Anna Tarasova

Robust modelling of solubility in supercritical carbon dioxide using Bayesian methods

Two sparse Bayesian methods were used to derive predictive models of solubility of organic dyes and polycyclic aromatic compounds in supercritical carbon dioxide (scCO(2)), over a wide range of temperatures (285.9-423.2K) and pressures (60-1400 bar): a multiple linear regression employing an expectation maximization algorithm and a sparse prior (MLREM) method and a non-linear Bayesian Regularized Artificial Neural Network with a Laplacian Prior (BRANNLP). A randomly selected test set was used to estimate the predictive ability of the models. The MLREM method resulted in a model of similar predictivity to the less sparse MLR method, while the non-linear BRANNLP method created models of substantially better predictivity than either the MLREM or MLR based models. The BRANNLP method simultaneously generated context-relevant subsets of descriptors and a robust, non-linear quantitative structure-property relationship (QSPR) model for the compound solubility in scCO(2). The differences between linear and non-linear descriptor selection methods are discussed.

AFM study of the stability of a dense affinity-bound liposome layer.

Liposomes that are surface-bound to a biomaterial such as a contact lens are of interest for localized delivery of therapeutic agents, but it is not known whether such liposome layers are sufficiently robust. The stability of a dense, PEG-functionalized layer of liposomes, affinity-bound onto a multilayer coated surface, was tested under various stress conditions using colloid-probe atomic force miscroscopy (AFM). The different stress effects were generated by varying the applied normal load of the probe and the impinging fluid shear through different approach velocities and by varying the applied lateral forces by scanning under increasing force loads. The effect of applied forces (normal and lateral) was further investigated by coating the probe with a layer of albumin. The liposomes remained intact following the ramping of both protein-coated and uncoated probes under the normal and lateral loads. The low-fouling nature of these liposomes, with respect to nonspecific protein adsorption, was also demonstrated from the interaction force measurements which showed only weak adhesion from the protein layer during the contact period of the albumin-coated probe. The observed adhesive interactions were concluded to be a direct result of the applied load from the probe, during the force measurements, rather than from attraction of the protein molecules for the surface-bound liposomes. The low frictional response of the liposome layer indicated the viscoelastic nature of these molecules, which enabled liposome structure retention during the continuous load application. The demonstrated stability of the liposomes presents a system of viable and localized drug delivery in, for example, ophthalmic applications.

Principal signalling complexes in haematopoiesis: Structural aspects and mimetic discovery

Blood production is a highly regulated process involving multiple inhibitory and stimulatory cytokines present in the haematopoietic stem cell niche. Small molecules mimics of these signalling molecules have substantial potential as drugs and in the development of bioreactors to generate blood products. We review the structural biology of the extracellular signalling domains of five of the most important cytokines, analyze their structure-property relationships, and summarize the progress in developing small molecule mimics using the molecular information from structural biology and mutation studies.

A thrombopoietin receptor antagonist is capable of depleting myelofibrosis hematopoietic stem and progenitor cells

Recently, interactions between thrombopoietin (TPO) and its receptor, the myeloproliferative leukemia (MPL) virus oncogene, have been shown to play a role in the development and progression of myeloproliferative neoplasms including myelofibrosis (MF). These observations have led to the development of strategies to disrupt the association of TPO with its receptor as a means of targeting MF hematopoietic stem cells (HSCs) and hematopoietic progenitor cells (HPCs). In this report, we show that although both splenic and peripheral blood MF CD34(+) cells expressed lower levels of MPL than normal CD34(+) cells, TPO promoted the proliferation of MF CD34(+) cells and HPCs in a dose-dependent fashion. Furthermore, the treatment of MF but not normal CD34(+) cells with a synthesized MPL antagonist, LCP4, decreased the number of CD34(+)Lin(-) cells and all classes of assayable HPCs (colony-forming unit-megakaryocyte [CFU-MK], CFU-granulocyte/macrophage, burst-forming unit-erythroid/CFU-erythroid, and CFU-granulocyte/erythroid/macrophage/MK) irrespective of their mutational status. In addition, LCP4 treatment resulted in the depletion of the number of MF HPCs that were JAK2V617F(+) Moreover, the degree of human cell chimerism and the proportion of malignant donor cells were significantly reduced in immunodeficient mice transplanted with MF CD34(+) cell grafts treated with LCP4. These effects of LCP4 on MF HSCs/HPCs were associated with inhibition of JAK-STAT activity, leading to the induction of apoptosis. These findings demonstrate that such specific anti-cytokine receptor antagonists represent a new class of drugs that are capable of targeting MF HSCs.

Modelling Atypical Small-Molecule Mimics of an Important Stem Cell Cytokine, Thrombopoietin

We report the first comprehensive 3D QSAR study of a large, structurally diverse set of compounds that act as atypical thrombopoietin (TPO) mimics by interacting with the transmembrane domain of the TPO receptor, c‐MPL. These agonists of c‐MPL were superimposed according to a pharmacophore hypothesis, resulting in 3D QSAR models of high statistical significance. The pharmacophore‐based superimposition and comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used to derive the QSAR models relating structure to the published in vitro bioactivities of the TPO mimics. The CoMFA and CoMSIA models gave high correlation coefficients of the bioactivities with the derived fields, resulting in robust prediction of agonist activity of the superimposed compounds. The models have been interpreted in terms of the requirements for binding to the transmembrane domain of the TPO receptor.

Zinc Is Not Required for Activity of TPO Agonists Acting at the c-Mpl Receptor Transmembrane Domain

Molecules that mimic the cytokine thrombopoietin that act by an atypical mechanism of binding to a receptor transmembrane (TM) domain are widely understood to require zinc for their biological activity. We investigated potent thrombopoietin mimetics from three chemical classes including the recently registered drug Eltrombopag, which operate via this novel mechanism, to determine whether zinc is essential for inducing cell proliferation. Using addition of zinc and a potent metal chelator, we show that the existing paradigm is incorrect and the compounds exhibit excellent thrombopoietin-mimetic activity even in the presence of high concentrations of EDTA. The implications of these findings for the mechanism of action are discussed.

Potent Agonists of a Hematopoietic Stem Cell Cytokine Receptor, c-Mpl

Several growth factors feature prominently in the control of hematopoiesis. Thrombopoietin, a class I hematopoietic cytokine, plays critical roles in regulating hematopoietic stem cell numbers and also stimulates the production and differentiation of megakaryocytes, the bone marrow cells that ultimately produce platelets. Thrombopoietin interacts with the c‐Mpl cell‐surface receptor. Recently, several peptide and small‐molecule agonists and antagonists of c‐Mpl have been reported. We conducted a bioinformatics and molecular modeling study aimed at understanding the agonist activities of peptides that bind to c‐Mpl, and developed new potent peptide agonists with low nanomolar activity. These agonists also show very high activity in human CD34+ primary cell cultures, and doubled the mean blood platelet counts when injected into mice.