Structure based designing of thiazolidinone-pyrimidine derivatives as ERK2 inhibitors: Synthesis and in vitro evaluation

Breast cancer has been associated with an overexpression of various molecular targets; accordingly, various target-specific chemotherapeutic agents have been developed. Inhibition of ERK2, a member of MAPK pathway, is an important target involved in the treatment of both oestrogen receptor-positive and triple-negative breast cancer. Thus, in continuation of our previous work on the ERK2 target, we here report novel inhibitors of this kinase. Out of three lead molecules reported in our previous study, we selected the thiazolidinone-pyrimidine scaffold for further development of small molecule inhibitors of ERK2. Analogues of the lead molecule were docked in the target kinase, followed by molecular dynamic simulations and MM-GBSA calculations. Analogues maintaining key interactions with amino acid residues in the ATP-binding domain of ERK2 were selected and duly synthesized. In vitro biochemical evaluation of these molecules against ERK2 kinase disclosed that two molecules possess significant kinase inhibitory potential with IC₅₀ values ≤ 0.5 µM.

Exploring RdRp-remdesivir interactions to screen RdRp inhibitors for the management of novel coronavirus 2019-nCoV

A novel coronavirus recently identified in Wuhan, China (2019-nCoV) has resulted in an increasing number of patients globally, and has become a highly lethal pathogenic member of the coronavirus family affecting humans. 2019-nCoV has established itself as one of the most threatening pandemics that human beings have faced, and therefore analysis and evaluation of all possible responses against infection is required. One such strategy includes utilizing the knowledge gained from the SARS and MERS outbreaks regarding existing antivirals. Indicating a potential for success, one of the drugs, remdesivir, under repurposing studies, has shown positive results in initial clinical studies. Therefore, in the current work, the authors have attempted to utilize the remdesivir-RdRp complex - RdRp (RNA-dependent RNA polymerase) being the putative target for remdesivir - to screen a library of the already reported RdRp inhibitor database. Further clustering on the basis of structural features and scoring refinement was performed to filter out false positive hits. Finally, molecular dynamics simulation was carried out to validate the identification of hits as RdRp inhibitors against novel coronavirus 2019-nCoV. The results yielded two putative hits which can inhibit RdRp with better potency than remdesivir, subject to further biological evaluation.

Overexpression of BLM promotes DNA damage and increased sensitivity to platinum salts in triple-negative breast and serous ovarian cancers

Background

Platinum-based therapy is an effective treatment for a subset of triple-negative breast cancer and ovarian cancer patients. In order to increase response rate and decrease unnecessary use, robust biomarkers that predict response to therapy are needed.

Patients and methods

We performed an integrated genomic approach combining differential analysis of gene expression and DNA copy number in sensitive compared with resistant triple-negative breast cancers in two independent neoadjuvant cisplatin-treated cohorts. Functional relevance of significant hits was investigated in vitro by overexpression, knockdown and targeted inhibitor treatment.

Results

We identified two genes, the Bloom helicase (BLM) and Fanconi anemia complementation group I (FANCI), that have both increased DNA copy number and gene expression in the platinum-sensitive cases. Increased level of expression of these two genes was also associated with platinum but not with taxane response in ovarian cancer. As a functional validation, we found that overexpression of BLM promotes DNA damage and induces sensitivity to cisplatin but has no effect on paclitaxel sensitivity.

Conclusions

A biomarker based on the expression levels of the BLM and FANCI genes is a potential predictor of platinum sensitivity in triple-negative breast cancer and ovarian cancer.

Abstract P5-06-04: Distinct BRCA1 and BRCA2 specific functions at stalled replication forks - Clinical implications for differences between BRCA1 and BRCA2 mutation driven cancer

This abstract was withdrawn by the authors.

Review of spectrum and sensitivity of bacterial bloodstream isolates in children with malignancy: A retrospective analysis from a single center

BACKGROUND

Febrile neutropenia is a life-threatening emergency in pediatric cancer patients. Its management is based on established guidelines that emphasize on prompt action. Consideration of local microbiologic spectrum and its susceptibility is pivotal in devising a rational protocol.

AIMS

To study the spectrum of bacterial isolates and its antibiotic sensitivity profile in bloodstream infections (BSIs) of pediatric cancer patients.

SETTINGS AND DESIGN

Retrospective study.

MATERIALS AND METHODS

This study was conducted at a tertiary cancer center for pediatric cancer patients. Blood culture samples sent during the evaluation of patients with clinical diagnosis of febrile neutropenia during the year of 2013 were analyzed. The microbiological and antibiotic sensitivity patterns were studied.

