Discovery of Mer kinase inhibitors by virtual screening using Structural Protein–Ligand Interaction Fingerprints

Abstract

Mer is a receptor tyrosine kinase implicated in acute lymphoblastic leukemia (ALL), the most common malignancy in children. The currently available data provide a rationale for development of Mer kinase inhibitors as cancer therapeutics that can target both cell autologous and immune-modulatory anti-tumor effects. We have previously reported several series of potent Mer inhibitors and the objective of the current report is to identify a chemically dissimilar back-up series that might circumvent potential, but currently unknown, flaws inherent to the lead series. To this end, we virtually screened a database of ∼3.8 million commercially available compounds using high-throughput docking followed by a filter involving Structural Protein-Ligand Interaction Fingerprints (SPLIF). SPLIF permits a quantitative assessment of whether a docking pose interacts with the protein target similarly to an endogenous or known synthetic ligand, and therefore helps to improve both sensitivity and specificity with respect to the docking score alone. Of the total of 62 experimentally tested compounds, 15 demonstrated reliable dose-dependent responses in the Mer in vitro kinase activity assay with inhibitory potencies ranging from 0.46 μM to 9.9 μM.

Role of the Receptor Tyrosine Kinase Axl and its Targeting in Cancer Cells

“…They also submitted to virtual screening 156 known TAM inhibitors (from public databases) docking most of them into the DFG-in model and only five into the DFG-out, finding that a terminal p-fluorophenyl group is crucial for type II inhibitors [10,107]. Very recently, the pyrazolopyrimidine TAM inhibitor UNC569 [107] has also been used as a reference compound in a virtual screening study aimed at finding Mer kinase inhibitors [108], owing to its high resolution crystal structure in complex with the Mer kinase domain [107]. Of note, UNC569 was found to be effective against lymphoblastic leukemia in vitro and in vivo [109].…”

Structure-Based Virtual Screening of Commercially Available Compound Libraries

“…Only four compounds of the 3200 screened have shown activity above a threshold of 30 % resulting in a hit rate of 0.12 % (4 hits/3200 tested). Therefore, our VS approach has demonstrated an $200-fold (24 %/0.12 %) improvement over a random screen [10]. This study also exemplifies that screening of commercial catalogs can yield tractable hits appropriate as starting points for the hit-to-lead progression.…”

“…Therefore, all possible means must be deployed to improve the odds of getting a sizable number of confirmed actives out of very small sets of virtual hits. We have recently demonstrated that a post-docking score based on structural protein-ligand interaction fingerprints (SPLIF) can greatly improve VS success rates [10,11]. The SPLIF-based score exploits the idea that a compound that can mimic "native" ligand-protein interactions (e.g., enzyme-substrate interactions) is more likely to be a true hit than a random compound with a decent docking score.…”

“…Due to a limited experimental effort and the possibility to use commercial compound libraries, VS is particularly suited for academic labs and small biotech companies that, unlike pharmaceutical companies, do not have physical access to rich small-molecule libraries. Here, we describe an SBVS protocol that has been used to identify inhibitors of Mer kinase, a promising therapeutic target against acute lymphoblastic leukemia (ALL) [10,14]. Prior to the start of this campaign, we had already identified a lead series of potent Mer inhibitors [15][16][17][18] and the objective of this VS campaign was to identify backup leads whose structures would significantly differ from the lead compound, UNC2025 [19].…”

Drug Design Strategies to Avoid Resistance in Direct-Acting Antivirals and Beyond

“…Protein–inhibitor interaction fingerprints are high-level presentations of these complexes, where the binding mode of a small molecule inhibitor is encoded in a series of physical interactions. The exact composition of such a fingerprint can vary significantly from simple binary representations that inform about the presence or absence of a particular interaction, to quantitative measurement of the strength of interactions between protein and ligand atoms. , Protein–ligand interaction fingerprints have been used extensively to characterize virtual screening results to identify small molecules that share a common mode of interaction with known binders . Fingerprinting has been used to characterize conserved binding modes across families of potential drug targets such as human kinases and G protein-coupled receptors. , One major advantage of fingerprinting is the ability to simultaneously evaluate a large number of protein–ligand complexes, which can identify signature interactions to guide SBDD.…”