Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories

Host immune responses play central roles in controlling SARS-CoV2 infection, yet remain incompletely characterized and understood. Here, we present a comprehensive immune response map spanning 454 proteins and 847 metabolites in plasma integrated with single-cell multi-omic assays of PBMCs in which whole transcriptome, 192 surface proteins, and T and B cell receptor sequence were co-analyzed within the context of clinical measures from 50 COVID19 patient samples. Our study reveals novel cellular subpopulations, such as proliferative exhausted CD8 ⁺ and CD4 ⁺ T cells, and cytotoxic CD4 ⁺ T cells, that may be features of severe COVID-19 infection. We condensed over 1 million immune features into a single immune response axis that independently aligns with many clinical features and is also strongly associated with disease severity. Our study represents an important resource towards understanding the heterogeneous immune responses of COVID-19 patients and may provide key information for informing therapeutic development.

Abstract 328: Targeting Mcl-1 enhances DNA replication stress sensitivity for cancer therapy

DNA double-strand breaks (DSBs) are mainly repaired by homologous recombination (HR) and non-homologous end-joining (NHEJ) pathways. Here we report that Mcl-1 acts as a functional switch in pathway choice between HR and NHEJ. Mcl-1 was cell cycle-regulated, with expression peaking in S/G2 phase when HR occurred. Endogenous Mcl-1 depletion reduced HR and enhanced NHEJ. Mcl-1 overexpression resulted in a net increase in HR over NHEJ. Mcl-1 directly interacted with Ku via its BH1 and BH3 domains, which are required for Mcl-1 to inhibit Ku-mediated NHEJ and promote Mre11 complex-mediated DNA resection and HR-dependent DSB repair. Using the Mcl-1 BH1 domain (aa256-265) as docking site, we identified a novel small molecule, MI-223, that directly bound to BH1 and blocked Mcl-1-stimulated HR DNA repair leading to a significant sensitization of cancer cells to hydroxyurea- or olaparib-induced DNA replication stress. Combined treatment with MI-223 and hydroxyurea or olaparib exhibited a strong synergy against lung cancer in vivo. This mechanism-driven combination of agents provides a highly attractive therapeutic strategy to improve lung cancer outcome.

Citation Format: Guo Chen, Andrew Magis, Ke Xu, Dongkyoo Park, David Yu, Taofeek Owonikoko, Gabriel Sica, Sarah Satola, Suresh Ramalingam, Walter Curran, Paul Doetsch, Xingming Deng. Targeting Mcl-1 enhances DNA replication stress sensitivity for cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 328.

Genomic, Transcriptional, and Phenotypic Analysis of the Glucose Derepressed Clostridium beijerinckii Mutant Exhibiting Acid Crash Phenotype

Clostridium beijerinckii is a predominant solventogenic bacterium that is used for the ABE fermentation. Various C. beijerinckii mutants are constructed for desirable phenotypes. The C. beijerinckii mutant BA105 harboring a glucose derepression phenotype was previously isolated and demonstrated the enhanced amylolytic activity in the presence of glucose. Despite its potential use, BA105 is not further characterized and utilized. Therefore, the authors investigate fermentation phenotypes of BA105 in this study. Under the typical batch fermentation conditions, BA105 consistently exhibits acid crash phenotype resulting in limited glucose uptake and cell growth. However, when the culture pH is maintained above 5.5, BA105 exhibits the increased glucose uptake and butanol production than did the wild-type. To further analyze BA105, the authors perform genome sequencing and RNA sequencing. Genome analysis identifies two SNPs unique to BA105, in the upstream region of AbrB regulator (Cbei_4885) and the ROK family glucokinase (Cbei_4895) which are involved in catabolite repression and regulation of sugar metabolism. Transcriptional analysis of BA105 reveals significant differential expression of the genes associated with the PTS sugar transport system and acid production. This study improves understanding of the acid crash phenomenon and provides the genetic basis underlying the catabolite derepression phenotype of C. beijericnkii.