RESULTS

A total of 27 isolates represented BSIs out of 412 blood cultures sent (6.5%). These were predominantly Gram-negative (92%) with Klebsiella contributing to the majority of them. Extended spectrum beta-lactamase production was seen in 59% of all isolates. Multidrug resistance phenotype was seen in 48%, extreme drug resistance in 32% and pan drug resistance in 16% of Gram-negative isolates. Klebsiella predominated in all of these isolates. Mortality resulted in 15% isolates, majorly contributed by Klebsiella. Colistin was the most sensitive antibiotic (75% sensitivity) and in significant number of cases the only salvage option.

CONCLUSION

Gram-negative bacteria are the most common etiologic agents. The emergence of drug resistant strains of Klebsiella and the poor sensitivity of most of these strains to common first choice empiric agents is alarming. Low prevalence of Gram-positive organisms questions the routine use of empiric vancomycin.

Hypoalbuminaemia is an independent predictor of poor outcome in metastatic Ewing's sarcoma family of tumours: a single institutional experience of 150 cases treated with uniform chemotherapy protocol

AIMS

Data on metastatic Ewing's sarcoma family of tumours (ESFT) with uniform chemotherapy protocol are minimal.

MATERIALS AND METHODS

This was a single institutional patient review of patients treated between June 2003 and November 2011 and evaluated on an intent-to-treat analysis. All patients received uniform chemotherapy: neoadjuvant chemotherapy (NACT), surgery and/or radiotherapy as local treatment followed by adjuvant chemotherapy. Local treatment was offered if the patient achieved a complete response and/or a partial response at both the primary and the metastatic site.

RESULTS

In total, 150/374 (40%) ESFT patients were metastatic, with a median age of 15 years (range: 2-50); a tumour diameter of 10 cm (range: 1.8-26). Most common metastatic sites were lung only (53; 35%), bone only (35; 23%) and combined bone/lung (25; 17%). Twenty patients underwent surgery; 55 patients received radical radiotherapy after NACT. After a median follow-up of 26.1 months (range: 1.6-101.6), 5 year event-free survival (EFS), overall survival and local control rate (LCR) were 9.1 ± 3.3%, 16.9 ± 5.2% and 31.8 ± 7.9%, respectively. Univariate analysis showed serum albumin ≤3.4 g/dl (P < 0.001) to predict inferior EFS. Tumour size >8 cm (P = 0.05), haemoglobin ≤10 g/dl (P = 0.04), hypoalbuminaemia (P = 0.003) and radical radiotherapy as local treatment (P = 0.03) predicted inferior overall survival. No factor significantly predicted LCR, although age ≤15 years (P = 0.08) and radical radiotherapy as local treatment (P = 0.09) had a trend towards inferior LCR. Hypoalbuminaemia was the only prognostic factor to predict EFS on multivariate analysis.

CONCLUSION

This was the largest study of metastatic ESFT from Asia and identified a unique prognostic factor. In view of dismal prognosis with conventional chemotherapy in metastatic ESFT with hypoalbuminaemia, palliative intent therapy may be a potential therapeutic alternative for this subgroup of patients, especially in resource-challenged situations.

Abstract P4-10-01: Edgetic perturbation of BRCT-mediated interactions caused by the BRCA1 H1686Q sequence variant

Background: The ever-increasing number of variants of uncertain significance (VUS) that result from BRCA1/BRCA2 genetic testing poses a challenge to healthcare providers, thus impacting clinical decision-making. Though a quantitative posterior probability model, mostly reliant on genetic data, has been developed to estimate the clinical relevance of individual VUS, indirect evidence derived from functional tests continues to be a sought-after adjunct to achieve VUS categorization. Using a multimodal approach, we previously demonstrated the deleterious effect on protein localization and function of the Italian founder sequence alteration BRCA1 V1688del, and the neutral effect of a neighboring variant, BRCA1 V1687I, identified in a patient with early onset triple negative breast cancer. Disease-causality has been suggested for the adjacent BRCA1 H1686Q variant that occurs in the evolutionarily conserved THV motif of the first BRCT repeat and was described in a breast/ovarian cancer family (Giannini et al., 2008). We aimed at substantiating the predicted pathogenicity of BRCA1 H1686Q by assessing its biological significance.

Methods: To investigate the structural and functional consequences of the BRCA1 H1686Q sequence alteration, we used a strategy that combined homology modeling with analysis of protein interactions (by immunoprecipitation and GST pull down techniques) and function (by a homologous recombination assay).

