Multiscale Nature of Thixotropy and Rheological Hysteresis in Attractive Colloidal Suspensions under Shear.

Colloids with short range attractions self-assemble into sample-spanning structures, whose dynamic nature results in a thermokinematic memory of the deformation history, also referred to as "thixotropy." Here, we study the origins of the thixotropic effect in these time- and rate-dependent materials by investigating hysteresis across different length scales: from particle-level local measurements of coordination number (microscale), to the appearance of density and velocity fluctuations (mesoscale), and up to the shear stress response to an imposed deformation (macroscale). The characteristic time constants at each scale become progressively shorter, and hysteretic effects become more significant as we increase the strength of the interparticle attraction. There are also strong correlations between the thixotropic effects we observe at each scale.

Microstructural Rearrangements and their Rheological Implications in a Model Thixotropic Elastoviscoplastic Fluid.

We identify the sequence of microstructural changes that characterize the evolution of an attractive particulate gel under flow and discuss their implications on macroscopic rheology. Dissipative particle dynamics is used to monitor shear-driven evolution of a fabric tensor constructed from the ensemble spatial configuration of individual attractive constituents within the gel. By decomposing this tensor into isotropic and nonisotropic components we show that the average coordination number correlates directly with the flow curve of the shear stress versus shear rate, consistent with theoretical predictions for attractive systems. We show that the evolution in nonisotropic local particle rearrangements are primarily responsible for stress overshoots (strain-hardening) at the inception of steady shear flow and also lead, at larger times and longer scales, to microstructural localization phenomena such as shear banding flow-induced structure formation in the vorticity direction.

Publisher's Note: Characterizing short-term stability for Boolean networks over any distribution of transfer functions [Phys. Rev. E 94, 012301 (2016)].

This corrects the article DOI: 10.1103/PhysRevE.94.012301.

Characterizing short-term stability for Boolean networks over any distribution of transfer functions.

We present a characterization of short-term stability of Kauffman's NK (random) Boolean networks under arbitrary distributions of transfer functions. Given such a Boolean network where each transfer function is drawn from the same distribution, we present a formula that determines whether short-term chaos (damage spreading) will happen. Our main technical tool which enables the formal proof of this formula is the Fourier analysis of Boolean functions, which describes such functions as multilinear polynomials over the inputs. Numerical simulations on mixtures of threshold functions and nested canalyzing functions demonstrate the formula's correctness.

Discovery and optimization of a highly efficacious class of 5-aryl-2-aminopyridines as FMS-like tyrosine kinase 3 (FLT3) inhibitors.

Based on a putative binding mode of quizartinib (AC220, 1), a potent FMS-like tyrosine kinase 3 (FLT3) inhibitor in Phase III clinical development, we have designed de novo a simpler aminopyridine-based hinge binding motif. Further optimization focusing on maximizing in vivo efficacy and minimizing CYP3A4 time-dependent inhibition resulted in a highly efficacious compound (6s) in tumor xenograft model for further preclinical development.

Phase I study of quizartinib administered daily to patients with relapsed or refractory acute myeloid leukemia irrespective of FMS-like tyrosine kinase 3-internal tandem duplication status.

