Literature-based automated discovery of tumor suppressor p53 phosphorylation and inhibition by NEK2.

Scientific progress depends on formulating testable hypotheses informed by the literature. In many domains, however, this model is strained because the number of research papers exceeds human readability. Here, we developed computational assistance to analyze the biomedical literature by reading PubMed abstracts to suggest new hypotheses. The approach was tested experimentally on the tumor suppressor p53 by ranking its most likely kinases, based on all available abstracts. Many of the best-ranked kinases were found to bind and phosphorylate p53 (P value = 0.005), suggesting six likely p53 kinases so far. One of these, NEK2, was studied in detail. A known mitosis promoter, NEK2 was shown to phosphorylate p53 at Ser315 in vitro and in vivo and to functionally inhibit p53. These bona fide validations of text-based predictions of p53 phosphorylation, and the discovery of an inhibitory p53 kinase of pharmaceutical interest, suggest that automated reasoning using a large body of literature can generate valuable molecular hypotheses and has the potential to accelerate scientific discovery.

Mitigation of off-target adrenergic binding and effects on cardiovascular function in the discovery of novel ribosomal S6 kinase 2 inhibitors.

We previously reported the discovery of a novel ribosomal S6 kinase 2 (RSK2) inhibitor, (R)-5-Methyl-1-oxo-2,3,4,5-tetrahydro-1H-[1,4]diazepino[1,2-a] indole-8-carboxylic acid [1-(3-dimethylamino-propyl)-1H-benzoimidazol-2-yl]-amide (BIX 02565), with high potency (IC(50) = 1.1 nM) targeted for the treatment of heart failure. In the present study, we report that despite nanomolar potency at the target, BIX 02565 elicits off-target binding at multiple adrenergic receptor subtypes that are important in the control of vascular tone and cardiac function. To elucidate in vivo the functional consequence of receptor binding, we characterized the cardiovascular (CV) profile of the compound in an anesthetized rat CV screen and telemetry-instrumented conscious rats. Infusion of BIX 02565 (1, 3, and 10 mg/kg) in the rat CV screen resulted in a precipitous decrease in both mean arterial pressure (MAP; to -65 ± 6 mm Hg below baseline) and heart rate (-93 ± 13 beats/min). In telemetry-instrumented rats, BIX 02565 (30, 100, and 300 mg/kg p.o. QD for 4 days) elicited concentration-dependent decreases in MAP after each dose (to -39 ± 4 mm Hg on day 4 at T(max)); analysis by Demming regression demonstrated strong correlation independent of route of administration and influence of anesthesia. Because of pronounced off-target effects of BIX 02565 on cardiovascular function, a high-throughput selectivity screen at adrenergic α(1A) and α(2A) was performed for 30 additional RSK2 inhibitors in a novel chemical series; a wide range of adrenergic binding was achieved (0-92% inhibition), allowing for differentiation within the series. Eleven lead compounds with differential binding were advanced to the rat CV screen for in vivo profiling. This led to the identification of potent RSK2 inhibitors (cellular IC(50) <0.14 nM) without relevant α(1A) and α(2A) inhibition and no adverse cardiovascular effects in vivo.

Indole RSK inhibitors. Part 2: optimization of cell potency and kinase selectivity.

A series of inhibitors for the 90 kDa ribosomal S6 kinase (RSK) based on an 1-oxo-2,3,4,5-tetrahydro-1H-[1,4]diazepino[1,2-a]indole-8-carboxamide scaffold were optimized for cellular potency and kinase selectivity. This led to the identification of compound 24, BIX 02565, an attractive candidate for use in vitro and in vivo to explore the role of RSK as a target for the treatment heart failure.

Indole RSK inhibitors. Part 1: discovery and initial SAR.

A series of inhibitors for the 90 kDa ribosomal S6 kinase (RSK) based on an 1-oxo-2,3,4,5-tetrahydro-1H-[1,4]diazepino[1,2-a]indole-8-carboxamide scaffold were identified through high throughput screening. An RSK crystal structure and exploratory SAR were used to define the series pharmacophore. Compounds with good cell potency, such as compounds 43, 44, and 55 were identified, and form the basis for subsequent kinase selectivity optimization.

Drug discovery using very large numbers of patents: general strategy with extensive use of match and edit operations.