Results: The three-dimensional model of the BRCA1 H1686Q BRCT domain suggested that the site and nature of the amino acid change could alter the interaction and relative orientation of secondary structure elements in the core region of the protein, thus possibly affecting the overall stability of the protein and triggering a long-range allosteric effect with repercussions on residues involved in phosphopeptide binding. Indeed, in transfected 293T cells, the recombinant BRCA1 H1686Q protein was less abundant than its wild-type counterpart. Moreover, while efficiently heterodimerizing, via its N-terminus, with the binding partner BARD1, the BRCA1 H1686Q protein displayed a peculiar behavior with regards to C-terminal, BRCT-mediated interactions as it bound BRIP1/FANCJ and not CtIP. These results, repeatedly observed in different cell lines, were confirmed by reciprocal immunoprecipitations as well as by GST pull down experiments using a recombinant BRCA1 H1686Q BRCT domain. Notably, the BRCA1 H1686Q protein displayed a homologous recombination defect similar to that observed for the clinically ascertained BRCA1 M1775R mutant protein.

Conclusions: Our data suggest that the BRCA1 H1686Q variant, by affecting the BRCT ligand recognition ability, causes an edgetic perturbation (i.e. selective disruption/retention) of BRCT-mediated interactions, which is yet sufficient to impair the homologous recombination function of the encoded protein. These findings provide valuable structure/function insights that could help elucidate the link between BRCA1 DNA repair and tumor suppression functions and aid development of functional tests for VUS screening and classification.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-10-01.

Preliminary assessment of binary ethylenimine inactivated and saponized cutaneous warts (BPV-2) therapeutic vaccine for enzootic bovine haematuria in hill cows

A preliminary therapeutic vaccine trial was conducted in hill cows to evaluate the therapeutic potential of binary ethylenimine (BEI) inactivated and saponized bovine papillomavirus-2 (BPV-2) for enzootic bovine haematuria (EBH). Although the vaccine failed to show favorable clinical vaccine results in treatment of EBH affected cows at 120 days post-vaccination but immunopathological responses were encouraging. A significant difference was observed in humoral (against Brucella abortus strain 19S) and cell-mediated (in vivo phytohaemagglutination delayed type hypersensitivity (PHA DTH) test and CD4+/CD8+ T-cells ratio by FACS analysis) immune responses following vaccination. The vaccinated animals grossly failed to show regression of bladder tumours but microscopically engorgement and marked perivascular infiltration of mononuclear cells was observed which are indicative of the induction of initial stages of tumour regression. Overall results indicated that the therapeutic vaccine developed can have potentials for treating EBH in cows, for which further modifications in vaccine dose and field trial is required.

BRCA1 c.5181_5183delGTT (p.Val1688del) is a true pathogenic mutation that affects both protein stability and function: implications for genetic counseling

Abstract #1106

Germ line mutations in the BRCA1 tumor suppressor gene are associated with a significantly increased lifetime risk of breast and/or ovarian cancers. Since genetic testing has become a routinely step in the clinical practice, the discrimination between pathogenic mutations and benign variants appears a mandatory task as it can facilitate risk estimation and surveillance, as well as implementation of cancer prevention and treatment strategies. Most of the deleterious BRCA1 mutations identified so far are frameshift or nonsense ones that result in a premature translational truncation of the protein; only a small percentage is represented by missense mutations residing in the N-terminal RING finger or in the C-terminal BRCT domains. Interestingly, a growing number of variants of unknown significance (VUSs) are being described, which lack ad hoc functional assays thus remaining unclassified with respect to their pathogenic or neutral effect.&#x2028; Recently, disease-causality was predicted, based upon a multifactorial likelihood approach, for a BRCA1 VUS, c.5181_5183delGTT (p.Val1688del), recurrent in Italian breast/ovarian cancer families (Malacrida et al., 2008). The same VUS was also identified in one of the families recruited at the Dana-Farber Cancer Institute: pedigree analysis revealed early onset breast cancer in both the proband and her mother; family history confirmed Italian descent.&#x2028; To gain insights into the specific risk associated with the BRCA1 c.5181_5183delGTT (p.Val1688del) VUS, we investigated its impact on BRCA1 function. The sequence variant causes a single amino acid in frame deletion that falls within the first of the two tandem BRCA1 BRCTs. A series of approaches, including protein stability assays and co-immunoprecipitation experiments, as well as structural modeling based on sequence alignment, were employed to characterize both the full-length mutant protein (ΔValBRCA1) and its C-terminal fragment.&#x2028; We observed that ΔValBRCA1 displayed decreased stability when compared to the wild type counterpart. Moreover, when tested, interactions with known BRCA1 partners, BRIP1 and CtIP, were completely abrogated. In addition, ΔValBRCA1 failed to interact with Rap80 and was deficient in DNA damage response and repair by homologous recombination. These results demonstrate that BRCA1 c.5181_5183delGTT (p.Val1688del) is a true pathogenic sequence alteration and provide the first evidence of its effect on the stability and function of the encoded protein. We believe that our findings will impact the genetic counseling of those patients who harbor this newly defined mutation and their family members thus allowing them to benefit of appropriate risk assessment, prevention and therapeutic strategies.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 1106.

