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Supplementary Data 3 from Increased Fibroblast Growth Factor-Inducible 14 Expression Levels Promote Glioma Cell Invasion via Rac1 and Nuclear Factor-κB and Correlate with Poor Patient Outcome

Supplementary Data 1 from Increased Fibroblast Growth Factor-Inducible 14 Expression Levels Promote Glioma Cell Invasion via Rac1 and Nuclear Factor-κB and Correlate with Poor Patient Outcome

Supplementary Data 2 from Increased Fibroblast Growth Factor-Inducible 14 Expression Levels Promote Glioma Cell Invasion via Rac1 and Nuclear Factor-κB and Correlate with Poor Patient Outcome

Supplementary Data 4 from Increased Fibroblast Growth Factor-Inducible 14 Expression Levels Promote Glioma Cell Invasion via Rac1 and Nuclear Factor-κB and Correlate with Poor Patient Outcome

Glial tumors progress to malignant grades by heightened proliferation and relentless dispersion throughout the central nervous system. Understanding genetic and biochemical processes that foster these behaviors is likely to reveal specific and effective targets for therapeutic intervention. Our current report shows that the fibroblast growth factor-inducible 14 (Fn14), a member of the tumor necrosis factor (TNF) receptor superfamily, is expressed at high levels in migrating glioma cells in vitro and invading glioma cells in vivo. Forced Fn14 overexpression stimulates glioma cell migration and invasion, and depletion of Rac1 by small interfering RNA inhibits this cellular response. Activation of Fn14 signaling by the ligand TNF-like weak inducer of apoptosis (TWEAK) stimulates migration and up-regulates expression of Fn14; this TWEAK effect requires Rac1 and nuclear factor-κB (NF-κB) activity. The Fn14 promoter region contains NF-κB binding sites, which mediate positive feedback causing sustained overexpression of Fn14 and enduring glioma cell invasion. Furthermore, Fn14 gene expression levels increase with glioma grade and inversely correlate with patient survival. These results show that the Fn14 cascade operates as a positive feedback mechanism for elevated and sustained Fn14 expression. Such a feedback loop argues for aggressive targeting of the Fn14 axis as a unique and specific driver of glioma malignant behavior. (Cancer Res 2006; 66(19): 9535-42)

A target-based drug discovery strategy has led to a bias away from low molecular weight (MWT) drug discovery. Analysis of the ACS chemistry registration system shows that most low MWT drugs were first made in the time era before target-based drug discovery. Therapeutic activity among most low MWT drugs was identified in the era of phenotypic drug discovery when drugs were selected based on their phenotypic effects and before in vitro screening, mechanism of action considerations and experiences with fragment screening became known. The common perception that drugs cannot be found among low MWT compounds is incorrect based on both drug discovery history and our own experience with MLR-1023. The greater proportion of low MWT compounds that are commercially available compared to higher MWT compounds is a factor that should facilitate biology study. We posit that low MWT compounds are more suited to identification of new therapeutic activity using phenotypic screens provided that the phenotypic screening method has enough screening capacity. On-target and off-target therapeutic activities are discussed from both a chemistry and biology perspective because of a concern that either phenotypic or low MWT drug discovery might bias towards promiscuous compounds that combine on-target and off-target effects. Among ideal drug repositioning candidates (late-stage pre-clinical or clinically-experience compounds), pleiotropic activity (multiple therapeutic actions) is far more likely due to on-target effects arising where a single target mediates multiple therapeutic benefits, a desirable outcome for drug development purposes compared to the off-target alternative. Our exemplar of a low MWT compound, MLR-1023, discovered by phenotypic screening and subsequently found to have a single mechanism of action would have been overlooked based on current era medicinal chemistry precedent. The diverse therapeutic activities described for this compound by us, and others arise from the same pleiotropic lyn kinase activation molecular target. MLR-1023 serves as a proof-of-principle that potent, on target, low MWT drugs can be discovered by phenotypic screening.

The drug discovery and development process is notoriously wrought with a high failure rate. A key contributor to this phenomenon is our significantly incomplete understanding of the biological systems that we are manipulating. We propose that an element of this lack of understanding is the degree to which the therapeutic targets that are modulated by drugs that we work with are involved in more biology, and thereby more therapeutic potential, than most investigators appreciate. This is reflected in the high rate at which drugs are used for indications other than the ones for which they were originally developed. We have coined this phenomenon of multi-therapeutic application for a single drug, pharmacological pleiotropy. MLR-1023, with its activation of Lyn kinase, provides an excellent illustration of pharmacological pleiotropy. Here we provide several examples detailed with scientific understanding across diverse therapeutic space, animal model validation in every case, and with at least two instances of clinical validation. The story also serves as a good example of the fact that there is much more to successful drug discovery and development beyond accomplishing the already arduous task of clinically proving that a drug is safe, well tolerated, and effective for the intended indication.

