An evaluation of indirubin analogues as phosphorylase kinase inhibitors

Abstract

Phosphorylase kinase (PhK) has been linked with a number of conditions such as glycogen storage diseases, psoriasis, type 2 diabetes and more recently, cancer (Camus S. et al., Oncogene 2012, 31, 4333). However, with few reported structural studies on PhK inhibitors, this hinders a structure based drug design approach. In this study, the inhibitory potential of 38 indirubin analogues have been investigated. 11 of these ligands had IC50 values in the range 0.170 -0.360 µM, with indirubin-3'-acetoxime (1c) the most potent. 7-bromoindirubin-3'-oxime (13b), an antitumor compound which induces caspase-independent cell-death (Ribas J. et al., Oncogene, 2006, 25, 6304) is revealed as a specific inhibitor of PhK (IC50 = 1.8 µM). Binding assay experiments performed using both PhK-holo and PhK-γtrnc confirmed the inhibitory effects to arise from binding at the kinase domain (γ subunit). High level computations using QM/MM-PBSA binding free energy calculations were in good agreement with experimental binding data, as determined using statistical analysis, and support binding at the ATP-binding site. The value of a QM description for the binding of halogenated ligands exhibiting σ-hole effects is highlighted. A new statistical metric, the 'sum of the modified logarithm of ranks' (SMLR), has been defined which measures performance of a model for both the "early recognition" (ranking earlier/higher) of active compounds and their relative ordering by potency. Through a detailed structure activity relationship analysis considering other kinases (CDK2, CDK5 and GSK-3α/β), 6'(Z) and 7(L) indirubin substitutions have been identified to achieve selective PhK inhibition. The key PhK binding site residues involved can also be targeted using other ligand scaffolds in future work.

Molecular dynamics-driven drug discovery: leaping forward with confidence

“…It has been 38 years since the first molecular dynamics (MD) simulations of bovine pancreatic trypsin inhibitor were carried out for 9.2 picoseconds. Since then, there has been tremendous growth in supercomputing power and significant developments [188] Multiple targets [189] NS2B/NS3 Dengue virus [190] Histone deacetylases [46,73,191] β-lactamase [192] HIV-1 RT RNase [193] Glycoprotein [194] Neurotoxin serotype A [195] ERCC1-XPF [114] Lysozyme [196] Phosphorylase kinase [197] STAT3 and STAT5 [198] Mad2 [199] Tubulin [200] Phosphorylase kinase [201]…”

Discovery of LDD‑1075 as a potent FLT3 inhibitor

“…Many indirubin derivatives have been synthesized, to develop anti-cancer drugs based on this information (13,(23)(24)(25). Depending on the substitutions of the indirubin derivatives, the compounds have been shown to inhibit kinases other than CDKs and GSK3β including, for example, the Jak family kinases (26), phosphorylase kinase (27), Aurora kinases (28), and dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) (29). Our lab has been investigating indirubin derivatives as FLT3 inhibitors (13); thus, here, we report compounds with an improved FLT3 inhibitory activity.…”

Recent Developments and Applications of the MMPBSA Method

“…For inflammatory disorders, targets such as COX-2 (Chaudhary and Aparoy, 2017 ), interleukin 6 (Verma R. et al, 2016 ), toll-like receptors (Shen et al, 2016 ), human leukocyte antigen (Kongkaew et al, 2015 ), chymase enzyme (Verma et al, 2017 ), tumor necrosis factor (Ivanisenko et al, 2014 ), and Nalp3 (Sahoo et al, 2014b ) were studied. For diabetes, analyses of targets included phosphorylase kinase (Begum et al, 2015 ), glycogen synthase kinase (Arfeen et al, 2015 ), protein kinase C beta II (Grewal and Sobhia, 2014 ), and dipeptidyl peptidase-4 enzyme (Gu et al, 2014 ; Sneha and Doss, 2016 ). In a search for compounds for the treatment of chronic kidney disease, Vitamin D receptor and cytochrome P450 were analyzed (Nagamani et al, 2016 ).…”