Abstract 2333: Modulation of Bax and mTOR for cancer therapeutics

Pharmacologic manipulation of the serine (S)184 phosphorylation site of Bax protein to functionally regulate its proapoptotic activity is an attractive anticancer strategy. We recently identified three small molecule Bax agonists. SMBA1 was selected as the lead compound based on its chemical structure and its drug-like properties, from which a more effective analog, CYD-2-11, was generated. CYD-2-11 targets the structural pocket around S184 in the C-terminal tail of Bax, directly activating its proapoptotic activity via 6A7 conformational change and formation of Bax homo-oligomers in mitochondrial membranes. CYD-2-11 suppresses tumor growth in SCLC, NSCLC and patient-derived lung cancer xenografts as well as the genetically engineered mutant KRAS-driven lung cancer model with no significant normal tissue toxicity. Inhibition of mTOR by RAD001 enhances S184 Bax phosphorylation in lung cancer cell lines and tumor tissues from lung cancer patients treated with RAD001, which inactivates the propaoptotic function of Bax, contributing to rapalog-resistance. Combined CYD-2-11 and RAD001 treatment not only displays strong synergistic activity against lung cancer but also overcomes rapalog-resistance in vitro and in vivo. Therefore, a mechanism-driven combination of Bax agonist and mTOR inhibitor represents a highly attractive therapeutic strategy to improve lung cancer patient outcomes.

Citation Format: Rui Li, Chunyong Ding, Jun Zhang, Maohua Xie, Dongkyoo Park, Ye Ding, Guo Chen, Guojing Zhang, Melissa Gilbert-Ross, Wei Zhou, Adam Marcus, Shi-Yong Sun, Zhuo Chen, Gabriel Sica, Suresh Ramalingam, Andrew Magis, Haian Fu, Fadlo Khuri, Walter Curran, Taofeek Owonikoko, Dong Shin, Jia Zhou, Xingming Deng. Modulation of Bax and mTOR for cancer therapeutics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2333. doi:10.1158/1538-7445.AM2017-2333

Abstract 2922: Development of Bcl2 BH4 antagonist for cancer therapy

The BH4 domain of Bcl2 is required for its antiapoptotic function, thus constituting a promising anticancer target. We identified a novel small molecule Bcl2-BH4 domain-antagonist (BDA-366) that binds BH4 with high affinity and selectivity. BDA-366-Bcl2 binding induces conformational change in Bcl2 that abrogates its antiapoptotic function, converting it from a survival to a cell death inducer. BDA-366 induces regression of lung cancer xenografts derived from cell line and patient without significant normal tissue toxicity at effective doses. mTOR inhibition up-regulates Bcl2 in lung cancer cells and tumor tissues from clinical trial patients. Combined BDA-366 and RAD001 treatment exhibits strong synergy against lung cancer in vivo. Development of this Bcl2-BH4 antagonist may provide a novel strategy to improve lung cancer outcome.

Citation Format: Bingshe Han, Dongkyoo Park, Rui Li, Maohua Xie, Taofeek Owonikoko, Gabriel Sica, Chunyong Ding, Jia Zhou, Andrew Magis, Suresh Ramalingam, Fadlo Khuri, Walter Curran, Xingming Deng. Development of Bcl2 BH4 antagonist for cancer therapy. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2922. doi:10.1158/1538-7445.AM2015-2922

Mitoxantrone targets the ATP-binding site of FAK, binds the FAK kinase domain and decreases FAK, Pyk-2, c-Src, and IGF-1R in vitro kinase activities

Focal Adhesion Kinase (FAK) is a non-receptor kinase that is overexpressed in many types of tumors and plays a key role in cell adhesion, spreading, motility, proliferation, invasion, angiogenesis, and survival. Recently, FAK has been proposed as a target for cancer therapy, and we performed computer modeling and screening of the National Cancer Institute (NCI) small molecule compounds database to target the ATP-binding site of FAK, K454. More than 140,000 small molecule compounds were docked into the crystal structure of the kinase domain of FAK in 100 different orientations using DOCK5.1 that identified small molecule compounds, targeting the K454 site, called A-compounds. To find the therapeutic efficacy of these compounds, we examined the effect of twenty small molecule compounds on cell viability by MTT assays in different cancer cell lines. One compound, A18 (1,4-bis(diethylamino)-5,8- dihydroxy anthraquinon) was a mitoxantrone derivative and significantly decreased viability in most of the cells comparable to the to the level of FAK kinase inhibitors TAE-226 (Novartis, Inc) and PF-573,228 (Pfizer). The A18 compound specifically blocked autophosphorylation of FAK like TAE-226 and PF-228. ForteBio Octet Binding assay demonstrated that mitoxantrone (1,4-dihydroxy- 5,8-bis[2-(2-hydroxyethylamino) ethylamino] anthracene-9,10-dione directly binds the FAK-kinase domain. In addition, mitoxantrone significantly decreased the viability of breast cancer cells in a dose-dependent manner and inhibited the kinase activity of FAK and Y56/577 FAK phosphorylation at 10-20 μM. Mitoxantrone did not affect phosphorylation of EGFR, but decreased Pyk-2, c-Src, and IGF-1R kinase activities. The data demonstrate that mitoxantrone decreases cancer viability, binds FAK-Kinase domain, inhibits its kinase activity, and also inhibits in vitro kinase activities of Pyk-2 and IGF-1R. Thus, this novel function of the mitoxantrone drug can be critical for future development of anti-cancer agents and FAK-targeted therapy research.