Increasingly, the pharmaceutical industry has been plagued with escalating costs coupled with decreasing productivity, leading to speculation that the pharmaceutical business model as we know it may be broken. It is in this context that many in the industry have been searching for innovative strategies to reduce cost as well as risk. Both phenotypic screening and drug repositioning represent discovery approaches that fit this description. Melior Discovery is unique among drug discovery organizations in its use of an in vivo phenotypic screening platform used to reposition discontinued clinical-stage compounds. The story of Melior's lead candidate, MLR-1023, illustrates this approach. We show that when dealing with “privileged” substrate (discontinued clinical-stage compounds that exhibit good human safety and tolerability characteristics and other favorable drug-like characteristics), an in vivo screening platform, comprising a wide array of animal models of human disease, is ideal. Many years of conducting these screens on hundreds of compounds has shown the frequency with which otherwise unpredicted therapeutic potential is associated with drug targets that were thought to be well-characterized.

The rule of five (Ro5), based on physicochemical profiles of phase II drugs, is consistent with structural limitations in protein targets and the drug target ligands. Three of four parameters in Ro5 are fundamental to the structure of both target and drug binding sites. The chemical structure of the drug ligand depends on the ligand chemistry and design philosophy. Two extremes of chemical structure and design philosophy exist; ligands constructed in the medicinal chemistry synthesis laboratory without input from natural selection and natural product (NP) metabolites biosynthesized based on evolutionary selection. Exceptions to Ro5 are found mostly among NPs. Chemistry chameleon-like behavior of some NPs due to intra-molecular hydrogen bonding as exemplified by cyclosporine A is a strong contributor to NP Ro5 outliers. The fragment derived, drug Navitoclax is an example of the extensive expertise, resources, time and key decisions required for the rare discovery of a non-NP Ro5 outlier.

Study objective We compare emergency department (ED) operational metrics obtained in the first year of a rotational patient assignment system (in which patients are assigned to physicians automatically according to an algorithm) with those obtained in the last year of a traditional physician self-assignment system (in which physicians assigned themselves to patients at physician discretion). Methods This was a pre-post retrospective study of patients at a single ED with no financial incentives for physician productivity. Metrics of interest were length of stay; arrival-to-provider time; rates of left before being seen, left subsequent to being seen, early returns (within 72 hours), and early returns with admission; and complaint ratio. Results We analyzed 23,514 visits in the last year of physician self-assignment and 24,112 visits in the first year of rotational patient assignment. Rotational patient assignment was associated with the following improvements (percentage change): median length of stay 232 to 207 minutes (11%), median arrival to provider time 39 to 22 minutes (44%), left before being seen 0.73% to 0.36% (51%), and complaint ratio 9.0/1,000 to 5.4/1,000 (40%). There were no changes in left subsequent to being seen, early returns, or early returns with admission. Conclusion In a single facility, the transition from physician self-assignment to rotational patient assignment was associated with improvement in a broad array of ED operational metrics. Rotational patient assignment may be a useful strategy in ED front-end process redesign.

Drug discovery requires the combination of medicinal chemistry and biology. In this article Chris Lipinski, the medicinal chemist, describes the chemical origins at Pfizer of Tolimidone1 the starting point for the repurposed MLR-1023 (Ochman et al., 2012). Andrew Reaume, the biologist, describes his motivation to develop a high quality (i.e. in vivo model) phenotypic screening platform as an ideal drug repositioning platform.

The “rule of 5” has become a mainstay of decision-making in the pharmaceutical industry as well as in nonindustrial (academic and institutional) drug development. However the authors of the original paper never intended for “double cutoffs” to preclude development of new drug leads for parasitic diseases., Graphical abstract Image 1, Highlights • “rule of 5” is a mainstay of decision-making in drug screening efforts. • Acts as an absorption-permeability alert procedure to guide medicinal chemists. • Never intended to apply to parasitic infectious diseases. • Should not impede anti-parasitic drug development.

The availability of structures and linked bioactivity data in databases is powerfully enabling for drug discovery and chemical biology. However, we now review some confounding issues with the divergent expansions of public and commercial sources of chemical structures. These are associated with not only expanding patent extraction but also increasingly large vendor collections amassed via different selection criteria between SciFinder from Chemical Abstracts Service (CAS) and major public sources such as PubChem, ChemSpider, UniChem, and others. These increasingly massive collections may include both real and virtual compounds, as well as so-called prophetic compounds from patents. We address a range of issues raised by the challenges faced resolving the NIH probe compounds. In addition we highlight the confounding of prior-art searching by virtual compounds that could impact the composition of matter patentability of a new medicinal chemistry lead. Finally, we propose some potential solutions.