PURPOSE: FMS-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) mutations in acute myeloid leukemia (AML) are associated with early relapse and poor survival. Quizartinib potently and selectively inhibits FLT3 kinase activity in preclinical AML models. PATIENTS AND METHODS: Quizartinib was administered orally at escalating doses of 12 to 450 mg/day to 76 patients (median age, 60 years; range, 23 to 86 years; with a median of three prior therapies [range, 0 to 12 therapies]), enrolled irrespective of FLT3-ITD mutation status in a phase I, first-in-human study in relapsed or refractory AML. RESULTS: Responses occurred in 23 (30%) of 76 patients, including 10 (13%) complete remissions (CR) of any type (two CRs, three CRs with incomplete platelet recovery [CRp], five CRs with incomplete hematologic recovery [CRi]) and 13 (17%) with partial remissions (PRs). Of 17 FLT3-ITD-positive patients, nine responded (53%; one CR, one CRp, two CRis, five PRs); of 37 FLT3-ITD-negative patients, five responded (14%; two CRps, three PRs); of 22 with FLT3-ITD-indeterminate/not tested status, nine responded (41%; one CR, three CRis, five PRs). Median duration of response was 13.3 weeks; median survival was 14.0 weeks. The most common drug-related adverse events (> 10% incidence) were nausea (16%), prolonged QT interval (12%), vomiting (11%), and dysgeusia (11%); most were ≤ grade 2. The maximum-tolerated dose was 200 mg/day, and the dose-limiting toxicity was grade 3 QT prolongation. FLT3-ITD phosphorylation was completely inhibited in an in vitro plasma inhibitory assay. CONCLUSION: Quizartinib has clinical activity in patients with relapsed/refractory AML, particularly those with FLT3-ITD, and is associated with an acceptable toxicity profile.

Transient exposure to quizartinib mediates sustained inhibition of FLT3 signaling while specifically inducing apoptosis in FLT3-activated leukemia cells.

Fms-like tyrosine kinase 3 (FLT3) is implicated in the pathogenesis of acute myeloid leukemia (AML). FLT3-activating internal tandem duplication (ITD) mutations are found in approximately 30% of patients with AML and are associated with poor outcome in this patient population. Quizartinib (AC220) has previously been shown to be a potent and selective FLT3 inhibitor. In the current study, we expand on previous observations by showing that quizartinib potently inhibits the phosphorylation of FLT3 and downstream signaling molecules independent of FLT3 genotype, yet induces loss of viability only in cells expressing constitutively activated FLT3. We further show that transient exposure to quizartinib, whether in vitro or in vivo, leads to prolonged inhibition of FLT3 signaling, induction of apoptosis, and drastic reductions in tumor volume and pharmacodynamic endpoints. In vitro experiments suggest that these prolonged effects are mediated by slow binding kinetics that provide for durable inhibition of the kinase following drug removal/clearance. Together these data suggest quizartinib, with its unique combination of selectivity and potent/sustained inhibition of FLT3, may provide a safe and effective treatment against FLT3-driven leukemia.

Discovery of highly potent and selective pan-Aurora kinase inhibitors with enhanced in vivo antitumor therapeutic index.

Serine/threonine protein kinases Aurora A, B, and C play essential roles in cell mitosis and cytokinesis. Currently a number of Aurora kinase inhibitors with different isoform selectivities are being evaluated in the clinic. Herein we report the discovery and characterization of 21c (AC014) and 21i (AC081), two structurally novel, potent, kinome-selective pan-Aurora inhibitors. In the human colon cancer cell line HCT-116, both compounds potently inhibit histone H3 phosphorylation and cell proliferation while inducing 8N polyploidy. Both compounds administered intravenously on intermittent schedules displayed potent and durable antitumor activity in a nude rat HCT-116 tumor xenograft model and exhibited good in vivo tolerability. Taken together, these data support further development of both 21c and 21i as potential therapeutic agents for the treatment of solid tumors and hematological malignancies.

CEP-32496: a novel orally active BRAF(V600E) inhibitor with selective cellular and in vivo antitumor activity.