A small-molecule inhibitor, 5'-O-tritylthymidine, targets FAK and Mdm-2 interaction, and blocks breast and colon tumorigenesis in vivo

Focal Adhesion Kinase (FAK) is overexpressed in many types of tumors and plays an important role in survival. We developed a novel approach, targeting FAK-protein interactions by computer modeling and screening of NCI small molecule drug database. In this report we targeted FAK and Mdm-2 protein interaction to decrease tumor growth. By macromolecular modeling we found a model of FAK and Mdm-2 interaction and performed screening of > 200,000 small molecule compounds from NCI database with drug-like characteristics, targeting the FAK-Mdm-2 interaction. We identified 5';-O-Tritylthymidine, called M13 compound that significantly decreased viability in different cancer cells. M13 was docked into the pocket of FAK and Mdm-2 interaction and was directly bound to the FAK-N terminal domain by ForteBio Octet assay. In addition, M13 compound affected FAK and Mdm-2 levels and decreased complex of FAK and Mdm-2 proteins in breast and colon cancer cells. M13 re-activated p53 activity inhibited by FAK with Mdm-2 promoter. M13 decreased viability, clonogenicity, increased detachment and apoptosis in a dose-dependent manner in BT474 breast and in HCT116 colon cancer cells in vitro. M13 decreased FAK, activated p53 and caspase-8 in both cell lines. In addition, M13 decreased breast and colon tumor growth in vivo. M13 activated p53 and decreased FAK in tumor samples consistent with decreased tumor growth. The data demonstrate a novel approach for targeting FAK and Mdm-2 protein interaction, provide a model of FAK and Mdm-2 interaction, identify M13 compound targeting this interaction and decreasing tumor growth that is critical for future targeted therapeutics.

Disruption of focal adhesion kinase and p53 interaction with small molecule compound R2 reactivated p53 and blocked tumor growth

BACKGROUND

Focal Adhesion Kinase (FAK) is a 125 kDa non-receptor kinase that plays a major role in cancer cell survival and metastasis.

METHODS

We performed computer modeling of the p53 peptide containing the site of interaction with FAK, predicted the peptide structure and docked it into the three-dimensional structure of the N-terminal domain of FAK involved in the complex with p53. We screened small molecule compounds that targeted the site of the FAK-p53 interaction and identified compounds (called Roslins, or R compounds) docked in silico to this site.

RESULTS

By different assays in isogenic HCT116p53+/+ and HCT116 p53-/- cells we identified a small molecule compound called Roslin 2 (R2) that bound FAK, disrupted the binding of FAK and p53 and decreased cancer cell viability and clonogenicity in a p53-dependent manner. In addition, dual-luciferase assays demonstrated that the R2 compound increased p53 transcriptional activity that was inhibited by FAK using p21, Mdm-2, and Bax-promoter targets. R2 also caused increased expression of p53 targets: p21, Mdm-2 and Bax proteins. Furthermore, R2 significantly decreased tumor growth, disrupted the complex of FAK and p53, and up-regulated p21 in HCT116 p53+/+ but not in HCT116 p53-/- xenografts in vivo. In addition, R2 sensitized HCT116p53+/+ cells to doxorubicin and 5-fluorouracil.

CONCLUSIONS

Thus, disruption of the FAK and p53 interaction with a novel small molecule reactivated p53 in cancer cells in vitro and in vivo and can be effectively used for development of FAK-p53 targeted cancer therapy approaches.

Abstract 3247: Novel small molecule inhibitors C9 and C10 specifically disrupt the FAK-VEGFR3 signaling axis in cancer cells

Introduction: FAK functions as both, a critical signaling kinase and a scaffolding protein to collectively mediate proliferation, survival, cell adhesion and migration signals. VEGFR3 is a receptor tyrosine kinase that acts as a key modulator of survival signals and lymphangiogenesis. Upregulation of FAK and VEGFR3 in multiple tumor types, with low levels in normal tissues make them attractive anti-cancer targets. Previously we have shown that VEGFR3 binds to FAK and the physical interaction between the two proteins confers a significant survival advantage to tumor cells. Subsequently we discovered small molecule C4 that specifically targets the VEGFR3 binding site on the FAT domain of FAK and exerts anti-tumor effects at moderate concentrations. In this study we designed, synthesized and characterized novel C4 analogs which show enhanced potency and specificity for the target site.

