Rathi et al., “Predicting ‘Hot’ and ‘Warm’ Spots for Fragment Binding.” J. Med. Chem., 2017, 60 (9), pp 4036-4046, DOI: 10.1021/acs.jmedchem.7b00366

Abstract

Computational fragment mapping methods aim to predict hotspots on protein surfaces where small fragments will bind. Such methods are popular for druggability assessment as well as structure-based design. However, to date researchers developing or using such tools have had no clear way of assessing the performance of these methods. Here, we introduce the first diverse, high quality validation set for computational fragment mapping. The set contains 52 diverse examples of fragment binding “hot” and “warm” spots from the Protein Data Bank (PDB). Additionally, we describe PLImap, a novel protocol for fragment mapping based on the Protein–Ligand Informatics force field (PLIff). We evaluate PLImap against the new fragment mapping test set, and compare its performance to that of simple shape-based algorithms and fragment docking using GOLD. PLImap is made publicly available from https://bitbucket.org/AstexUK/pli.

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Rathi et al., “Predicting ‘Hot’ and ‘Warm’ Spots for Fragment Binding.” J. Med. Chem., 2017, 60 (9), pp 4036-4046, DOI: 10.1021/acs.jmedchem.7b00366

2015_ESH-AML: Baseline biomarkers and DNA demethylation correlate w. clinical responses in SGI-110

Summary

Guadecitabine (SGI-110) is a novel hypomethylating dinucleotide of decitabine (DAC) and deoxyguanosine that is resistant to degradation by cytidine deaminase and results in prolonged in vivo exposure to its active moiety DAC. The differentiated pharmacokinetic profile offers the potential of improved biological and clinical activity and safety over currently available HMAs. We reported previously results from the Phase 1 dose-escalation study in AML and MDS1 and the Phase 2 randomized dose-response study in r/r AML patients of SGI-110 given SC at 2 doses (60 and 90 mg/m2) in a 5-day regimen2 or at 60 mg/m2 in a 10-day regimen3. Here we report an overall assessment of the association between clinical responses, global DNA demethylation assessed by LINE1 assay and baseline expression of a panel of 7 genes (CDA, P15, P21, DNMT3B, DNMT3A, DNMT1 and CTCF) assessed by qRT-PCR.

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2015_ESH-AML: Baseline biomarkers and DNA demethylation correlate w. clinical responses in SGI-110

2015 EHA: Late response & OS long term follow up of randomized P2 Study of SGI-110 in elderly AML

Summary

  • We previously reported results from a multicenter study of guadecitabine randomized to a 5-day regimen at either 60 or 90 mg/m2 in 51 treatment naïve elderly AML patients not eligible for intensive chemotherapy
  • There were no significant differences in overall composite complete response (CRc: CR+CRp+CRi) or safety between the two doses; however 14 patients were still on treatment at the time of the prior analysis
  • We present here current results on these patients with a median follow-up of 24 months (20.2-33) during which 38 death events occurred in the 51 patients treated (75%)

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2015 EHA: Late response & OS long term follow up of randomized P2 Study of SGI-110 in elderly AML

2015 ASCO: Epigenome and Genome Alterations in Platinum Resistant Ovarian Cancer

Summary

Background : Epigenetic changes, particularly in DNA methylation, have been implicated in acquired resistance to platinum in ovarian cancer (OC). Methods: An ongoing phase I/II multi-institutional clinical trial uses the novel DNA methyltransferase (DNMT) inhibitor guadecitabine (SGI-110) to re-sensitize recurrent platinum resistant OC to carboplatin. Patients enrolled in this trial had recurrent platinum resistant OC and multiple lines of prior therapy. Tumor biopsies were collected at baseline and after two cycles of guadecitabine administered daily for 5 days in low dose (30mg/m2). The goal of the current study was to analyze and integrate global RNA expression and DNA methylation profiles of platinum resistant tumors and to measure genomic and epigenomic changes induced by guadecitabine in tumors. RNA and DNA were extracted from 48 and 57 baseline tumors and analyzed using next generation sequencing (RNA-seq) and Infinium Human Methylation450 (HM450) arrays, respectively. Differential gene expression and DNA methylation profiles were generated and used for Ingenuity Pathway Analysis (IPA) to identify the top altered pathways in response to guadecitabine. Results: Analysis of a limited number of paired samples before and after treatment (n=8) revealed significant changes in global gene expression profiles induced by SGI-110, with 960 altered genes representing immunopathway enrichment including: cytokine production in macrophages and T helper cells by IL-17A and IL-17F, granulocyte /agranulocyte adhesion and inflammation, IL-8 signaling, p38 MAPK signaling, cAMP-mediated signaling, and innate immunity. HM450 analysis showed a greater number of hypermethylated genes in baseline tumors compared to primary OC samples in The Cancer Genome Atlas (TCGA) and demethylation (decreased β-values relative to baseline) of a large number of loci (381 gene promoters) after guadecitabine treatment. IPA analysis of baseline tumor transcriptome and methylome demonstrated significant enrichment in a wide range of pathways associated with cancer, stem cells, inflammation and the immune system. Conclusions: These data suggest that treatment with a DNMT inhibitor induces a reactivation of immune responses in human OC. Correlations between methylation changes and expression profiles are being explored.

