Molecular dynamics investigations of structural and functional changes in Bcl-2 induced by the novel antagonist BDA-366

<p>Apoptosis is a fundamental biological phenomenon, in which anti- or proapoptotic proteins of the Bcl-2 family regulate a committed step. Overexpression of Bcl-2, the prototypical antiapoptotic protein in this family, is associated with therapy resistance in various human cancers. Accordingly, Bcl-2 inhibitors intended for cancer therapy have been developed, typically against the BH3 domain. Recent experimental evidences have shown that the antiapoptotic function of Bcl-2 is not immutable, and that BDA-366, a novel antagonist of the BH4 domain, converts Bcl-2 from a survival molecule to an inducer of cell death. In this study, the underlying mechanisms of this functional conversion were investigated by accelerated molecular dynamics simulation. Results revealed that Pro127 and Trp30 in the BH4 domain rotate to stabilize BDA-366 via π-π interactions, and trigger a series of significant conformational changes of the α3 helix. This rearrangement blocks the hydrophobic binding site (HBS) in the BH3 domain and further prevents binding of BH3-only proteins, which consequently allows the BH3-only proteins to activate the proapoptotic proteins. Analysis of binding free energy confirmed that BDA-366 cross-inhibits BH3-only proteins, implying negative cooperative effects across separate binding sites. The newly identified blocked conformation of the HBS along with the open to closed transition pathway revealed by this study advances the understanding of the Bcl-2 transition from antiapoptotic to proapoptotic function, and yielded new structural insights for novel drug design against the BH4 domain.</p> <p>Communicated by Ramaswamy H. Sarma</p> <p>The ability of the small molecule BDA-366 to convert Bcl-2 from an antiapoptotic to a proapoptotic molecule was investigated by accelerated molecular dynamics simulation. Results show that BDA-366 blocks or reduces the affinity of Bcl-2 for BH3-only proteins like Bid via negative cooperative effects, thereby releasing such proteins and unleashing their proapoptotic effects.</p

Distribution of ADPRT and APE1 genotype among breast cancer of cases and controls in the meta-analysis.

a<p>A represents the major allele, B represents the minor allele.</p><p>HWE: Hardy-Weinberg equilibrium; MAF: minor allele frequencies.</p

Forest plots for meta-analysis of the association between APE1 Asp148Glu polymorphism and breast cancer risk.

<p>A: Asp/Glu vs. Asp/Asp; B: Glu/Glu vs. Asp/Asp; C: Dominant model; D: Recessive model.</p

Characteristics of studies included in the meta-analysis for ADPRT and APE1.

<p>Characteristics of studies included in the meta-analysis for ADPRT and APE1.</p

Summary ORs and 95% CI of the association between polymorphisms in the two BER genes (ADPRT Val762Ala and APE1 Asp148Glu) and breast cancer risk.

<p>Summary ORs and 95% CI of the association between polymorphisms in the two BER genes (ADPRT Val762Ala and APE1 Asp148Glu) and breast cancer risk.</p

Flow diagram of study identification.

<p>Flow diagram of study identification.</p

Forest plots for meta-analysis of the association between ADPRT Val762Ala polymorphism and breast cancer risk.

<p>A: Val/Ala vs. Val/Val; B: Ala/Ala vs. Val/Val; C: Dominant model; D: Recessive model.</p

Funnel plot of publication bias for ADPRT Val762Ala and APE1 Asp148Glu polymorphism with breast cancer risk.

<p>Note: Funnel plot with pseudo 95% confidence limits was used. A: Funnel plot of publication bias for ADPRT (Val/Ala vs. Val/Val); B: Funnel plot of publication bias for APE1 (Asp/Glu vs. Asp/Asp).</p