Methods: Modifications were made on the C4 moiety and the resulting analogs were screened for anti-cancer inhibitory effects in different cancer cell lines by MTS assay. Effects of C4 analogs on cancer cell lines were determined by MTS assay (viability), Clonogenecity assay, Western blot (phosphorylation, apoptosis), Immunofluorescence staining (apoptosis) and Flow cytometry (apoptosis). Computer modeling, target specificity (immunoprecipitation) and binding confirmation (Forte-Bio's Octet Red assay) of all analogs were tested. In vitro wound healing and cell invasion assays were also performed. In vivo anti-tumor activity of lead analogs was done using a subcutaneous xenograft mouse model of pancreatic cancer.

Results: Based on the preliminary screening results in several cancer cell lines, we selected analogs C9 and C10 for further analyses. Both analogs inhibit colony formation of pancreatic cancer cells and show target specificity by disrupting FAK-VEGFR3 interaction at ≤10μM. Binding of C9 and C10 to the FAT domain of FAK was confirmed with Octet method. Induction of apoptosis after treatment with C9 and C10 was confirmed via caspase 3/7 activation, caspase-3 and PARP cleavage. Down-regulation of phosphorylated forms of Akt, Erk1/2, Jnk, Grb2 and paxillin was seen in a dose and time dependent manner after 24h treatment with C9 and C10. These drugs also inhibited migration and invasion of pancreatic cancer cells at ≤10μM. In vivo, 30 days treatment with low doses of C9 and C10 led to massive reduction in tumor growth when treated as single agents (P<0.05).

Conclusions: FAK-VEGFR3 targeted therapeutics represents a novel approach towards anti-cancer treatment options. Our promising results thereby form the basis for future clinical applications of FAK-VEGFR3 small molecule inhibitors for cancer therapy.

Citation Format: Priyanka A. Agharkar, Manivannan Ethirajan, Andrew Magis, Jian Liao, Michael Yemma, William Cance, Ravindra Pandey, Elena Kurenova. Novel small molecule inhibitors C9 and C10 specifically disrupt the FAK-VEGFR3 signaling axis in cancer cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3247. doi:10.1158/1538-7445.AM2013-3247

Kinetic characterization of newly discovered inhibitors of various constructs of human T-cell leukemia virus-1 (HTLV-1) protease and their effect on HTLV-1-infected cells

BACKGROUND

Human T-cell leukemia virus-1 (HTLV-1) was the first identified human retrovirus and was shown to be associated with diseases such as adult T-cell leukemia lymphoma and tropical spastic paraparesis/HTLV-1 associated myelopathy. Retroviral proteases (PRs) are essential for viral replication by processing viral Gag and Gag-(Pro)-Pol polyproteins during maturation. Full-length HTLV-1 PR is 125 residues long; whether the C-terminal region is required for catalytic activity is still controversial. In this study, we characterized the effect of C-terminal amino acids of HTLV-1 PR for PR activity and examined the binding of compounds identified by in silico screening. One compound showed inhibition against the virus in infected cells.

METHODS

Truncated (116-, 121- and 122-residue) forms of HTLV-1 PR were prepared and proteins from expression of the genes were purified. In silico screening was performed by docking small molecules into the active site of HTLV-1 PR. The kinetic constants k(cat), K(m), k(cat)/K(m) and inhibition constants K(i) for inhibitors identified by the computational screening were determined. Western blot and ELISA analyses were used to determine the effect of the most potent PR inhibitors on HTLV-1 protein processing in infected cells.

RESULTS

The constructs showed similar catalytic efficiency constants (k(cat)/K(m)); thus HTLV-1 PR C-terminal amino acids are not essential for full activity. Computational screening revealed new PR inhibitors and some were shown to be inhibitory in enzyme assays. In HTLV-1-infected cells, one of the small molecules inhibited HTLV-1 gag cleavage and decreased the amount of HTLV-1 p19 produced in the cells.

CONCLUSIONS

We have identified an HTLV-1 PR inhibitor that is biologically functional. Inhibitor screening will continue to develop possible drugs for therapy of HTLV-1 infection.