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2015 ASCO: Epigenome and Genome Alterations in Platinum Resistant Ovarian Cancer

2015: AACR First Results of a 10-Day Regimen of SGI-110 in Previously Untreated Elderly AML

Summary

  • Elderly and unfit individuals with AML are often ineligible to receive intensive chemotherapy
  • Hypomethylating agents (HMA) such as decitabine and azacitidine have shown efficacy and acceptable safety in these patients
  • SGI-110 (guadecitabine) is a next generation HMA given as a small volume subcutaneous (SC) administration
  • We previously presented Phase 2 data of SGI-110 using the standard 5-day regimen which showed good good clinical activity in these patients
  • We present here , the preliminary results (minimum follow up of 3 months) of a 10-day regimen of SGI-110 in treatment naïve (TN) AML patients who are ineligible for intensive chemotherapy (IC)

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2015: AACR First Results of a 10-Day Regimen of SGI-110 in Previously Untreated Elderly AML

2015: AACR PD and PK Results of SGI-110 in Patients with HCC after Progression on Sorafenib

Summary

  • Hepatocellular Carcinoma (HCC) is the sixth most common cancer and the third most common cause of cancer death worldwide (1)
  • Sorafenib treatment improves survival in advanced disease, but no therapy has demonstrated significant activity after progression on sorafenib (2)
  • SGI-110, a dinucleotide of decitabine and deoxyguanosine (Fig 1), affords increased in vivo exposure of decitabine by protecting it from deamination due to slow release upon SQ injection
  • In Phase 1 AML/MDS studies, SGI-110 provides longer exposure and more potent hypomethylation compared to decitabine (3)
  •  Preclinical studies demonstrated:
    • In vitro, SGI-110 induced significant hypomethylation of tumor suppressor genes RASSF1A, SOCS1 and DAB2IP in human HCC cell lines HuH7 an HepG2 and resulted in a potent reduction in colony formation at low nanomolar concentrations of SGI-110 (4)
    • SGI-110 efficiently sensitizes HCC cells and xenografts to oxaliplatin by inhibiting distinct signaling pathways, allowing for high antitumor activity without systemic toxicity (Kuang et al., AACR 2015, Abst 2533)
    • Numerous epigenetic alterations accumulate during hepatocarcinogenesis, leading to activation of oncogenes or loss of tumor suppressor genes in HCC. Specifically, increased methylation of genes implicated in HCC tumorigenesis has been associated with pathogenesis and poor outcome
  • In this study, we evaluated therapeutic and biologic effects of SGI-110, a hypomethylating agent (HMA)in patients with HCC. PK and PD results of this open-label, phase 2 study in patients with HCC are presented here

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2015: AACR PD and PK Results of SGI-110 in Patients with HCC after Progression on Sorafenib

2015 AACR Novel Combination Therapy of SGI-110 and BMN-673 for BRCA-Proficient Ovarian Cancer

Summary

  • Ovarian cancer (OC) is initially chemoresponsive but the majority of patients relapse after first line platinum-, taxane-based chemotherapy.
  • Recurrence has been shown to be associated with increased DNA damage response (DDR) mediated by poly-(ADP)-ribose polymerase 1/2 (PARP1/2), which can be therapeutically targeted by PARP inhibitors (PARPi). Although PARPi are indicated for platinum-responsive, BRCA-mutated OC, most OC patients have BRCA-proficient disease.
  • Based on our previous studies supporting a role for DNA methylation in chemoresistant OC, mediated by the enzyme DNA methyltransferase 1 (DNMT1), and reports on a functional role for DNMT1 in DNA double strand break repair mediated by BRCA1/2, we hypothesize that combining the DNMTi SGI-110 and the PARPi talazoparib (BMN673) will impair BRCA-mediated DDR, resulting in cytotoxicity. CONCLUSION: Combination SGI-110 + talazoparib treatment significantly reduced cancer cell colony formation. Regardless of BRCA and platinum sensitivity status, co-administration of SGI-110 and talazoparib reduced cell survival, albeit %survival was dependent on drug dose and cancer cell line.