Mutations in the BRAF gene have been identified in approximately 7% of cancers, including 60% to 70% of melanomas, 29% to 83% of papillary thyroid carcinomas, 4% to 16% colorectal cancers, and a lesser extent in serous ovarian and non-small cell lung cancers. The V600E mutation is found in the vast majority of cases and is an activating mutation, conferring transforming and immortalization potential to cells. CEP-32496 is a potent BRAF inhibitor in an in vitro binding assay for mutated BRAF(V600E) (K(d) BRAF(V600E) = 14 nmol/L) and in a mitogen-activated protein (MAP)/extracellular signal-regulated (ER) kinase (MEK) phosphorylation (pMEK) inhibition assay in human melanoma (A375) and colorectal cancer (Colo-205) cell lines (IC(50) = 78 and 60 nmol/L). In vitro, CEP-32496 has multikinase binding activity at other cancer targets of interest; however, it exhibits selective cellular cytotoxicity for BRAF(V600E) versus wild-type cells. CEP-32496 is orally bioavailable in multiple preclinical species (>95% in rats, dogs, and monkeys) and has single oral dose pharmacodynamic inhibition (10-55 mg/kg) of both pMEK and pERK in BRAF(V600E) colon carcinoma xenografts in nude mice. Sustained tumor stasis and regressions are observed with oral administration (30-100 mg/kg twice daily) against BRAF(V600E) melanoma and colon carcinoma xenografts, with no adverse effects. Little or no epithelial hyperplasia was observed in rodents and primates with prolonged oral administration and sustained exposure. CEP-32496 benchmarks favorably with respect to other kinase inhibitors, including RAF-265 (phase I), sorafenib, (approved), and vemurafenib (PLX4032/RG7204, approved). CEP-32496 represents a novel and pharmacologically active BRAF inhibitor with a favorable side effect profile currently in clinical development.

Identification of 1-(3-(6,7-dimethoxyquinazolin-4-yloxy)phenyl)-3-(5-(1,1,1-trifluoro-2-methylpropan-2-yl)isoxazol-3-yl)urea hydrochloride (CEP-32496), a highly potent and orally efficacious inhibitor of V-RAF murine sarcoma viral oncogene homologue B1 (BRAF) V600E.

The Ras/RAF/MEK/ERK mitogen-activated protein kinase (MAPK) signaling pathway plays a central role in the regulation of cell growth, differentiation, and survival. Expression of mutant BRAF(V600E) results in constitutive activation of the MAPK pathway, which can lead to uncontrolled cellular growth. Herein, we describe an SAR optimization campaign around a series of quinazoline derived BRAF(V600E) inhibitors. In particular, the bioisosteric replacement of a metabolically sensitive tert-butyl group with fluorinated alkyl moieties is described. This effort led directly to the identification of a clinical candidate, compound 40 (CEP-32496). Compound 40 exhibits high potency against several BRAF(V600E)-dependent cell lines and selective cytotoxicity for tumor cell lines expressing mutant BRAF(V600E) versus those containing wild-type BRAF. Compound 40 also exhibits an excellent PK profile across multiple preclinical species. In addition, significant oral efficacy was observed in a 14-day BRAF(V600E)-dependent human Colo-205 tumor xenograft mouse model, upon dosing at 30 and 100 mg/kg BID.

Discovery of AC710, a Globally Selective Inhibitor of Platelet-Derived Growth Factor Receptor-Family Kinases.

A series of potent, selective platelet-derived growth factor receptor-family kinase inhibitors was optimized starting from a globally selective lead molecule 4 through structural modifications aimed at improving the physiochemical and pharmacokinetic properties, as exemplified by 18b. Further clearance reduction via per-methylation of the α-carbons of a solubilizing piperidine nitrogen resulted in advanced leads 22a and 22b. Results from a mouse tumor xenograft, a collagen-induced arthritis model, and a 7 day rat in vivo tolerability study culminated in the selection of compound 22b (AC710) as a preclinical development candidate.

Influence and dynamic behavior in random boolean networks.

We present a rigorous mathematical framework for analyzing dynamics of a broad class of boolean network models. We use this framework to provide the first formal proof of many of the standard critical transition results in boolean network analysis, and offer analogous characterizations for novel classes of random boolean networks. We show that some of the assumptions traditionally made in the more common mean-field analysis of boolean networks do not hold in general. For example, we offer evidence that imbalance (internal inhomogeneity) of transfer functions is a crucial feature that tends to drive quiescent behavior far more strongly than previously observed.