A small molecule focal adhesion kinase (FAK) inhibitor, targeting Y397 site: 1-(2-hydroxyethyl)-3, 5, 7-triaza-1-azoniatricyclo [3.3.1.1(3,7)]decane; bromide effectively inhibits FAK autophosphorylation activity and decreases cancer cell viability, clonogenicity and tumor growth in vivo

Focal adhesion kinase (FAK) is a protein tyrosine kinase that is overexpressed in most solid types of tumors and plays an important role in the survival signaling. Recently, we have developed a novel computer modeling combined with a functional assay approach to target the main autophosphorylation site of FAK (Y397). Using these approaches, we identified 1-(2-hydroxyethyl)-3, 5, 7-triaza-1-azoniatricyclo [3.3.1.1(3,7)]decane; bromide, called Y11, a small molecule inhibitor targeting Y397 site of FAK. Y11 significantly and specifically decreased FAK autophosphorylation, directly bound to the N-terminal domain of FAK. In addition, Y11 decreased Y397-FAK autophosphorylation, inhibited viability and clonogenicity of colon SW620 and breast BT474 cancer cells and increased detachment and apoptosis in vitro. Moreover, Y11 significantly decreased tumor growth in the colon cancer cell mouse xenograft model. Finally, tumors from the Y11-treated mice demonstrated decreased Y397-FAK autophosphorylation and activation of poly (ADP ribose) polymerase and caspase-3. Thus, targeting the major autophosphorylation site of FAK with Y11 inhibitor is critical for development of cancer therapeutics and carcinogenesis field.

Abstract 3582: Targeting the FAK amino terminus F2 subdomain to disrupt growth factor receptor protein interactions, signaling and function

Introduction: Focal adhesion kinase (FAK), IGF-1R and the c-MET are tyrosine kinases that induce cell proliferation, invasion, metastases and survival. We have previously shown that FAK physically interacts with growth factor receptors in pancreatic cancer cells and is involved in tumor progression. Since IGF-1R and c-MET have significant structural similarity, we hypothesize that both interact with a similar conserved amino acid “patch” on FAK. We also hypothesize that this patch can be targeted with small molecules to inhibit pancreatic cancer essential signaling pathways and induce apoptosis.

Methods: Based on Lipinski rules, we screened a chemical library of 240,000 compounds against a conserved patch on the F2 subdomain of FAK using in silico high throughput screening. We obtained the top scoring compounds from the National Cancer Institute Developmental Therapeutics Program and evaluated their effects on: 1) FAK protein interactions with c-MET and IGF-1R, 2) FAK, IGF-1R and c-MET kinase activity, 3)cell viability and apoptosis, and 4) growth of Panc-1 and Miapaca-2 pancreatic cancer cells in both orthotopic and direct xenograft mouse tumor models.

Results: Based on co-immunoprecipitation assays, our lead compound blocked the interaction of FAK with both c-MET and IGF-1R in pancreatic cancer cells, without altering their kinase activity. Treatment with our lead compound led to decreased phosphorylation of AKT, inhibited cell viability and induced apoptosis in a dose-dependent manner (range 2-20μM). In addition, the combination of our lead compound with either 5-FU or gemcitabine chemotherapy resulted in a synergistic decrease in pancreatic cancer cell viability. More importantly, 10mg/kg of lead compound via subcutaneous injection, effectively (p<0.05) caused pancreatic tumor regression in vivo in both an orthotopic and direct xenograft model of pancreatic cancer. Conclusions: Our data suggest that targeting the protein interactions of FAK with growth factor receptors including c-MET and IGF-1R has specific therapeutic effects that can increase the sensitivity of pancreatic cancer cells to conventional chemotherapy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3582. doi:10.1158/1538-7445.AM2011-3582

Noise contributions in an inducible genetic switch: a whole-cell simulation study

Stochastic expression of genes produces heterogeneity in clonal populations of bacteria under identical conditions. We analyze and compare the behavior of the inducible lac genetic switch using well-stirred and spatially resolved simulations for Escherichia coli cells modeled under fast and slow-growth conditions. Our new kinetic model describing the switching of the lac operon from one phenotype to the other incorporates parameters obtained from recently published in vivo single-molecule fluorescence experiments along with in vitro rate constants. For the well-stirred system, investigation of the intrinsic noise in the circuit as a function of the inducer concentration and in the presence/absence of the feedback mechanism reveals that the noise peaks near the switching threshold. Applying maximum likelihood estimation, we show that the analytic two-state model of gene expression can be used to extract stochastic rates from the simulation data. The simulations also provide mRNA–protein probability landscapes, which demonstrate that switching is the result of crossing both mRNA and protein thresholds. Using cryoelectron tomography of an E. coli cell and data from proteomics studies, we construct spatial in vivo models of cells and quantify the noise contributions and effects on repressor rebinding due to cell structure and crowding in the cytoplasm. Compared to systems without spatial heterogeneity, the model for the fast-growth cells predicts a slight decrease in the overall noise and an increase in the repressors rebinding rate due to anomalous subdiffusion. The tomograms for E. coli grown under slow-growth conditions identify the positions of the ribosomes and the condensed nucleoid. The smaller slow-growth cells have increased mRNA localization and a larger internal inducer concentration, leading to a significant decrease in the lifetime of the repressor–operator complex and an increase in the frequency of transcriptional bursts.