A patent data base of 6.7 million compounds generated by a very high performance computer (Blue Gene) requires new techniques for exploitation when extensive use of chemical similarity is involved. Such exploitation includes the taxonomic classification of chemical themes, and data mining to assess mutual information between themes and companies. Importantly, we also launch candidates that evolve by "natural selection" as failure of partial match against the patent data base and their ability to bind to the protein target appropriately, by simulation on Blue Gene. An unusual feature of our method is that algorithms and workflows rely on dynamic interaction between match-and-edit instructions, which in practice are regular expressions. Similarity testing by these uses SMILES strings and, less frequently, graph or connectivity representations. Examining how this performs in high throughput, we note that chemical similarity and novelty are human concepts that largely have meaning by utility in specific contexts. For some purposes, mutual information involving chemical themes might be a better concept.

Annotating patents with Medline MeSH codes via citation mapping.

Both patents and Medline are important document collections for discovering new relationships between chemicals and biology, searching for prior art for patent applications and retrieving background knowledge for current research activities. Finding relevance to a topic within patents is often made difficult by poor categorization, badly written descriptions, and even intentional obfuscation. Unlike patents, the Medline corpus has Medical Subject Heading (MeSH) keywords manually added to their articles, giving a medically relevant taxonomy to the 18 million article abstracts. Our work attempts to accurately recognize the citations made in patents to Medline-indexed articles, linking them to their corresponding PubMed ID and exploiting the associated MeSH to enhance patent search by annotating the referencing patents with their Medline citations' MeSH codes. The techniques, system features, and benefits are explained.

ChemBrowser: a flexible framework for mining chemical documents.

The ability to extract chemical and biological entities and relations from text documents automatically has great value to biochemical research and development activities. The growing maturity of text mining and artificial intelligence technologies shows promise in enabling such automatic chemical entity extraction capabilities (called "Chemical Annotation" in this paper). Many techniques have been reported in the literature, ranging from dictionary and rule-based techniques to machine learning approaches. In practice, we found that no single technique works well in all cases. A combinatorial approach that allows one to quickly compose different annotation techniques together for a given situation is most effective. In this paper, we describe the key challenges we face in real-world chemical annotation scenarios. We then present a solution called ChemBrowser which has a flexible framework for chemical annotation. ChemBrowser includes a suite of customizable processing units that might be utilized in a chemical annotator, a high-level language that describes the composition of various processing units that would form a chemical annotator, and an execution engine that translates the composition language to an actual annotator that can generate annotation results for a given set of documents. We demonstrate the impact of this approach by tailoring an annotator for extracting chemical names from patent documents and show how this annotator can be easily modified with simple configuration alone.

Two differing presentations, treatments, and outcomes of malignant choroidal melanoma.

BACKGROUND: Choroidal melanomas represent the most common primary malignancy of the eye. As primary eye care providers, optometrists must be able to identify suspicious lesions to facilitate proper referrals and timely treatment. Metastasis occurs in approximately 75% of cases. Ongoing studies such as the Collaborative Ocular Melanoma Study are bringing new information on how to best manage choroidal melanoma. Current treatments include enucleation, plaque brachytherapy, and transpupillary thermotherapy. CASE REPORT: Two patients presented to the Veterans Affairs (VA) Illiana Health Care System optometry clinic for routine visits and had malignant melanomas diagnosed. The first patient was in for a 6-month routine glaucoma follow-up, noting that the right eye seemed to be worse. The second patient was new, complaining of a painful, red eye. Both were referred to a retinal specialist and later treated by an ocular oncologist with enucleation and plaque brachytherapy, respectively. Their differing chief complaints and cases are discussed. CONCLUSION: Patients with malignant choroidal melanomas present with a wide variety of complaints, and optometrists need to be diligent in properly assessing the cause of seemingly common conditions, such as anterior uveitis, as well as performing routine dilated fundus examinations. Given the relationship between size and prognosis, early detection is important.

Human immunodeficiency virus-positive patient with bilateral corneal endothelial deposits.

BACKGROUND: Ocular disorders associated with the human immunodeficiency virus are numerous as are ocular side effects from medications used to treat all of the manifestations of the virus. This report presents a unique case of bilateral, peripheral, and corneal endothelial deposits that may be a result of either the human immunodeficiency virus or the medication rifabutin. Rifabutin was the only medication prescribed that is known to cause endothelial deposits. Rifabutin is part of a multidrug therapy to prevent or treat Mycobacterium avium complex, a common pulmonary disease of immunocompromised individuals. CASE REPORT: A 69-year-old man with a 20-year history of being human immunodeficiency virus-positive presented with bilateral, asymptomatic, peripheral, and corneal endothelial deposits of unknown etiology. Literature research suggested that the deposits did not appear like cytomegalovirus retinitis-related deposits but rather a variant of rifabutin-associated deposits. CONCLUSIONS: These rifabutin-associated deposits differed from known rifabutin-associated deposits previously reported in the literature. These deposits have increased in pigmentation and density 5 years after the patient discontinued the drug. This case may represent another variation of rifabutin-associated endothelial deposits. Knowledge of human immunodeficiency virus and all the associated ocular findings (owing to both the condition and its treatment) is important, because the length of time patients are living with human immunodeficiency virus is increasing.

