T-score, the association between TBS category and previous fracture was only significant in CA men (OR 1.47 per worsening category, 95% CI 1.10-1.95), though analysis was somewhat limited by small fracture numbers.

CONCLUSIONS

The association of fracture and TBS varies by race/ethnicity and gender with weaker association observed in AA and MA women. More research is needed to define the proper use of TBS for predicting fractures in minority groups.

Pharmacological Reperfusion Therapy with Tenecteplase in 7,668 Indian Patients with ST Elevation Myocardial Infarction - A Real World Indian Experience

OBJECTIVE

This real-world, observational, prescription event monitoring study was conducted to evaluate safety and efficacy of indigenous tenecteplase (TNK-tPA) in Indian patients presenting with ST elevation myocardial infarction (STEMI).

METHODS

This is a multi-centric, observational, prescription event monitoring study. Data was collected for 7,668 patients from 1,307 investigator sites across India from January 2011 to February 2016.

RESULTS

Overall, 76.71% patients were hypertensive, 47.97% patients were diabetic, 42.01% had dyslipidemia, 24.35% had ischemic heart disease and 40.82% patients were smokers. The overall rate for achieving clinically successful thrombolysis by TNK was 93.34%. Delayed administration of tenecteplase yielded lower success rate (84.66%) as against those patients who received tenecteplase within 3 hours of symptoms (94.34%). 93.2% patients had chest pain resolution after pharmacological fibrinolysis. Overall 91.1% patients had 50% resolution of ST elevation at 90 minutes and mean time for 50% ST resolution was 72.06 minutes. Overall 53 patients died (mortality of 0.69%) before discharge. The incidence of bleeding (excluding stroke) was 1.77%, any stroke without ICH was 0.18% and any ICH was 0.38%.

CONCLUSION

The findings of this study further reinforce the safety and efficacy of indigenous TNK-tPA in Indian patients presenting with STEMI, including high-risk sub-groups. The study also highlights the importance of early reperfusion therapy.

Induction of cell death by tospoviral protein NSs and the motif critical for cell death does not control RNA silencing suppression activity

Groundnut bud necrosis virus induces necrotic symptoms in different hosts. Previous studies showed reactive oxygen species-mediated programmed cell death (PCD) resulted in necrotic symptoms. Transgenic expression of viral protein NSs mimics viral symptoms. Here, we showed a role for NSs in influencing oxidative burst in the cell, by analyzing H2O2 accumulation, activities of antioxidant enzymes and expression levels of vacuolar processing enzymes, H2O2-responsive microRNA 319a.2 plus its possible target metacaspase-8. The role of NSs in PCD, was shown using two NSs mutants: one in the Trp/GH3 motif (a homologue of pro-apototic domain) (NSsS189R) and the other in a non-Trp/GH3 motif (NSsL172R). Tobacco rattle virus (TRV) expressing NSsS189R enhanced the PCD response, but not TRV-NSsL172R, while RNA silencing suppression activity was lost in TRV-NSsL172R, but not in TRV-NSsS189R. Therefore, we propose dual roles of NSs in RNA silencing suppression and induction of cell death, controlled by different motifs.

Examining the influence of specificity ligands and ATP-competitive ligands on the overall effectiveness of bivalent kinase inhibitors

Background

Identifying selective kinase inhibitors remains a major challenge. The design of bivalent inhibitors provides a rational strategy for accessing potent and selective inhibitors. While bivalent kinase inhibitors have been successfully designed, no comprehensive assessment of affinity and selectivity for a series of bivalent inhibitors has been performed. Here, we present an evaluation of the structure activity relationship for bivalent kinase inhibitors targeting ABL1.

Methods

Various SNAPtag constructs bearing different specificity ligands were expressed in vitro. Bivalent inhibitor formation was accomplished by synthesizing individual ATP-competitive kinase inhibitors containing a SNAPtag targeting moiety, enabling the spontaneous self-assembly of the bivalent inhibitor. Assembled bivalent inhibitors were incubated with K562 lysates, and then subjected to affinity enrichment using various ATP-competitive inhibitors immobilized to sepharose beads. Resulting eluents were analyzed using Tandem Mass Tag (TMT) labeling and two-dimensional liquid chromatography-tandem mass spectrometry (2D–LC-MS/MS). Relative binding affinity of the bivalent inhibitor was determined by calculating the concentration at which 50% of a given kinase remained bound to the affinity matrix.

Results

The profiling of three parental ATP-competitive inhibitors and nine SNAPtag conjugates led to the identification of 349 kinase proteins. In all cases, the bivalent inhibitors exhibited enhanced binding affinity and selectivity for ABL1 when compared to the parental compound conjugated to SNAPtag alone. While the rank order of binding affinity could be predicted by considering the binding affinities of the individual specificity ligands, the resulting affinity of the assembled bivalent inhibitor was not predictable. The results from this study suggest that as the potency of the ATP-competitive ligand increases, the contribution of the specificity ligand towards the overall binding affinity of the bivalent inhibitor decreases. However, the affinity of the specificity components in its interaction with the target is essential for achieving selectivity.