Expressing genes in a bacterial cell is noisy and random. A colony of bacteria grown from a single cell can show remarkable differences in the copy number per cell of a given protein after only a few generations. In this work we use computer simulations to study the variation in how individual cells in a population express a set of genes in response to an environmental signal. The modeled system is the lac genetic switch that Escherichia coli uses to find, collect, and process lactose sugar from the environment. The noise inherent in the genetic circuit controlling the cell's response determines how similar the cells are to each other and we study how the different components of the circuit affect this noise. Furthermore, an estimated 30–50% of the cell volume is taken up by a wide variety of large biomolecules. To study the response of the circuit caused by crowding, we simulate the circuit inside a three-dimensional model of an E. coli cell built using data from cryoelectron tomography reconstructions of a single cell and proteomics data. Correctly including random effects of molecular crowding will be critical to developing fully dynamic models of living cells.

The constitutive activation of Jak2-V617F is mediated by a π stacking mechanism involving phenylalanines 595 and 617

Somatic mutations in the Jak2 allele that lead to constitutive kinase activation of the protein have been identified in human disease conditions such as the myeloproliferative neoplasms (MPNs). The most common mutation in these patients is a V617F substitution mutation, which is believed to play a causative role in the MPN pathogenesis. As such, identifying the molecular basis for the constitutive activation of Jak2-V617F is important for understanding its clinical implications and potential treatment. Here, we hypothesized that conversion of residue 617 from Val to Phe resulted in the formation of novel π stacking interactions with neighboring Phe residues. To test this, we first examined the Jak2 structure via molecular modeling and identified a potential π stacking interaction between F594, F595, and F617. Disruption of this interaction through site-directed mutagenesis impaired Jak2 autophosphorylation, Jak2-dependent gene transcription, and in vitro kinase activity of the Jak2-V617F protein. Further, substitution of F594 and F595 with Trp did not affect Jak2 function significantly, but replacement with charged residues did, showing the importance of aromaticity and hydropathy index conservation at these positions. Using molecular dynamics (MD) simulations, we found that the π stacking interaction between residues 595 and 617 in the Jak2-V617F protein was of much greater energy and conformed to the properties of π stacking, relative to the Jak2-WT or Jak2-V617F/F594A/F595A. In summary, we have identified a π stacking interaction between F595 and F617 that is specific to and is critical for the constitutive activation of Jak2-V617F.

Structure-function correlation of G6, a novel small molecule inhibitor of Jak2: indispensability of the stilbenoid core

Somatic mutations in the Jak2 protein, such as V617F, cause aberrant Jak/STAT signaling and can lead to the development of myeloproliferative neoplasms. This discovery has led to the search for small molecule inhibitors that target Jak2. Using structure-based virtual screening, our group recently identified a novel small molecule inhibitor of Jak2 named G6. Here, we identified a structure-function correlation of this compound. Specifically, five derivative compounds of G6 having structural similarity to the original lead compound were obtained and analyzed for their ability to (i) inhibit Jak2-V617F-mediated cell growth, (ii) inhibit the levels of phospho-Jak2, phospho-STAT3, and phospho-STAT5; (iii) induce apoptosis in human erythroleukemia cells; and (iv) suppress pathologic cell growth of Jak2-V617F-expressing human bone marrow cells ex vivo. Additionally, we computationally examined the interactions of these compounds with the ATP-binding pocket of the Jak2 kinase domain. We found that the stilbenoid core-containing derivatives of G6 significantly inhibited Jak2-V617F-mediated cell proliferation in a time- and dose-dependent manner. They also inhibited phosphorylation of Jak2, STAT3, and STAT5 proteins within cells, resulting in higher levels of apoptosis via the intrinsic apoptotic pathway. Finally, the stilbenoid derivatives inhibited the pathologic growth of Jak2-V617F-expressing human bone marrow cells ex vivo. Collectively, our data demonstrate that G6 has a stilbenoid core that is indispensable for maintaining its Jak2 inhibitory potential.

