Comparative Analysis of Virtual Screening Approaches in the Search for Novel EphA2 Receptor Antagonists

Donatella Callegari, Daniele Pala, Laura Scalvini, Massimiliano Tognolini, Matteo Incerti, Silvia Rivara, Marco Mor, Alessio Lodola
2015 Molecules  
The EphA2 receptor and its ephrin-A1 ligand form a key cell communication system, which has been found overexpressed in many cancer types and involved in tumor growth. Recent medicinal chemistry efforts have identified bile acid derivatives as low micromolar binders of the EphA2 receptor. However, these compounds suffer from poor physicochemical properties, hampering their use in vivo. The identification of compounds able to disrupt the EphA2-ephrin-A1 complex lacking the bile acid scaffold may
more » ... e acid scaffold may lead to new pharmacological tools suitable for in vivo studies. To identify the most promising virtual screening (VS) protocol aimed at finding novel EphA2 antagonists, we investigated the ability of both ligand-based and structure-based approaches to retrieve known EphA2 antagonists from libraries of decoys with similar molecular properties. While ligand-based VSs were conducted using UniPR129 and ephrin-A1 ligand as reference structures, structure-based VSs were performed with Glide, using the X-ray structure of the EphA2 receptor/ephrin-A1 complex. A comparison of enrichment factors showed that ligand-based approaches outperformed the structure-based ones, suggesting ligand-based methods using the G-H loop of ephrin-A1 ligand as template as the most promising protocols to search for novel EphA2 antagonists. The erythropoietin-producing hepatocellular carcinoma (Eph) receptors constitute the largest family of tyrosine kinase receptors in mammals and it includes at least fourteen members, such as the EphA1-EphA8, EphA10, EphB1-B4 and EphB6 receptor subtypes [1] . The Eph receptors are activated by membrane-anchored proteins, called ephrins, which are divided in ephrinA1-A5 and ephrinB1-B3 subclasses, respectively [2]. The Eph receptors and their ephrin ligands constitute a cell-cell communication system, which is essential for the regulation of several processes during the embryonic morphogenesis [3] . Eph-ephrin system preserves the cellular architecture in various epithelia and modulates tissue renewal in the adult. A deregulation of this system, and in particular of the activity of EphA2/ephrin-A1 signaling complex, has been related to cancer insurgence and progression [4] . Indeed, the EphA2 receptor has been found overexpressed in several cancer types [5] , while the inhibition of EphA2 receptor with monoclonal antibodies [6] or soluble receptors [7] has been shown to effectively suppress cancer progression and angiogenesis in animal models [8] . For these reasons [9], the EphA2/ephrin-A1 interface is currently explored as a target for the development of new antitumorigenic and antiangiogenic treatments [10, 11] . A screening campaign recently conducted in our laboratories allowed the identification of small molecules able to inhibit the EphA2/ephrin-A1 interaction, including the (3α,5β)-3-hydroxycholan-24-oic acid (lithocholic acid, LCA, Figure 1, [12] ) which turned out to be a competitive antagonist of the EphA2 receptor [13] . Further medicinal chemistry efforts [14, 15] led to the identification of the L-β-homo-tryptophan derivative of LCA (UniPR129, Figure 1 ) as a potent antagonist of the EphA2 receptor, having an inhibitory constant (Ki) of 370 nM [16] . However, this compound had modest solubility, which hampered its use in vivo by the oral route [17] . The identification of new compounds able to disrupt the EphA2/ephrin-A1 complex may lead to pharmacological tools featured by better physicochemical properties and thus suitable for in vivo investigations. To search for better EphA2 antagonists, we recently screened in silico a small collection of carboxylic acid derivatives available from Sigma-Aldrich (Saint Louis, MO, USA). A bunch of top-ranked compounds was purchased and tested in a wet binding assay. Among them, the 3β-hydroxy-Δ 5 -cholenic acid and the 4-(4-cyclopentylnaphthalen-1-yl)-4-oxobutanoic acid (Figure 1) were identified as inhibitors of the EphA2/ephrin-A1 interaction [18] , with potency in the medium/high micromolar range. The ability of in silico screening approaches to identify novel EphA2 receptor antagonists, prompted us to evaluate the performance of a variety of virtual screening (VS) approaches, starting from known chemical libraries of ready-to-ship compounds, typically used in VS campaigns. In the present work, we carried out a computational analysis where we compared the ability of standard ligandand structure-based approaches to retrieve known EphA2 antagonists from different libraries of decoys. We applied shape-similarity and pharmacophore match techniques available in the Phase software package [19], and flexible ligand docking available in the Glide program [20]. The EphA2 antagonist
doi:10.3390/molecules200917132 pmid:26393553 fatcat:mqvliqrszra5fmfycvku5rs6qe