In a decade with over half a billion dollars of investment, more than 300 chemical probes have been identified to have biological activity through NIH funded screening efforts. We have collected the evaluations of an experienced medicinal chemist on the likely chemistry quality of these probes based on a number of criteria including literature related to the probe and potential chemical reactivity. Over 20% of these probes were found to be undesirable. Analysis of the molecular properties of these compounds scored as desirable suggested higher pKa, molecular weight, heavy atom count, and rotatable bond number. We were particularly interested whether the human evaluation aspect of medicinal chemistry due diligence could be computationally predicted. We used a process of sequential Bayesian model building and iterative testing as we included additional probes. Following external validation of these methods and comparing different machine learning methods, we identified Bayesian models with accuracy comparable to other measures of drug-likeness and filtering rules created to date.

The terminal carbonate complex of southeast Spain is a Miocene (Messinian) unit of oolite, microbialite, and coralgal reefs deposited in association with glacioeustasy and evaporitic drawdown. The relationship between paleotopography and sea level history is useful for prediction of microbialite and oolite reservoir facies in the subsurface. Four sequences record sea level change with minimum amplitudes of 32–77 m (105–253 ft). Sequences commonly have local basal stromatolites overlain by local thrombolites, ooid grainstone, volcaniclastic-rich planar-bedded ooid grainstone, and fenestral ooid grainstone. At low substrate positions, thrombolite boundstones are thicker and laterally more continuous than at higher positions. At intermediate substrate positions (relative to sea level history), sequences have a build-and-fill architecture, characterized by a relief-building phase and a relief-filling phase, with thin sequences draping paleotopography. Microbialites dominate during the relative sea level rises and build topographic relief. Oolites dominate during the relative sea level falls and fill topographic relief. At higher substrate positions, close to highstand, sequences thicken and yield stratigraphic character that is inconsistent with a build-and-fill model. Apparently, the build-and-fill model requires an intermediate-elevation substrate position and nonoptimal carbonate productivity during rapid sea level change. Sequences progressively show increasing diversity and more normal marine organisms, possibly caused by decreasing aridity. Lithofacies of the La Molata area show evidence of more restricted conditions compared to the La Rellana-Ricardillo area lithofacies, likely because La Molata was in an embayment. These results show that distribution of oolite, microbialite, and reef facies are predictable given known interaction among sea level, paleotopography of the depositional surface (substrate), and coastline configuration.

Static three-dimensional (3-D) reservoir analog models were constructed for the Miocene terminal carbonate complex (TCC) in southeastern Spain. The models used field data collected from two areas containing exceptional 3-D exposures (La Molata; La Rellana-Ricardillo). Four TCC sequences in each area are composed of oolite, microbialite (thrombolites, stromatolites), bioclastic sands, and coralgal reefs deposited over paleotopographic relief of 33–76 m (108–249 ft). The models integrate field, laboratory, and petrophysical data with results providing a workflow and reservoir analogs useful in evaluating oolilte and microbialite reservoir characteristics in relation to paleotopography and sea level change. Results from this study reveal favorable reservoir-quality values with the potential for substantial hydrocarbon storage for many lithofacies. Flow and baffle facies were distinguished for the models based on thickness, lateral distribution, porosity, and permeability values. Trough cross-bedded ooid grainstone is volumetrically the most abundant lithofacies within both models, is laterally extensive across the entirety of sequences, has large storage capacities with good permeability, and has good connectivity with other flow facies. This facies represents the best reservoir-quality facies and would be the primary target for hydrocarbon exploitation. Microbialites act both as reservoir and baffle facies. Thrombolites, in particular, are concentrated downslope and in a more restricted embayment but vary between porous and nonporous facies. Stromatolites and fenestral ooid grainstones are concentrated at sequence boundaries and would create laterally extensive baffles with significant thicknesses at the sequence boundaries. Sea level interacting with both paleotopography and paleogeography were identified as the main controls on sequence development and reservoir heterogeneity. An understanding of these controls can aid in exploitation and identification of oolite-microbialite sequences.

Telemedical physician triage (TPT) is a potential application of telemedicine in the emergency department (ED). We report the technical success, patient satisfaction, and effect on ED throughput metrics (length of stay [LOS] and time to physician evaluation [TPE]) of TPT performed on a mobile platform.Patients underwent standard nursing triage with or without TPT. Technical success is reported as raw data. Patient satisfaction is reported as raw data±standard deviation on a 5-point (low-to-high) scale. LOS and TPE are reported as mean±SD [95% CI] values. Statistical analyses of LOS and TPE are via two-sample t test.One hundred six patients were registered during intervention periods, and TPT was completed in 36 (34%). One hundred ninety-six patients were registered during control periods. The technical success rate was 95%. Average patient satisfaction was 4.7 on a 5-point scale. The primary analysis (106 patients) showed no change in LOS (266±101 [244-288] min versus 258±172 [234-282] min) but a trend toward improved TPE with TPT (35±28 [29-41] min versus 42±31 [38-46] min) (p=0.052). A secondary analysis (36 patients) showed no change in LOS (273±125 [231-316] min versus 258±172 [234-282] min) but improved TPE with TPT (16±15 [11-21] min versus 42±31 [38-46] min) (p0.0001).TPT in the ED on a mobile platform was technically successful, well accepted by patients, and associated with a decrease in TPE but not LOS.