Abstract C137: Pinpointing a protein-protein interaction site of focal adhesion kinase and VEGFR-3 suppresses cancer growth in vivo

Tumor cell survival depends on activation of signaling pathways that suppress the apoptotic stimuli of invasion and metastasis. FAK and VEGFR-3 are tyrosine kinases that have been identified as critical signaling molecules for these processes. Previously we have shown that VEGFR-3 and FAK physically interact and are overexpressed in cancer cells to provide a significant survival advantage for the tumor cells. We subsequently identified a novel small molecule inhibitor that targeted VEGFR-3-FAK site of interaction and disrupted the survival function of these two proteins. We utilized the crystal structure of the FAK focal adhesion targeting (FAT) domain for molecular docking of small molecules that targeted the VEGFR-3 binding site on FAK. We identified a small molecule C4 (Chloropyramine hydrochloride), that disrupted VEGFR-3-FAK binding, and abrogated the phosphorylation of VEGFR-3 while reducing the phosphorylation of FAK. In vitro testing of this compound resulted in the selective growth inhibition, reduction in motility and invasion, and induction of apoptosis in a time- and dose-dependent manner in many cancer cell lines, especially those that overexpressed VEGFR-3. In vivo, C4 showed a marked reduction of tumor growth and was synergistic with doxorubicin chemotherapy in breast cancer xenograft models, with dacarbazine in melanoma xenograft models, and with gemcitabine in pancreatic cancer xenograft models. These results demonstrate that targeting the FAK-VEGFR-3 interaction with a small molecules inhibited the survival function of these two tyrosine kinases, representing a unique approach for molecular-targeted highly-specific cancer therapeutics.

Citation Information: Mol Cancer Ther 2009;8(12 Suppl):C137.

Targeting of the protein interaction site between FAK and IGF-1R

The interaction of focal adhesion kinase (FAK) and insulin-like growth factor-1 receptor (IGF-1R) plays an important role in cancer cell survival. Targeting this interaction with small molecule drugs could be a novel strategy in cancer therapy. By a series of pull-down assays using GST-tagged FAK fragments and His-tagged IGF-1R intracellular fragments, we showed that the FAK-NT2 (a.a. 127-243) domain directly interacts with the N-terminal part of the IGF-1R intracellular domain. Overexpressed FAK-NT2 domain was also shown to co-localize with IGF-1R in pancreatic cells. Computational modeling was used to predict the binding configuration of these two domains and to screen for small molecules binding to the interaction site. This strategy successfully identified a lead compound that disrupts FAK/IGF-1R interaction.

A novel small molecule inhibitor of FAK decreases growth of human pancreatic cancer

Focal adhesion kinase (FAK) is a cytoplasmic tyrosine kinase that is overexpressed in many types of tumors, including pancreatic cancer, and plays an important role in cell adhesion and survival signaling. Pancreatic cancer is a lethal disease and is very resistant to chemotherapy, and FAK has been shown recently to assist in tumor cell survival. Therefore, FAK is an excellent potential target for anti-cancer therapy. We identified a novel small molecule inhibitor (1,2,4,5-Benzenetetraamine tetrahydrochloride, that we called Y15) targeting the main autophosphorylation site of FAK and hypothesized that it would be an effective treatment strategy against human pancreatic cancer. Y15 specifically blocked phosphorylation of Y397-FAK and total phosphorylation of FAK. It directly inhibited FAK autophosphorylation in a dose- and time-dependent manner. Furthermore, Y15 increased pancreatic cancer cell detachment and inhibited cell adhesion in a dose-dependent manner. Y15 effectively caused human pancreatic tumor regression in vivo, when administered alone and its effects were synergistic with gemcitabine chemotherapy. This was accompanied by a decrease in Y397-phosphorylation of FAK in the tumors treated with Y15. Thus, targeting the Y397 site of FAK in pancreatic cancer with the small molecule inhibitor, 1,2,4,5-Benzenetetraamine tetrahydrochloride, is a potentially effective treatment strategy in this deadly disease.

A small molecule inhibitor, 1,2,4,5-benzenetetraamine tetrahydrochloride, targeting the y397 site of focal adhesion kinase decreases tumor growth

Focal adhesion kinase (FAK) is a nonreceptor kinase that is overexpressed in many types of tumors. We developed a novel cancer-therapy approach, targeting the main autophosphorylation site of FAK, Y397, by computer modeling and screening of the National Cancer Institute (NCI) small molecule compounds database. More than 140,000 small molecule compounds were docked into the N-terminal domain of the FAK crystal structure in 100 different orientations that identified 35 compounds. One compound, 14 (1,2,4,5-benzenetetraamine tetrahydrochloride), significantly decreased viability in most of the cells to the levels equal to or higher than control FAK inhibitor 1a (2-[5-chloro-2-[2-methoxy-4-(4-morpholinyl)phenylamino]pyrimidin-4-ylamino]-N-methylbenzamide, TAE226) from Novartis, Inc. Compound 14 specifically and directly blocked phosphorylation of Y397-FAK in a dose- and time-dependent manner. It increased cell detachment and inhibited cell adhesion in a dose-dependent manner. Furthermore, 14 effectively caused breast tumor regression in vivo. Thus, targeting the Y397 site of FAK with 14 inhibitor can be effectively used in cancer therapy.

