Networks of biological molecules are key to cellular function, governing processes ranging from signal cascade propagation to metabolic pathway regulation. Genetic duplication processes give rise to sets of regulatory proteins that have evolved from a common ancestor, leading to interactomes whose dysregulation is often associated with disease. A better understanding of the determinants of specificity at interfaces shared by functionally related proteins is crucial to the rational design of novel pharmacotherapeutic agents. To this end, a comprehensive data set of drug and drug-like binders was assembled for the Bcl-xL and Bcl-2 antiapoptotic proteins-archetypal examples of regulatory systems governed by evolutionarily conserved protein-protein interactions. These were first used to derive a two-dimensional quantitative structure-activity relationship (2D QSAR) model, predicting ligand specificity for these homologous proteins. The strengths and weaknesses of high-throughput 2D QSAR were then compared and contrasted to those of theoretically rigorous thermodynamic integration calculations performed on 14 complexes of Bcl-xL-specific, Bcl-2-specific, and potent dual binders bound to the Bcl-xL and Bcl-2 proteins. We demonstrate that free energy calculations provide an added layer of essential information, which traditional QSAR cannot capture. Moreover, we show that protein energetic responses to different ligands, expressed as per-residue energy values, can be used to fingerprint the protein-ligand interaction, extending the framework of four-dimensional molecular dynamics/quantitative structure-activity relationships (4D-MD/QSAR) toward the facilitation of future drug design strategies.

Downregulation of apoptosis has been proposed as a mechanism of clonal expansion in low-grade B cell neoplasms. We have previously described an unusual case of CD5+ B cell lymphoma characterized by cycles of leukemic phase alternating with spontaneous remission. In the present study, we examined the involvement of apoptosis-related proteins in the progression of this cyclic lymphoma ex vivo. During the leukemic phases, the clonal cells were activated blasts expressing elevated levels of wild-type (wt) p53, Bcl-2, Bcl-x(L), and Bax, while Bak expression increased during the decline of lymphocytosis. Bax heterodimerized with Bcl-2 but not with Bcl-x(L). The anti-apoptotic Bcl-2/Bax heterodimers peaked during early leukemic phases and declined during regression. The elevation in Bcl-2, Bcl-x(L) and Bax expression during early leukemic phases seems to result from cell activation since a similar increase was induced by activating the remission phase leukemic cells in culture. The data suggest that wt p53, Bcl-x(L), and Bcl-2/Bax heterodimers support the accumulation of activated leukemic cells during the leukemic phases, while Bax and Bak may be involved in their decline during regression.