Discovery of a Novel Chemotype of Tyrosine Kinase Inhibitors by Fragment-Based Docking and Molecular Dynamics

Abstract

ABSTRACT:We have discovered a novel chemical class of inhibitors of the EphB4 tyrosine kinase by fragment-based high-throughput docking followed by explicit solvent molecular dynamics simulations for assessment of the binding mode. The synthesis of a single derivative (compound 7) of the hit identified in silico has resulted in an improvement of the inhibitory potency in an enzymatic assay from 8.4 μM to 160 nM and a ligand efficiency of 0.39 kcal/mol per non-hydrogen atom. Such remarkable improvement in affinity is due to an additional hydroxyl group involved in two favorable (buried) hydrogen bonds as predicted by molecular dynamics and validated by the crystal structure of the complex with EphA3 solved at 1.7 Å resolution. KEYWORDS: In silico screening, EphB4 kinase, angiogenesis, cancer, explicit solvent MD T he Eph-ephrin system, including the EphA2 and EphB4 receptors, plays a critical role in tumor and vascular functions during carcinogenesis.1,2 Recently, it has been shown that delivery of chemotherapeutic drugs by an EphA2 targeting peptide into EphA2-expressing cancer cells led to dramatically improved efficacy in inhibiting tumor growth.3 So far, a few Eph inhibitors have been identified, including the marketed drug Dasatinib ( Figure S1 in the Supporting Information). 4−12Although their role is still controversial for certain types of cancer, e.g., non small cell lung cancer, 13 the identification of selective inhibitors of Eph tyrosine kinases will help to elucidate their involvement in deregulated signaling.Previously, we have developed an efficient in silico procedure called ALTA, which stays for anchor-based library tailoring approach, to interrogate a library of compounds for highthroughput docking.14 First, small and mainly rigid virtual fragments are docked in the binding site. The fragments with most favorable calculated binding free energy (anchors) are used to identify the compounds with 2D structure containing one of these anchors, which are then submitted to flexibleligand docking. In this letter, we report a new approach for in silico screening based on the synergistic combination of the ALTA procedure for docking followed by explicit solvent molecular dynamics simulations for further validation of the binding poses.The flowchart of the ALTA procedure is shown in Figure 1. First, the nearly 9 million compounds in the ZINC-all now library 15 (version of August 2011) were decomposed into 563,774 fragments by in house developed software ( Figure S2 in the Supporting Information). Just like its in vitro counterpart of fragment-based drug discovery, 16,17 the success of the ALTA in silico screening approach depends on the choice of fragments. The use of virtual fragments by computational decomposition of a real compound library offers opportunities to explore a much greater fragmental space, with no limitations in availability. To obtain fragments with high chemical richness

Structured Water Molecules in the Binding Site of Bromodomains Can Be Displaced by Cosolvent

“…Moreover, the position of structured water molecules that are replaced by (m)ethanol can be used to design hydroxy substituents of initial hits, which can improve the affinity by up to two orders of magnitude. [46][47][48]…”

New strategies in achieving antiangiogenic effect: Multiplex inhibitors suppressing compensatory activations of RTKs

“…They combined fragment-based approach for docking and accurate evaluation of binding affinity. 147 The third optimization campaign was performed on a quinoxaline scaffold affording nanomolar inhibitors (43)(44)(45). Qui-B4 exhibited inhibition on VEGF-A-induced HUVEC sprouting with an IC 50 value of 1.5 M. These results confirmed the importance of the quinoxaline derivatives for further optimization as EphB4 inhibitors.…”

“…Pyr‐B1 is a nanomolar EphB4 inhibitor with high potency and ligand efficiency. They combined fragment‐based approach for docking and accurate evaluation of binding affinity . The third optimization campaign was performed on a quinoxaline scaffold affording nanomolar inhibitors ( 43–45 ).…”

Using Fragment Based Drug Discovery to Target Epigenetic Regulators in Cancer

“…First, the ZINC library was filtered for compounds that are 200-400 Dalton, > 1 hydrogen-bond acceptor, < 8 rotatable bond, and have 2 to 6 rings. This processed library was then automatically decomposed into 375,897 fragments by a published algorithm [67] and again filtered to 238,408 fragments against the criteria that each fragment possess a MW between 60-300 Dalton, have ≥ 1 hydrogen-bond acceptor, and contain < 4 rotatable bonds [39]. This focused fragment library was docked into BRD4(I) and 17,179 fragments were selected as anchor fragments to retrieve 665,184 molecules from the original filtered ZINC library for high throughput docking onto the BRD4 (1) structure.…”