Z3, a novel Jak2 tyrosine kinase small-molecule inhibitor that suppresses Jak2-mediated pathologic cell growth

Jak2 tyrosine kinase is essential for animal development and hyperkinetic Jak2 function has been linked to a host of human diseases. Control of this pathway using Jak2-specific inhibitors would therefore potentially serve as a useful research tool and/or therapeutic agent. Here, we used a high-throughput program called DOCK to predict the ability of 20,000 small molecules to interact with a structural pocket adjacent to the ATP-binding site of murine Jak2. One small molecule, 2-methyl-1-phenyl-4-pyridin-2-yl-2-(2-pyridin-2-ylethyl)butan-1-one (herein designated as Z3), bound to Jak2 with a favorable energy score. Z3 inhibited Jak2-V617F and Jak2-WT autophosphorylation in a dose-dependent manner but was not cytotoxic to cells at concentrations that inhibited kinase activity. Z3 selectively inhibited Jak2 kinase function with no effect on Tyk2 or c-Src kinase function. Z3 significantly inhibited proliferation of the Jak2-V617F-expressing, human erythroleukemia cell line, HEL 92.1.7. The Z3-mediated reduction in cell proliferation correlated with reduced Jak2 and STAT3 tyrosine phosphorylation levels as well as marked cell cycle arrest. Finally, Z3 inhibited the growth of hematopoietic progenitor cells isolated from the bone marrow of an essential thrombocythemia patient harboring the Jak2-V617F mutation and a polycythemia vera patient carrying a Jak2-F537I mutation. Collectively, the data suggest that Z3 is a novel specific inhibitor of Jak2 tyrosine kinase.

Human pharmacokinetics of N-L-leucyl-doxorubicin, a new anthracycline derivative, and its correlation with clinical toxicities

A pharmacokinetic study of N-L-leucyl-doxorubicin, a new derivative of doxorubicin, has been undertaken during a phase I trial in 19 patients with advanced cancer after intravenous bolus administration at doses ranging from 30 to 240 mg/m2. The pharmacokinetics of N-L-leucyl-doxorubicin was linear with a total body clearance of 41.3 +/- 25.7 L/hr/m2. N-L-leucyl-doxorubicin was extensively metabolized into doxorubicin, which appeared in plasma immediately after N-L-leucyl-doxorubicin infusion. The mean molar doxorubicin/N-L-leucyl-doxorubicin area under the curve (AUC) ratio was 0.49 +/- 0.22 and was independent of the administered dose. A relationship has been established between the doxorubicin AUC (r = 0.74; p less than 0.001) and the surviving factor in white blood cell counts. Other toxic side effects (thrombocytopenia or stomatitis) did not correlate with any pharmacokinetic parameter. These findings suggest that the degree of metabolization of N-L-leucyl-doxorubicin into doxorubicin may be responsible for the toxicity, that is, N-L-leucyl-doxorubicin may simply represent a pro-drug for doxorubicin.

Infections in patients in intensive care units: can the combination of a monobactam and a penicillin replace the classic combination of a beta-lactam agent and an aminoglycoside?

An open, comparative, randomized study was performed in two medical intensive care units to compare the efficacy of the combination of aztreonam and either cloxacillin or oxacillin [(cl)oxacillin] with that of the combination of tobramycin and a cephalosporin. Of the 92 patients who were included in the study, 76 were evaluable. All patients suffered from severe, mostly pulmonary, infections and received ventilatory support. The aztreonam combination yielded an 80% rate of clinical cure; mortality was 15%. Use of the aminoglycoside combination resulted in a 51% rate of clinical cure; mortality was 23%. The difference in cure rate between the two combinations was statistically significant. Adverse effects were negligible in patients who received the aztreonam combination, and superinfection was seen in only 2%. Of the patients who received the aminoglycoside combination, 20% developed a superinfection and 11% developed a new renal insufficiency. Therefore, the combination of aztreonam and (cl)oxacillin is a valuable alternative to the combination of an aminoglycoside and a cephalosporin.