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2015 AACR Novel Combination Therapy of SGI-110 and BMN-673 for BRCA-Proficient Ovarian Cancer

2015 AACR: Determinants of hypomethylation and clinical response in r/r AML pts treated with SGI-110

Summary

SGI-110 (guadecitabine) is a dinucleotide of decitabine and deoxyguanosine and a novel subcutaneous (SQ) hypomethylating agent. In a previous Phase 1 (dose escalation) study, we found in relapsed/refractory (r/r) AML patients who were treated with SGI-110 (36 mg/m2-125 mg/m2) subcutaneously (SQ) daily for 5 days a correlation between low LINE-1 demethylation induction, a three gene expression classifier score (low CDA, low P15 and high DNMT3B) and resistance to SGI-110. Here, we analyzed r/r AML patients (n=122) from Phase 1/2 studies treated at harmacologically effective doses of SGI-110 looking for determinants of hypomethylation and response. Phase 1 patients with r/r AML (n=27) who were treated at a therapeutic dose range of SGI-110 (36 mg/m2 – 125 mg/m2) by SQ daily for 5 days. Phase 2 study r/r AML patients received 60 mg/m2 SQ daily for 5 days (n=22), 90 mg/m2 SQ daily for 5 days (n=25) and 60 mg/m2 SQ daily for 10 days (n=48). Global DNA methylation at pre/post treatment was estimated by bisulfite-pyrosequencing for the LINE-1 repetitive sequence. We also examined expression of a panel of genes (CDA, P15, P21, DNMT3B, DNMT3A, DNMT1, and CTCF) at baseline by quantitative RT-PCR.

We analyzed samples from 122 patients with r/r AML. Median age was 59.6 (range, 23–86), 75 were males (61.5%). Overall, peak LINE-1 demethylation generally occurred on day 8 after daily x 5 treatment, or on day 8 or 15 after daily x 10 treatment(Fig.1). In individual patients, peak LINE-1 demethylation ranged from +4.9% to -56.3%. In 122 r/r AML patients, 28 showed overall remission (23.0 %, 15 CR and 13 CRi/CRp). Unsupervised clustering by expression of a panel of genes at baseline grouped the patients into two clusters: A (N=95, response rate = 29.5 %) and B (N=27, response rate = 0 %).

Cluster B is characterized by high DNMT3b expression, low P15 expression, low CDA expression (average Z-score 1.44 ± 0.26 in cluster B compared to -1.26 ± 0.14 in clusters A, p<0.0001) and reduced demethylation (demethylation average -14.2 ± 1.90 % in cluster B compared to -26.1 ± 1.38 % in clusters A, p<0.0001)(Fig. 2). Peak LINE-1 demethylation was significantly higher in responders than non-responders (average demethylation -32.33 ± 1.91 % in responders compared to -21.25 ± 1.42 % in non-responders, p=0.0001). (Fig.3) A three gene classifier score (low CDA, low P15 and high DNMT3B) was associated with low LINE-1 demethylation (R=0.27, p=0.0034) as well as resistance to SGI-110 (mean Z-score -0.75 in non-responders compared to -1.67
in responders, p=0.014)(Fig.4).

In a phase 1/2 study of SGI-110, we identified in r/r AML patients a gene expression signature (high DNMT3B, low P15, and low CDA) associated with reduced demethylation and resistance to SGI-110 and we found strong trends for associations between demethylation and response.

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2015 AACR: Determinants of hypomethylation and clinical response in r/r AML pts treated with SGI-110

2015 Keystone Conf: DNA Methylome Alterations in Platinum Resistant Ovarian Cancer Tumors

Summary

Epigenetic changes, particularly DNA methylation aberrations have been implicated in acquired resistance to platinum in ovarian cancer. An ongoing phase I/II multi-institutional clinical trial uses the novel DNA methyl transferase (DNMT) inhibitor SGI-110 to resensitize recurrent platinum resistant ovarian cancer to carboplatin.

Tumor biopsies or malignant ascites were collected at baseline and after two cycles of SGI-110 administered daily for 5 days in low dose (30mg/m2). The goal of the current study was to analyze
global DNA methylation profiles of platinum resistant tumors and compare them to the methylome of untreated, platinum-sensitive ovarian tumors. LINE1 methylation and promoter methylation of
selected genes (MAGE-A2, MAGE-A3, MAGE-A11, NY-ESO, RASSF1, MLH1, and HOXA11) were quantified by pyrosequencing before and after SGI-110 treatment (n=12 paired samples).

Epigenetic profiling using the Infinium HumanMethylation450 BeadChip (HM450) revealed extensive methylation changes when comparing recurrent platinum resistant ovarian tumors (n=42) to
primary, untreated ovarian cancer specimens analyzed as part of the TCGA project (n=10). Six hundred and four promoters were significantly differentially methylated (adjusted p<0.05, absolute methylation changes β>0.2), among which, 498 and 106 were hypermethylated or hypomethylated respectively in recurrent platinum resistant ovarian tumors. DNMT1, 3A, and 3B mRNA
levels in the tumors were highly variable (n=19). Analysis of a limited number of paired samples (n=7) revealed no significant changes in global methylation or in DNMT expression levels
induced by treatment with SGI-110 (adjusted p>0.05). However, the DNMT inhibitor induced significant methylome alterations in selected patients. Significant hypomethylation of MAGE-A3 and
MAGE–A11 promoters (p<0.05) was detected. Correlations between methylation changes and clinical outcomes are being explored.

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2015 Keystone Conf: DNA Methylome Alterations in Platinum Resistant Ovarian Cancer Tumors