Ectopic expression of alkaline phosphatase in proximal tubular brush border membrane of human renal cell carcinoma

The present study was conducted to find out any alteration in the expression and activity of alkaline phosphatase in the brush border membrane (BBM) from renal cell carcinoma (RCC) in comparison to normal renal BBM. The specific activity of alkaline phosphatase was drastically reduced in homogenate as well as BBM from RCC kidney when compared to ALP activity in BBM of normal kidney. Kinetic studies revealed that diminished activity of alkaline phosphatase in BBM isolated from RCC was fraternized with decrease in maximal velocity (V(max)) and increase in affinity constant (K(m)) of the enzyme. SDS-PAGE studies showed that the BBM proteins having molecular weights ranging from 95 to 170 kDa were poorly expressed in RCC BBM in relative to normal kidney BBM. Incubation of SDS-PAGE gel with BCIP/NBT dye clearly showed that the expression of ALP in tumor renal BBM was markedly reduced as compared to normal kidney. Further, Western blot analysis using anti-alkaline phosphatase antibody also confirmed the reduced expression of ALP in tumor renal BBM. Lipid composition in reference to phospholipids, glycolipids and cholesterol in tumor renal BBM was altered to that of normal renal BBM, indicating alteration in membrane fluidity of tumor renal BBM.

A general model for site-specific recombination by the integrase family recombinases

We present here a general model for integrase family site-specific recombination using the geometric relationships of the cleavable phosphodiester bonds and the disposition of the recombinase monomers (defined by their binding planes) with respect to them. The 'oscillation model' is based largely on the conformations of the recombinase-bound DNA duplexes and their dynamics within Holliday junctions. The duplex substrate or the Holliday junction intermediate is capable of 'oscillating' between two cleavage-competent asymmetric states with respect to corres-ponding chemically inert 'equilibrium positions'. The model accommodates several features of the Flp system and predicts two modes of DNA cleavage during a normal recombination event. It is equally applicable to other systems that mediate recombination across 6, 7 or 8 bp long strand exchange regions (or spacers). The model is consistent with approximately 0-1, 1-2 and 2-3 bp of branch migration during recombination reactions involving 6, 7 and 8 bp spacers, respectively.

Flp ribonuclease activities. Mechanistic similarities and contrasts to site-specific DNA recombination

The ribonuclease active site harbored by the Flp site-specific recombinase can act on two neighboring phosphodiester bonds to yield mechanistically distinct chain breakage reactions. One of the RNase reactions apparently proceeds via a covalent enzyme intermediate and targets the phosphodiester position involved in DNA recombination (Flp RNase I activity). The second activity (Flp RNase II) targets the phosphodiester immediately to the 3' side but appears not to involve an enzyme-linked intermediate. Flp RNase I is absolutely dependent upon Tyr-343 of Flp and is competitive with respect to the normal strand joining reaction. It can utilize the 2'-hydroxyl group from any one of the four ribonucleotides with comparable efficiencies in the cleavage reaction. On the other hand, the RNase II reaction mediated by Flp(Y343F) is specific for U and cannot utilize the 2'-hydroxyl group from ribo-A, -G, or -C under standard reaction conditions. The RNase II activity is also sensitive to the 3'-neighboring base. Although dT is functional, the activity is stimulated by U or U-2'-OMe. The Flp RNase II reaction effectively competes with the normal strand cleavage reaction mediated by Tyr-343, even though their phosphodiester targets are not the same.

Structural alterations and conformational dynamics in Holliday junctions induced by binding of a site-specific recombinase

Binding of a cleavage-incompetent mutant of the Flp recombinase induces a roughly square-planar geometry in synthetic immobile Holliday junctions. The branch points, which are rigidly fixed in these junctions in their free forms, tend to be more flexible in their protein-bound forms. Our results (1) suggest a plausible mechanism for the switching of the recombination complex from the Holliday-forming mode to the Holliday-resolving mode, (2) provide a rationale for previous observations that Flp resolves preformed immobile Holliday structures in the parental or in the recombinant mode in a relatively unbiased manner, and (3) accommodate two modes of DNA cleavage by Flp (transhorizontal or transdiagonal) in Holliday substrates.