Background Bioassay data analysis continues to be an essential, routine, yet challenging task in modern drug discovery and chemical biology research. The challenge is to infer reliable knowledge from big and noisy data. Some aspects of this problem are general with solutions informed by existing and emerging data science best practices. Some aspects are domain specific, and rely on expertise in bioassay methodology and chemical biology. Testing compounds for biological activity requires complex and innovative methodology, producing results varying widely in accuracy, precision, and information content. Hit selection criteria involve optimizing such that the overall probability of success in a project is maximized, and resource-wasteful “false trails” are avoided. This “fail-early” approach is embraced both in pharmaceutical and academic drug discovery, since follow-up capacity is resource-limited. Thus, early identification of likely promiscuous compounds has practical value. Results Here we describe an algorithm for identifying likely promiscuous compounds via associated scaffolds which combines general and domain-specific features to assist and accelerate drug discovery informatics, called Badapple: bioassay-data associative promiscuity pattern learning engine. Results are described from an analysis using data from MLP assays via the BioAssay Research Database (BARD) http://bard.nih.gov. Specific examples are analyzed in the context of medicinal chemistry, to illustrate associations with mechanisms of promiscuity. Badapple has been developed at UNM, released and deployed for public use two ways: (1) BARD plugin, integrated into the public BARD REST API and BARD web client; and (2) public web app hosted at UNM. Conclusions Badapple is a method for rapidly identifying likely promiscuous compounds via associated scaffolds. Badapple generates a score associated with a pragmatic, empirical definition of promiscuity, with the overall goal to identify “false trails” and streamline workflows. Unlike methods reliant on expert curation of chemical substructure patterns, Badapple is fully evidence-driven, automated, self-improving via integration of additional data, and focused on scaffolds. Badapple is robust with respect to noise and errors, and skeptical of scanty evidence. Electronic supplementary material The online version of this article (doi:10.1186/s13321-016-0137-3) contains supplementary material, which is available to authorized users.

Importance of the field: The focal adhesion tyrosine kinases FAK and Pyk2 are uniquely situated to act as critical mediators for the activation of signaling pathways that regulate cell migration, proliferation and survival. By coordinating adhesion and cytoskeletal dynamics with survival and growth signaling, FAK and Pyk2 represent molecular therapeutic targets in cancer as malignant cells often exhibit defects in these processes.Areas covered in this review: This review examines the structure and function of the focal adhesion kinase Pyk2 and intends to provide a rationale for the employment of modulating strategies that include both catalytic and extra-catalytic approaches that have been developed in the last 3 – 5 years.What the reader will gain: Targeting tyrosine kinases in oncology has focused on the ATP binding pocket as means to inhibit catalytic activity and downregulate pathways involved in tumor invasion. This review discusses the available catalytic inhibitors and compares them to the alternat...

Disease progression of glioblastoma involves a complex interplay between tumor cells and the peri-tumor microenvironment. The propensity of malignant glioma cells to disperse throughout the brain typifies the disease and portends a poor response to surgical resection, radio-therapy, and current chemotherapeutics. The focal adhesion kinases FAK and Pyk2 function as important signaling effectors in glioma through stimulation of pro-migratory and proliferative signaling pathways. In the current study, we examined the importance of Pyk2 and FAK in the pathobiology of malignant glioma in an intracranial xenograft model. We show that mice with xenografts established with glioma cells with specific knockdown of Pyk2 or FAK expression by RNA interference had significantly increased survival compared to control mice. Furthermore, the effect of inhibition of Pyk2 activity in xenografts was compared to the effect of knockdown of Pyk2 expression. Inhibition of Pyk2 activity by stable expression an autonomous FERM domain in glioma cells slowed disease progression in the intracranial xenograft model. In contrast, expression of a variant FERM domain that does not inhibit Pyk2 activity did not alter survival. These results substantiate the disease relevance of both Pyk2 and FAK in glioma and suggest a novel approach to target Pyk2 for therapeutic benefit.

We propose a framework with simple proxies to dissect the relative energy contributions responsible for standard drug discovery binding activity. We explore a rule of thumb using hydrogen-bond donors, hydrogen-bond acceptors and rotatable bonds as relative proxies for the thermodynamic terms. We apply this methodology to several datasets (e.g., multiple small molecules profiled against kinases, Mycobacterium tuberculosis (Mtb) high throughput screening (HTS) and structure based drug design (SBDD) derived compounds, and FDA approved drugs). We found that Mtb active compounds developed through SBDD methods had statistically significantly larger PEnthalpy values than HTS derived compounds, suggesting these compounds had relatively more hydrogen bond donor and hydrogen bond acceptors compared to rotatable bonds. In recent FDA approved medicines we found that compounds identified via target-based approaches had a more balanced enthalpic relationship between these descriptors compared to compounds identified via phenotypic screens As it is common to experimentally optimize directly for total binding energy, these computational methods provide alternative calculations and approaches useful for compound optimization alongside other common metrics in available software and databases.