Small molecule inhibitors of KDR (VEGFR-2) kinase: an overview of structure activity relationships.

The Kinase insert Domain containing Receptor (KDR), alternatively referred to as VEGFR-2, is a receptor for Vascular Endothelial Growth Factors (VEGFs) and functions as a key regulator of angiogenesis, the process by which new capillaries are created from preexisting blood vessels. The induction of angiogenesis, or the "angiogenic switch," is a critical step in tumor progression, and inhibitors of KDR have been demonstrated both to induce tumor regression and reduce metastatic potential in preclinical models. In the last few years, medicinal chemists have expanded the kinase selectivity profile of known inhibitor classes to include KDR, and also identified novel classes of KDR inhibitors. This review presents structure activity relationships (SAR) of small molecule inhibitors of KDR, with an emphasis on the pharmacophore elements of the scaffolds employed. Binding hypotheses based on X-ray crystallographic analyses will also be described. Additionally, the efficacy of representative compounds in in vitro and in vivo models of tumor progression and angiogenesis are discussed.

Inhibition of hypoxia-induced gene transcription by substituted pyrazolyl oxadiazoles: initial lead generation and structure-activity relationships.

The transcription factors hypoxia-inducible factor-1 and -2 (HIF-1 and HIF-2) orchestrate a multitude of processes that allow tumor cells to survive under conditions of low oxygen and nutrients, and that lead to resistance to some apoptotic pathways and facilitate invasion and metastasis. Therefore, inhibition of transactivation by HIF has become an attractive target in cancer research. Herein we present the results of a cell-based screening approach that led to the discovery of substituted 1H-pyrazole-3-carboxamides. Chemical optimization of the hit class with respect to potency and metabolic stability is described; it resulted in novel 5-(1H-pyrazol-3-yl)-1,2,4-oxadiazoles that inhibit the hypoxia-induced accumulation of HIF-1α and HIF-2α. The HIF inhibitory potency in the screening cell system was improved from IC50 190 to 0.7 nM, and significant parts of the SAR are disclosed. For a key compound, the ability to suppress the hypoxia-induced expression of HIF target genes was studied in A549 human lung adenocarcinoma cells. The same compound shows a favorable pharmacokinetic profile in rats after i.v. and p.o. administration.

Identification of a potent sodium hydrogen exchanger isoform 1 (NHE1) inhibitor with a suitable profile for chronic dosing and demonstrated cardioprotective effects in a preclinical model of myocardial infarction in the rat.

Sodium-hydrogen exchanger isoform 1 (NHE1) is a ubiquitously expressed transmembrane ion channel responsible for intracellular pH regulation. During myocardial ischemia, low pH activates NHE1 and causes increased intracellular calcium levels and aberrant cellular processes, leading to myocardial stunning, arrhythmias, and ultimately cell damage and death. The role of NHE1 in cardiac injury has prompted interest in the development of NHE1 inhibitors for the treatment of heart failure. This report outlines our efforts to identify a compound suitable for once daily, oral administration with low drug-drug interaction potential starting from NHE1 inhibitor sabiporide. Substitution of a piperidine for the piperazine of sabiporide followed by replacement of the pyrrole moiety and subsequent optimization to improve potency and eliminate off-target activities resulted in the identification of N-[4-(1-acetyl-piperidin-4-yl)-3-trifluoromethyl-benzoyl]-guanidine (60). Pharmacological evaluation of 60 revealed a remarkable ability to prevent ischemic damage in an ex vivo model of ischemia reperfusion injury in isolated rat hearts.

Rapid analysis of pharmacology for infectious diseases.

Pandemic, epidemic and endemic infectious diseases are united by a common problem: how do we rapidly and cost-effectively identify potential pharmacological interventions to treat infections? Given the large number of emerging and neglected infectious diseases and the fact that they disproportionately afflict the poorest members of the global society, new ways of thinking are required to developed high productivity discovery systems that can be applied to a larger number of pathogens. The growing availability of parasite genome data provides the basis for developing methods to prioritize, a priori, the potential drug target and pharmacological landscape of an infectious disease. Thus the overall objective of infectious disease informatics is to enable the rapid generation of plausible, novel medical hypotheses of testable pharmacological experiments, by uncovering undiscovered relationships in the wealth of biomedical literature and databases that were collected for other purposes. In particular our goal is to identify potential drug targets present in a pathogen genome and prioritize which pharmacological experiments are most likely to discover drug-like lead compounds rapidly against a pathogen (i.e. which specific compounds and drug targets should be screened, in which assays and where they can be sourced). An integral part of the challenge is the development and integration of methods to predict druggability, essentiality, synthetic lethality and polypharmacology in pathogen genomes, while simultaneously integrating the inevitable issues of chemical tractability and the potential for acquired drug resistance from the start.