Noncooperatively optimized tolerance: decentralized strategic optimization in complex systems.

We introduce noncooperatively optimized tolerance (NOT), a game theoretic generalization of highly optimized tolerance (HOT), which we illustrate in the forest fire framework. As the number of players increases, NOT retains features of HOT, such as robustness and self-dissimilar landscapes, but also develops features of self-organized criticality. The system retains considerable robustness even as it becomes fractured, due in part to emergent cooperation between players, and at the same time exhibits increasing resilience against changes in the environment, giving rise to intermediate regimes where the system is robust to a particular distribution of adverse events, yet not very fragile to changes.

4-Quinazolinyloxy-diaryl ureas as novel BRAFV600E inhibitors.

Aryl phenyl ureas with a 4-quinazolinoxy substituent at the meta-position of the phenyl ring are potent inhibitors of mutant and wild type BRAF kinase. Compound 7 (1-(5-tert-butylisoxazol-3-yl)-3-(3-(6,7-dimethoxyquinazolin-4-yloxy)phenyl)urea hydrochloride) exhibits good pharmacokinetic properties in rat and mouse and is efficacious in a mouse tumor xenograft model following oral dosing.

Novel series of pyrrolotriazine analogs as highly potent pan-Aurora kinase inhibitors.

The synthesis and SAR for a novel series of pyrrolotriazines as pan-Aurora kinase inhibitors are described. Optimization of the cyclopropane carboxamide terminus of lead compound 1 resulted in analogs with high cellular activity and improved rat PK profiles. Notably, compound 17l demonstrated tumor growth inhibition in a mouse xenograft model.

Activation state-dependent binding of small molecule kinase inhibitors: structural insights from biochemistry.

Interactions between kinases and small molecule inhibitors can be activation state dependent. A detailed understanding of inhibitor binding therefore requires characterizing interactions across multiple activation states. We have systematically explored the effects of ABL1 activation loop phosphorylation and PDGFR family autoinhibitory juxtamembrane domain docking on inhibitor binding affinity. For a diverse compound set, the affinity patterns correctly classify inhibitors as having type I or type II binding modes, and we show that juxtamembrane domain docking can have dramatic negative effects on inhibitor affinity. The results have allowed us to associate ligand-induced conformational changes observed in cocrystal structures with specific energetic costs. The approach we describe enables investigation of the complex relationship between kinase activation state and compound binding affinity and should facilitate strategic inhibitor design.

AC220 is a uniquely potent and selective inhibitor of FLT3 for the treatment of acute myeloid leukemia (AML).

Activating mutations in the receptor tyrosine kinase FLT3 are present in up to approximately 30% of acute myeloid leukemia (AML) patients, implicating FLT3 as a driver of the disease and therefore as a target for therapy. We report the characterization of AC220, a second-generation FLT3 inhibitor, and a comparison of AC220 with the first-generation FLT3 inhibitors CEP-701, MLN-518, PKC-412, sorafenib, and sunitinib. AC220 exhibits low nanomolar potency in biochemical and cellular assays and exceptional kinase selectivity, and in animal models is efficacious at doses as low as 1 mg/kg given orally once daily. The data reveal that the combination of excellent potency, selectivity, and pharmacokinetic properties is unique to AC220, which therefore is the first drug candidate with a profile that matches the characteristics desirable for a clinical FLT3 inhibitor.

Initial stage of spinodal decomposition in a rigid-rod system.