Intellectual property considerations decrease research productivity in subtle and unanticipated ways. Chemical probe exchange between Pharma and academia is hindered by academic IP interests. These are perceived as a subtle nuisance by the academic researcher. Novel ligands for oral targets are historically few and numbers of economically attractive oral drug targets are limited. Economically speculative targets lie in the academic domain but the medicinal chemistry to explore these in a drug discovery sense lies in Pharma and cooperation between the two is hindered by very different academic and Pharma views on chemical quality. Tools and probes for academic target validation can accommodate looser chemical quality criteria as opposed to the very strict chemical quality criteria required in Pharma drug discovery.

Dissolution of organic compounds in DMSO in HTS plate or tube format is a difficult problem as users move to higher compression plate formats. Precipitation of compounds from DMSO screening stocks is a recognized problem in the HTS materials management process. The adverse effect of freeze thaw cycles on DMSO stock solutions stored in plate format as a result of cherry picking operations has led to the gradual replacement of plate-based storage with tube-based storage so as to minimize the number of freeze thaw cycles. Compound solubility in DMSO is markedly decreased by uptake of small quantities of water. We attribute this effect to the non ideal properties of DMSO water mixtures such that cavity formation in solvent, a necessary step in dissolution, is more difficult in wet DMSO than in dry DMSO or in pure water. We report here that efficient compound dissolution is possible even in 384 well format by the use of in-well plate-based sonication. Surprisingly, compounds precipitated from DMSO stocks either by water uptake or repeated freeze thaw cycles can be re-dissolved by low energy sonication. Finally, we demonstrate that precipitation of compound from DMSO stock solutions is synergistically enhanced by water uptake into DMSO compound stock solutions as well as by increasing the number of freeze thaw cycles.

Citations in CAS SciFinder to the rule-of-five (RO5) publication will exceed 1000 by year-end 2004. Trends in the RO5 literature explosion that can be discerned are the further definitions of drug-like. This topic is explored in terms of drug-like physicochemical features, drug-like structural features, a comparison of drug-like and non-drug-like in drug discovery and a discussion of how drug-like features relate to clinical success. Physicochemical features of CNS drugs and features related to CNS blood-brain transporter affinity are briefly reviewed. Recent literature on features of non-oral drugs is reviewed and how features of lead-like compounds differ from those of drug-like compounds is discussed. Most recently, partly driven by NIH roadmap initiatives, considerations have arisen as to what tool-like means in the search for chemical tools to probe biology space. All these topics frame the scope of this short review/perspective.

Background Although the use of a physician and nurse team at triage has been shown to improve emergency department (ED) throughput, the mechanism(s) by which these improvements occur is less clear. Objectives 1) To describe the effect of a Rapid Medical Assessment (RMA) team on ED length of stay (LOS) and rate of left without being seen (LWBS); 2) To estimate the effect of RMA on different groups of patients. Methods For Objective 1, we compared LOS and LWBS on dates when we utilized RMA to comparable dates when we did not. For Objective 2, we utilized patient logs to divide patients into groups and estimated the effects of the RMA on each. Results Objective 1. LOS fell from 297.8 min pre-RMA to 261.7 min during RMA, an improvement of 36.1 (95% confidence interval 21.8–50.4) min; LWBS did not change significantly. Objective 2. Patients seen and dispositioned by the RMA had an estimated decrease in LOS of 117.8 min (estimated decrease in LOS of 45%), but patients seen by the RMA whose care was transitioned to the main ED had an estimated increase in LOS of 25.0 min (estimated increase in LOS of 8%). Conclusions On a system level, the addition of an RMA shift at a single facility was associated with an improvement in LOS, but not LWBS. On a mechanistic level, it seems that improvements occurred as a result of the rapid disposition component of the RMA rather than placing advanced orders at triage.

Experimental and computational approaches to estimate solubility and permeability in discovery and development settings are described. In the discovery setting 'the rule of 5' predicts that poor absorption or permeation is more likely when there are more than 5 H-bond donors, 10 H-bond acceptors, the molecular weight (MWT) is greater than 500 and the calculated Log P (CLogP) is greater than 5 (or MlogP > 4.15). Computational methodology for the rule-based Moriguchi Log P (MLogP) calculation is described. Turbidimetric solubility measurement is described and applied to known drugs. High throughput screening (HTS) leads tend to have higher MWT and Log P and lower turbidimetric solubility than leads in the pre-HTS era. In the development setting, solubility calculations focus on exact value prediction and are difficult because of polymorphism. Recent work on linear free energy relationships and Log P approaches are critically reviewed. Useful predictions are possible in closely related analog series when coupled with experimental thermodynamic solubility measurements.