Conclusion

Through comprehensive chemical proteomic profiling, this work provides the first insight into the influence of ATP-competitive and specificity ligands binding to their intended target on a proteome-wide scale. The resulting data suggest a subtle interplay between the ATP-competitive and specificity ligands that cannot be accounted for by considering the specificity or affinity of the individual components alone.

Electronic supplementary material

The online version of this article (doi:10.1186/s12953-017-0125-1) contains supplementary material, which is available to authorized users.

First record of Pepper cryptic virus 2 in chilli (Capsicum annuum) in India

The occurrence of Pepper cryptic virus 2 was confirmed by RT-PCR and partial sequencing of coat protein gene in chilli cultivars Jwalamukhi and Jwalasakhi grown in the experimental farm at IARI, New Delhi. To the best of our knowledge this is the first report of occurrence of cryptovirus in chilli in India.

Functional Outcome of Bipolar Prosthesis versus Total Hip Replacement in the Treatment of Femoral Neck Fracture in Elderly Patients

Introduction

The present study was performed to compare cemented total hip replacement (THR) with cemented bipolar prosthesis in the treatment of displaced fracture neck of femur in elderly patients.

Materials and Methods

This prospective study included 47 patients of greater than 60 years of age and having fracture of neck of femur, out of which 25 patients were managed by cemented bipolar prosthesis and remaining 22 were managed by cemented THR between June 2011 and June 2013. These patients were followed up post-operatively for two years, at 6, 12 and 24 months, for functional analysis using Modified Harris Hip Score.

Results

Modified Harris Hip Score was significantly higher in the THR group as compared to the bipolar prosthesis group at 6, 12 and 24 months post-operatively. Pain was almost similar in both the groups at all follow-up periods. Gait and range of motion was significantly higher in THR group as compared to bipolar prosthesis group at all-time point intervals.

Conclusion

Cemented THR is a better option as compared to cemented bipolar prosthesis based on our short term functional outcome for the management of fracture of neck of femur in elderly patients.

African Americans have lower TBS than whites among densitometry patients at a Chicago academic center

Trabecular bone score, an indirect measure of bone structure, may differ between ethnicities. We found that African Americans had lower trabecular bone score than do whites referred for densitometry, even when controlling for age and abdominal soft tissue thickness.

PURPOSE

Trabecular bone score (TBS), an indirect measure of bone structure, has been shown to predict fractures in predominantly white populations. Analysis of NHANES data revealed lower TBS in African Americans than in whites. However, it is not clear if this is true in patients referred for densitometry (where fracture risk stratification is most pertinent) or if ethnic differences in TBS may be related to differences in abdominal soft tissue (tissue thickness), which was not controlled for in the NHANES study.

METHODS

We retrospectively analyzed all BMD scans obtained at a university hospital in Chicago between 2011 and 2016.

RESULTS

There were 3187 women (51 % African American) and 675 men (32 % African American). African American women were older (69.6 ± 10.4 vs. 64.8 ± 1.3) and heavier (BMI 28.3 ± 4.7 vs. 25.4 ± 4.5) than whites were, while men were of similar age and BMI. African American women had higher T-scores at all sites (the lowest of T-scores, termed LowT, -1.5 ± 1.2 vs. -1.9 ± 1.0, p < 0.001) but lower TBS than white women even when adjusting for age and tissue thickness (1.231 ± 0.130 versus 1.251 ± 0.130, p < 0.001). While LowT was higher in African American men (-1.1 ± 1.2 vs. -1.5 ± 1.4, p < 0.001), TBS was lower than in white men even after adjusting for age and tissue thickness (1.232 ± 0.144 vs. 1.275 ± 0.144, p < 0.001).

CONCLUSIONS

African Americans had lower TBS than whites did, even with adjustment for age and tissue thickness. Ethnic differences in TBS should be considered when assessing fracture risk in clinical practice.

A Photoaffinity Labeling-Based Chemoproteomics Strategy for Unbiased Target Deconvolution of Small Molecule Drug Candidates

The combination of photoaffinity labeling (PAL) and quantitative chemoproteomics enables the comprehensive, unbiased determination of protein interaction profiles to support target identification of bioactive small molecules. This approach is amenable to cells in culture and compatible with pharmacologically relevant transmembrane target classes like G-protein coupled receptors and ions channels which have been notoriously hard to access by conventional chemoproteomics approaches. Here, we describe a strategy that combines PAL probe titration and competition with excess parental compounds with the goal of enabling the identification of specific interactors as well as assessing the functional relevance of a binding event for the phenotype under investigation.