The initial stage of spinodal decomposition is investigated for a rigid-rod system. Spinodal decomposition proceeds through either of two mechanisms: (1) The randomly aligned rods rotate toward a common director with no inherent length scale. (2) The rods diffuse axially and segregate into regions of common alignment with a selected length scale [script-l]. Previous studies on spinodal decomposition yielded radically different conclusions about which mechanism is dominant. A computational method is employed to analyze the growth rate and properties of the dominant fluctuation mode through an eigenvalue analysis of the linearized Doi diffusion equation in Fourier space. The linearized operator is discretized in Fourier mode and orientation space (k,theta,phi) space, and the maximum eigenvalue and corresponding eigenvector of the operator are calculated. Our analysis generalizes the results of previous studies and shows that the conflicts seen in those studies are due to differences in the diffusivities for rotational motion, motion perpendicular to the rod axis, and motion along the rod axis. For a given system density, a plot of the dominant perturbation wave number k(max) as a function of the diffusivity ratios shows two separate regions corresponding to mechanisms (1) and (2). High rotational diffusivity corresponds to mechanism (1), whereas high axial diffusivity corresponds to mechanism (2). The transition between the two mechanisms depends on the ratio of diffusivities and on system density. Also, the dominant wave number increases with increasing density indicating that a deeper quench into the spinodal regime leads to a smaller characteristic length scale.

Computation of the nonhomogeneous equilibrium states of a rigid-rod solution.

The nonhomogeneous equilibrium phase behavior of a solution of rigid rods is analyzed for a periodic one-dimensional system. Stable and unstable equilibrium solutions for the distribution function are computed as extrema of the free energy of the system expressed by the nonhomogeneous generalization of Onsager's [Ann. N.Y. Acad. Sci. 51, 627 (1949)] theory, which models interaction between rods on the scale of a single rod length. Biaxial equilibrium solutions are computed in a periodic system by discretizing the Euler-Lagrange nonlinear integral equation by the finite-element method and using Newton's method to solve the resulting set of nonlinear equations. Stable states for isotropic-nematic coexistence are computed in a periodic system rather than the semi-infinite system used in previous calculations. The density and order parameter profiles evolve monotically from the isotropic phase to the nematic phase. Unstable, nonhomogeneous, equilibrium states are also computed for concentrations of rods that exceed the value for spinodal decomposition. These nonhomogeneous states are characterized by combinations of bend, twist, and splay distortions in physical space and correspond to unstable attractors in the dynamic process of isotropic-nematic spinodal decomposition. For large systems, the nonhomogeneous states develop wide, bulklike nematic regions separated by thin regions with sharp gradients in orientation. The free energy formulation was also used to compute the accurate neutral stability curve; this curve shows the limits of applicability of the low-wave-number approximations frequently used in the study of spinodal decomposition.

An inhibitor of Bcl-2 family proteins induces regression of solid tumours.

Proteins in the Bcl-2 family are central regulators of programmed cell death, and members that inhibit apoptosis, such as Bcl-X(L) and Bcl-2, are overexpressed in many cancers and contribute to tumour initiation, progression and resistance to therapy. Bcl-X(L) expression correlates with chemo-resistance of tumour cell lines, and reductions in Bcl-2 increase sensitivity to anticancer drugs and enhance in vivo survival. The development of inhibitors of these proteins as potential anti-cancer therapeutics has been previously explored, but obtaining potent small-molecule inhibitors has proved difficult owing to the necessity of targeting a protein-protein interaction. Here, using nuclear magnetic resonance (NMR)-based screening, parallel synthesis and structure-based design, we have discovered ABT-737, a small-molecule inhibitor of the anti-apoptotic proteins Bcl-2, Bcl-X(L) and Bcl-w, with an affinity two to three orders of magnitude more potent than previously reported compounds. Mechanistic studies reveal that ABT-737 does not directly initiate the apoptotic process, but enhances the effects of death signals, displaying synergistic cytotoxicity with chemotherapeutics and radiation. ABT-737 exhibits single-agent-mechanism-based killing of cells from lymphoma and small-cell lung carcinoma lines, as well as primary patient-derived cells, and in animal models, ABT-737 improves survival, causes regression of established tumours, and produces cures in a high percentage of the mice.