The changes in screening philosophy over a 40 year period from in vivo phenotypic screening to a reductionist mechanism-based in vitro search for a single selective compound against a single target are described. Examples are given of the shortcomings of the reductionist paradigm and the advantages of the phenotypic and multi-target screening approaches towards drug discovery and repurposing. Non-mechanism biased phenotypic screening offers the advantages of enhanced target opportunity space and is a good match for screening of ligands covering narrow chemistry space, e.g. natural products. Retrospective analysis suggests that phenotypic screening is better than mechanistic screening in finding first in class compounds, particularly for the more complex disease targets.

2(1H)-pyrimidinone,5-(3-methylphenoxy) (MLR-1023) is a candidate for the treatment of type 2 diabetes. The current studies were aimed at determining the mechanism by which MLR-1023 mediates glycemic control. In these studies, we showed that MLR-1023 reduced blood glucose levels without increasing insulin secretion in vivo. We have further determined that MLR-1023 did not activate peroxisome proliferator-activated α, δ, and γ receptors or glucagon-like peptide-1 receptors or inhibit dipeptidyl peptidase-4 or α-glucosidase enzyme activity. However, in an in vitro broad kinase screen MLR-1023 activated the nonreceptor-linked Src-related tyrosine kinase Lyn. MLR-1023 increased the V(max) of Lyn with an EC(50) of 63 nM. This Lyn kinase activation was ATP binding site independent, indicating that MLR-1023 regulated the kinase through an allosteric mechanism. We have established a link between Lyn activation and blood glucose lowering with studies showing that the glucose-lowering effects of MLR-1023 were abolished in Lyn knockout mice, consistent with existing literature linking Lyn kinase and the insulin-signaling pathway. In summary, these studies describe MLR-1023 as a unique blood glucose-lowering agent and show that MLR-1023-mediated blood glucose lowering depends on Lyn kinase activity. These results, coupled with other results (J Pharmacol Exp Ther 342:23-32, 2012), suggest that MLR-1023 and Lyn kinase activation may be a new treatment modality for type 2 diabetes.

MLR-1023 [Tolimidone; CP-26154; 2(1H)-pyrimidinone, 5-(3-methylphenoxy)] is an allosteric Lyn kinase activator that reduces blood glucose levels in mice subjected to an oral glucose tolerance test (J Pharmacol Exp Ther 342:15-22, 2012). The current studies were designed to define the role of insulin in MLR-1023-mediated blood glucose lowering, to evaluate it in animal models of type 2 diabetes, and to compare it to the activities of selected existing diabetes therapeutics. Results from these studies show that in an acute oral glucose tolerance test MLR-1023 evoked a dose-dependent blood glucose-lowering response that was equivalent in magnitude to that of metformin without eliciting a hypoglycemic response. In streptozotocin-treated, insulin-depleted mice, MLR-1023 administration did not affect blood glucose levels. However, MLR-1023 potentiated the glucose-lowering activity of exogenously administered insulin, showing that MLR-1023-mediated blood glucose lowering was insulin-dependent. In a hyperinsulinemic/euglycemic clamp study, orally administered MLR-1023 increased the glucose infusion rate required to sustain blood glucose levels, demonstrating that MLR-1023 increased insulin receptor sensitivity. In chronically treated db/db mice, MLR-1023 elicited a dose-dependent and durable glucose-lowering effect, reduction in HbA1c levels and preservation of pancreatic β-cells. The magnitude of effect was equivalent to that seen with rosiglitazone but with a faster onset of action and without causing weight gain. These studies show that MLR-1023 is an insulin receptor-potentiating agent that produces a rapid-onset and durable blood glucose-lowering activity in diabetic animals.

This commentary describes two simple procedures using commercially available software packages that greatly facilitate the creation of and replication of data sets intended for quantitative structure activity relationship (QSAR) and quantitative structure property relationship (QSPR) studies. Used properly, the procedures allow the capture of individual chemical structures from the Chemical Abstracts Service (CAS) SciFinder software in a computer readable format that is recognized by most chemical database and computational calculation software packages. The researcher need not draw in a chemical structure to create a Molecular Design Limited (MDL) mol file, the 2D connection table format most commonly used to create the chemical depiction of compound or drug. The MDL mol format is needed so that properties can be calculated from the chemical structure alone. All that is required is that the compound or drug be located in SciFinder. The procedures are described in considerable detail because the key procedures for capturing structures from Chemical Abstracts Service (CAS) SciFinder through the use of Accelrys’Accord for Excel software are undocumented in either software. Also described is a batch procedure that allows search of CAS SciFinder for the exact chemical structure of up to 25 compounds. Without use of this procedure, Scifinder can only be searched for an exact chemical structure a single compoundat a time using a query consisting of a drawn in structure. Both the single-mode structure retrieval and batch-mode compound search procedures result in very significant time savings to the researcher creating or replicating QSAR/QSPR data sets and likelymay enable structure searches that previously might not have been attempted because of researcher time constraints. These procedures do not affect positively or negatively the cost to the user of the searches against the SciFinder software. These costs are determined by CAS policy, and depend on the numbers of structures/compounds searched. Locating a compound or drug in SciFinder is most accurately done using the CAS Registry Number. The CAS Registry Number uniquely identifies a specific compound and salt form. Older deleted CAS Registry Numbers for a specific compound may be encountered, but a search on the current (or older) CAS Registry Numbers will always bring up the correct compound. If different salt forms of the same compound exist in the CAS databases, they will have different CAS Registry Numbers. By contrast, a search by compound or drug namemay fail. IUPAC names for compounds are of no value in searches against SciFinder because IUPAC Names are not listed in the records. Commonly used drug names work fairly well. However, it is frequent to find variant or misspelled drug names in the scientific literature. A deviation between a search input name and the names stored in CAS databases in only a single letter or number will result in a search failure. Searchesusingdrug tradenames (as invery recent drugs) or company code numbers (as in early discovery stage compounds) fail more frequently than searches using common names.

