A Computational Model for Overcoming Drug Resistance Using Selective Dual-Inhibitors for Aurora Kinase A and Its T217D Variant

The human Aurora kinase-A (AK-A) is an essential mitotic regulator that is frequently overexpressed in several cancers. The recent development of several novel AK-A inhibitors has been driven by the well-established association of this target with cancer development and progression. However, resistance and cross-reactivity with similar kinases demands an improvement in our understanding of key molecular interactions between the Aurora kinase-A substrate binding pocket and potential inhibitors. Here, we describe the implementation of state-of-the-art virtual screening techniques to discover a novel set of Aurora kinase-A ligands that are predicted to strongly bind not only to the wild type protein, but also to the T217D mutation that exhibits resistance to existing inhibitors. Furthermore, a subset of these computationally screened ligands was shown to be more selective toward the mutant variant over the wild type protein. The description of these selective subsets of ligands provides a unique pharmacological tool for the design of new drug regimens aimed at overcoming both kinase cross-reactivity and drug resistance associated with the Aurora kinase-A T217D mutation

B cell subset frequencies are unchanged in HCV patients compared to controls.

<p>(<b>A–C</b>) 7.5×10⁵ freshly isolated PBMCs from chronically infected HCV patients (n = 54) or healthy controls (n = 50) were incubated with fluorescently labeled antibodies to CD19, CD27 and CD5 for multi-color flow cytometry analysis. (<b>A</b>) The total percent of CD19+ B cells within the lymphocyte gate and number of B cells per ml of blood based on our isolations. (<b>B</b>) The percent of memory (CD19+CD27+) and naïve (CD19+CD27−) and number of each subset per ml of blood. <b>(C)</b> The percent and number per ml of CD5+CD19+ B cells. Horizontal lines on graphs represent means +/− SEM (percentages) or median (number of cells/ml) values. In (C) only 48 HCV and 47 healthy control samples were tested for CD5. *, P<0.05; n.s., not significant.</p

Clinical characteristics of HCV+ patients and healthy controls in study.

<p>Abbreviations: N/A, not applicable, ALT, alanine aminotransferase (normal values = <50), GGT, gamma-glutamyl transpeptidase (normal levels = <70 (males), <55 (females)), IU, International units, IFN, interferon.</p>*<p>determined from biopsy or Fibroscan.</p

HCV patients with advanced fibrosis have increased expression of CD86 on memory B cells.

<p>Fibrosis scores were determined as outlined in the Materials and Methods, where scores of 3–4 are considered advanced fibrosis/cirrhosis (F4). PBMCs were freshly isolated and analyzed by flow cytometry as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068308#pone-0068308-g003" target="_blank">Figure 3</a>. The expression level and percent positive of cells expressing CD86 (geometric mean fluorescent intensity (MFI) or percent positive compared to mouse isotype controls) were calculated for memory (CD19+CD27+) and naïve (CD19+CD27−) B cells. Horizontal lines represent median values. *, P<0.05; n.s., not significant.</p

Memory, but not naïve B cells from cryoglobulin positive HCV patients express higher levels of activation markers compared to B cells from cryoglobulin negative HCV patients.

<p>PBMCs were freshly isolated and analyzed by flow cytometry as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068308#pone-0068308-g003" target="_blank">Figure 3</a> except that this analysis compares cryoglobulin+ (n = 20, cryo+) and cryoglobulin- (n = 34, cryo-) HCV patients. Antibodies to CD86, CD71, HLA-DR and CD183 were added in combinations with CD19 and CD27 to gate on memory (CD19+CD27+) and naïve (CD19+CD27−) B cells. The percent positive was calculated based on mouse isotype controls and the geometric mean fluorescent intensities (MFI) for each marker were determined. Horizontal lines on graphs represent median values. For CD71 analysis, 18 cryo+ and 30 cryo- HCV samples were stained. ***, P<0.001, **, P<0.01, *, P<0.05, n.s., not significant.</p

PBMC and B cell quantification and clinical characteristics of cryoglobulin positive versus cryoglobulin negative HCV patients.

<p>(<b>A–B</b>) PBMCs were freshly isolated and analyzed by flow cytometry as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068308#pone-0068308-g002" target="_blank">Figure 2</a> except that this analysis compares cryoglobulin+ (n = 20, cryo+) and cryoglobulin- (n = 34, cryo-) HCV patients. (<b>A</b>) The total percent of CD19+ B cells within the lymphocyte gate and number of B cells per ml of blood based on our isolations. (<b>B</b>) The percent of memory (CD19+CD27+) and naïve (CD19+CD27−) and number of each subset per ml of blood. (<b>C</b>) The number of total PBMCs isolated per ml of blood. (<b>D</b>) The alanine aminotransferase (ALT) and gamma-glutamyl transpeptidase (GGT) levels were measured in the serum in units/L (U/L) for 54 (ALT) or 48 (GGT) HCV patients. (<b>E</b>) Serum HCV RNA titers were quantified by qRT-PCR as described in the Materials and Methods for all 54 HCV patients. Horizontal lines on graphs represent mean +/− SEM (A-B, percentages, C) or median (A–B numbers, D, E) values. *, P<0.05, n.s., not significant. IU/ml, international units/ml.</p

Geometric mean fluorescent intensities of each marker on memory and naïve B cells.

<p>Abbreviation: MFI, mean fluorescent intensity.</p

Summary of significant correlations between B cell activation marker expression and liver clinical tests.

<p>Abbreviations: ALT = alanine aminotransferase, GGT = gamma-glutamyl transpeptidase, AFP = alpha-fetoprotein, Geo MFI = geometric mean fluorescent intensity.</p

Gating strategy for flow cytometry analysis of memory and naïve B cell activation.

<p>Lymphocytes were gated by FSC/SSC properties and memory B cells (CD19+CD27+) and naïve B cells (CD19+CD27−) were analyzed within the lymphocyte gate for the expression of 6 different markers described in the Materials and Methods. Histograms show a representative example of the expression of CD183 (numbers represent geometric mean fluorescent intensity) on memory and naïve B cells from a healthy control (HCV-) and chronic HCV patient (HCV+).</p

A Refined Model of the HCV NS5A Protein Bound to Daclatasvir Explains Drug-Resistant Mutations and Activity against Divergent Genotypes

Many direct-acting antiviral agents (DAAs) that selectively block hepatitis C virus (HCV) replication are currently under development. Among these agents is Daclatasvir, a first-in-class inhibitor targeting the NS5A viral protein. Although Daclatasvir is the most potent HCV antiviral molecule yet developed, its binding location and mode of binding remain unknown. The drug exhibits a low barrier to resistance mutations, particularly in genotype 1 viruses, but its efficacy against other genotypes is unclear. Using state-of-the-art modeling techniques combined with the massive computational power of Blue Gene/Q, we identified the atomic interactions of Daclatasvir within NS5A for different HCV genotypes and for several reported resistant mutations. The proposed model is the first to reveal the detailed binding mode of Daclatasvir. It also provides a tool to facilitate design of second generation drugs, which may confer less resistance and/or broader activity against HCV