Two presentations of nonarteritic ischemic optic neuropathy.

BACKGROUND: Nonarteritic ischemic optic neuropathy (NAION) is the most common acute optic neuropathy in adults over the age of 50. Patients affected notice sudden and painless loss of vision in 1 eye, often upon awaking. Studies have found that the opposite eye may be affected in approximately 15% to 20% of cases within a 5-year period. NAION vision loss results from an ischemic event often affecting the short posterior ciliary arteries. This results in optic nerve pallor, nerve fiber layer defects, and corresponding visual field defects. CASE REPORTS: Two cases of NAION are discussed here. The first patient, a 57-year-old woman, had a 10-year history of visual symptoms, and the second, a 66-year-old man, presented in less than a week after first noticing symptoms. Both had predisposing systemic risk factors and resultant visual field loss and decreased visual acuity. CONCLUSIONS: Predisposing factors for NAION include small cup-to-disc ratios of the optic nerve, obstructive sleep apnea, nocturnal hypotension, diabetes, and other vascular diseases. The vision loss is irreversible, and there is no known effective treatment to prevent subsequent disc atrophy or recurring episodes.

Two differing presentations of chronic bilateral anterior uveitis.

BACKGROUND: Bilateral, recurrent, or chronic anterior uveitis requires a diagnostic evaluation to rule out any systemic cause. An understanding of the possible etiologies and their diagnostic criteria is needed to manage these patients. Treating any systemic cause can decrease the recurrent or chronic nature of the uveitis and favorably alter the course. Many possible systemic conditions are capable of causing anterior uveitis, including sarcoidosis. CASE REPORTS: Two cases of chronic, recurrent, bilateral uveitis are presented. Both were evaluated for any systemic etiology. After extensive systemic workups, the first case had no identifiable systemic etiology, whereas the second case was associated with systemic sarcoidosis. CONCLUSION: Although a medical workup may be necessary, it will not always lead to a systemic diagnosis. The literature indicates that up to about 50% of uveitic cases have no identified causes.

Additive effect of dorzolamide hydrochloride to patients taking travoprost: a retrospective study.

BACKGROUND: A retrospective chart review study at a Veterans Affairs hospital evaluated intraocular pressure change after dorzolamide hydrochloride 2% was administered to patients already using travoprost. A literature search found no other study that looked specifically at this combination of drugs. METHODS: A chart review of 46 patients at the Veterans Affairs Illiana Health Care System was performed evaluating the intraocular pressures after dorzolamide hydrochloride was added to travoprost. Baseline intraocular pressures were obtained on patients who had been on travoprost at least 4 months. Endpoint intraocular pressures were then obtained from the visit closest to 6 months after the addition of dorzolamide hydrochloride. RESULTS: An average intraocular pressure reduction of an additional 20.6% was observed after adding only dorzolamide hydrochloride to travoprost. CONCLUSIONS: This study confirmed our clinical observations that dorzolamide hydrochloride added to travoprost is an excellent and safe choice to further lower intraocular pressures.

Mining patents using molecular similarity search.

Text analytics is becoming an increasingly important tool used in biomedical research. While advances continue to be made in the core algorithms for entity identification and relation extraction, a need for practical applications of these technologies arises. We developed a system that allows users to explore the US Patent corpus using molecular information. The core of our system contains three main technologies: A high performing chemical annotator which identifies chemical terms and converts them to structures, a similarity search engine based on the emerging IUPAC International Chemical Identifier (InChI) standard, and a set of on demand data mining tools. By leveraging this technology we were able to rapidly identify and index 3,623,248 unique chemical structures from 4,375,036 US Patents and Patent Applications. Using this system a user may go to a web page, draw a molecule, search for related Intellectual Property (IP) and analyze the results. Our results prove that this is a far more effective way for identifying IP than traditional keyword based approaches.

RAF modulators and methods of use.

Exelixis claims a series of RAF kinase inhibitors based on a 3-oxo-2,3-dihydro-1H-isoindol-1-yl core structure. Both the chemical matter and the biochemical target appear to be new for Exelixis, and many examples have IC(50) values < 100 nM. These compounds are claimed to have the potential to treat diseases that are associated with uncontrolled, abnormal and/or unwanted cellular activities such as cancer.