There is an urgent need for new drugs against tuberculosis which annually claims 1.7-1.8 million lives. One approach to identify potential leads is to screen in vitro small molecules against Mycobacterium tuberculosis (Mtb). Until recently there was no central repository to collect information on compounds screened. Consequently, it has been difficult to analyze molecular properties of compounds that inhibit the growth of Mtb in vitro. We have collected data from publically available sources on over 300 000 small molecules deposited in the Collaborative Drug Discovery TB Database. A cheminformatics analysis on these compounds indicates that inhibitors of the growth of Mtb have statistically higher mean logP, rule of 5 alerts, while also having lower HBD count, atom count and lower PSA (ChemAxon descriptors), compared to compounds that are classed as inactive. Additionally, Bayesian models for selecting Mtb active compounds were evaluated with over 100 000 compounds and, they demonstrated 10 fold enrichment over random for the top ranked 600 compounds. This represents a promising approach for finding compounds active against Mtb in whole cells screened under the same in vitro conditions. Various sets of Mtb hit molecules were also examined by various filtering rules used widely in the pharmaceutical industry to identify compounds with potentially reactive moieties. We found differences between the number of compounds flagged by these rules in Mtb datasets, malaria hits, FDA approved drugs and antibiotics. Combining these approaches may enable selection of compounds with increased probability of inhibition of whole cell Mtb activity.

Despite widespread use of anti-CD20 antibodies as therapeutic agents for oncologic and autoimmune indications, precise descriptions of killing mechanisms remain incomplete. Complement-dependent cytolysis and antibody-dependent cell-mediated cytotoxicity are indicated as modes of target cell depletion; however, the importance of apoptosis induction is controversial. Studies showing that the therapeutic anti-CD20 antibody rituximab (Rituxan) mediates apoptosis of tumor cell targets in vitro after cross-linking by anti-Fc reagents suggest that enhancement strategies applied to Fc-independent activities for anti-CD20 antibodies could improve therapeutic efficacy. An anti-CD20 antibody designated DXL625, with autophilic properties such as increased binding avidity, is shown here to independently induce caspase-mediated apoptosis of an established B-cell lymphoma line in vitro. Depletion of membrane cholesterol or chelation of extracellular calcium abrogated the pro-apoptotic activity of DXL625, indicating that intact lipid rafts and calcium are required for this activity. The Fc-mediated complement-dependent and antibody-dependent cellular killing mechanisms are maintained by DXL625 despite conjugation of the parental Rituxan antibody to the autophilic DXL peptide sequence. This study shows a strategy for improving anti-CD20 immunotherapy by endowing therapeutic antibodies with self-interacting properties.

Olfactory and gustatory hallucinations are not often encountered in the acute care setting but may represent the subtle presenting features of a significant underlying disease process. We describe a patient whose most striking presenting symptoms were of olfactory and gustatory hallucinations and in whom the diagnosis and treatment of a new brain tumor and partial status epilepticus occurred entirely in the emergency department. The lesion was subsequently identified as glioblastoma multiforme involving the hippocampus and amygdala.

Between 2004 and 2008, the US National Institutes of Health Molecular Libraries and Imaging initiative pilot phase funded 10 high-throughput screening centers, resulting in the deposition of 691 assays into PubChem and the nomination of 64 chemical probes. We crowdsourced the Molecular Libraries and Imaging initiative output to 11 experts, who expressed medium or high levels of confidence in 48 of these 64 probes.

The invasion of malignant glioma cells into the surrounding normal brain precludes effective clinical treatment. In this report, we investigated the role of the NH2-terminal FERM domain in the regulation of the promigratory function of Pyk2. We report that the substitution of residues that constitute a small cleft on the surface of the F3 module of the FERM domain do not significantly alter Pyk2 expression but result in the loss of Pyk2 phosphorylation. A monoclonal antibody, designated 12A10, specifically targeting the Pyk2 FERM domain was generated and recognizes an epitope located on the β5C-α1C surface of the F3 module of the FERM domain. Amino acid substitutions in the F3 module that resulted in the loss of Pyk2 phosphorylation also inhibited the binding of 12A10, suggesting that the 12A10 epitope overlaps a site that plays a role in Pyk2 activity. Conjugation of 12A10 to a membrane transport peptide led to intracellular accumulation and inhibition of glioma cell migration in a concentration-dependent manner. A single chain Fv fragment of 12A10 was stable when expressed in the intracellular environment, interacted directly with Pyk2, reduced Pyk2 phosphorylation, and inhibited glioma cell migration in vitro. Stable intracellular expression of the 12A10 scFv significantly extended survival in a glioma xenograft model. Together, these data substantiate a central role for the FERM domain in regulation of Pyk2 activity and identify the F3 module as a novel target to inhibit Pyk2 activity and inhibit glioma progression. [Mol Cancer Ther 2009;8(6):1505–14]

A medicinal chemist combines organic synthesis expertise and the ability to optimize chemistry structure-activity relationships (SAR) based on relevant biomedical information so as to achieve project goals. The ability to optimize chemistry SAR consists of both the easier to explain logical stepwise structural modification that is often described by quantitative structure-activity relationships (QSAR) and the more difficult to explain exercise of high-order pattern recognition. Optimizing SAR is full of traps for the unwary. What are the pros and cons of various types of screens Should one believe the screening data How does one optimize against multiple sometimes conflicting properties What types of compounds are worth screening How does one judge the quality of a screening hit Very importantly, drug discovery is a team exercise in which the medicinal chemist plays a key facilitating role. Given good interpersonal skills, the medicinal chemist's training is broad enough to enable cooperative interactions across the whole discovery team. Chemistry pattern recognition is the unique skill that the medicinal chemist contributes to drug discovery. The ability to relate chemistry structure to biological activity and to change chemistry structure so as to change a variety of biomedical parameters in a desired direction leads to the successful “drug hunter.”

Log P values have been measured for twenty phenyl and benzyl five membered heterocycles and alicyclic analogs that might function as acidic bioisosteres. pKa's have been measured by potentiometric titration in water and 1:1 dioxane-water. From this experimental data, twelve missing fragmental CLOGP values are derived for use in calculating Log P values according to the Pomona College MedChem program. Log P values of some of the simple benzyl and phenyl heterocycles are compared to those measured for four clinically used drugs containing the same acidic moieties. Sulfonyl urea and acyl sulfonamide moieties have similar pKa and Log P values suggesting that these groups might be explored as bioisosteres.

Two positions on the acetylcholinesterase (AChE) inhibitor, 9-amino-1,2,3,4-tetrahydroacridine (THA), have been identified which can be modified to vary log P, log D and pKa values. Most importantly, these changes can be carried out without altering its AChE activity.

Publisher Summary Considerable literature supports the stability over time of the physicochemical properties of an approved drug. This chapter focuses on the recent changes in synthetic chemistry practices, shows how these changes are modulated by the target impact on compound properties, and provides guidance on how the pattern of early compound properties can be improved. Changes in medicinal chemistry synthetic practice can be broadly characterized into three main areas: changes related to synthesis of one compound at a time and moderate output parallel synthesis, the more radical changes related to combinatorial chemistry, and the chemistry involved in generation of fragment screening libraries. This chapter primarily emphasizes issues related to the design of combinatorial libraries and secondarily with the newer area of fragment libraries. The design of combinatorial libraries with drug-like properties is a trade-off between efficient chemistry and therefore better numerical compound output on one side and increasingly difficult chemistry but better physicochemical properties on the other. Effectiveness of ADME (absorption, distribution, metabolism, excretion) design implementation depends on whether chemistry protocol development or chemistry production is rate determining. Computational models for ADME properties work best when the models are based on single mechanism experimental assays.

The synthesis, stability, X-ray structural characterization and 13 C nmr shifts of N-1 ' , N-3'-dichloro and N-1'-monochlorohydantoin derivatives of the anticonvulsant dilantin and the aldose reductase inhibitor sorbinil are described. These chlorinated derivatives may be involved in drug induced hypersensitivity reactions.

A systematic approach to the replacement of acidic groups with potential bioisosteres is described. The strategy involves simple nucleophilic displacement of a common alkyl halide precursor with a variety of mercaptoazoles and related molecules. The mercaptoazoles and their oxidized derivatives (sulfinyl- and sulfonylazoles) represent a series of possible surrogates for acidic groups which span a pKa range from about 4.5-11.5. This simple strategy was extended to include 2-hydroxy- or 2-aminothiophenyl groups which function as relatively nonacidic isosteres for a phosphonic acid. By replacing the phosphonic acid of 2-amino-7-phosphonoheptanoate (AP-7) with these groups, we have synthesized novel N-methyl-d-aspartate (NMDA) antagonists.