The rational design of a novel potent analogue of the 5′-AMP-activated protein kinase inhibitor compound C with improved selectivity and cellular activity

Abstract

We have designed and synthesized analogues of compound C, a non-specific inhibitor of 5'-AMPactivated protein kinase (AMPK), using a computational fragment-based drug design (FBDD) approach. Synthesizing only twenty-seven analogues yielded a compound that was equipotent to compound C in the inhibition of the human AMPK (hAMPK) α2 subunit in the heterotrimeric complex in vitro, exhibited significantly improved selectivity against a subset of relevant kinases, and demonstrated enhanced cellular inhibition of AMPK. KeywordsFragment-based drug design; FBDD; 5'-AMP-activated protein kinase; AMPK; compound C 5'-AMP-activated protein kinase (AMPK) is a major regulator of normal cellular energy metabolism [1]. AMPK activity is sensitive to the cellular AMP:ATP ratio, which is increased by physiological stresses such decreased oxygen and glucose concentrations (hypoxia and hypoglycemia). AMPK activity is also associated with the growth of solid tumors, which commonly contain regions of pathologic hypoxia and hypoglycemia [2]. AMPK cooperates with hypoxia-inducible factor-1 (HIF-1), the primary transcriptional regulator of the mammalian response to hypoxia and other metabolic stresses that lower cellular ATP levels, in pathophysiological tumor microenvironments [3,4]. Thus, in the context of microenvironmental stress, AMPK may represent a novel target for the treatment of solid tumors. The successful design of potent and selective inhibitors of AMPK that exhibit activity is an important first step toward establishing the proof-of-concept for the therapeutic value of AMPK inhibition in solid tumor microenvironments.This Letter describes our efforts to design a Type I inhibitor of AMPK with a superior biological profile than that of compound C (Figure 1), which is a commonly used experimental direct inhibitor of the enzyme [5], through the use of our proprietary fragmentbased drug design (FBDD) software [6][7][8][9] Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. We discuss the SAR of a series of pyrazolopyrimidine and aminooxazole analogues of compound C and present their general binding mode obtained through the use of homology modeling and Grand Canonical Monte Carlo (GCMC) fragment simulations [9]. A focused kinase selectivity profile for the most active subset of these compounds is presented, as well as the cellular AMPK inhibition data for the most promising pyrazolopyrimidine. NIH Public AccessWe generated a model of the catalytic α2 subunit of AMPK with the DFG-loop in the 'in' conformation using MOE [12]. The crystal structure of the AMPK α2 subunit (RCSB ID# 2H6D, ...

Farnesoid X Receptor Activation by Chenodeoxycholic Acid Induces Detoxifying Enzymes through AMP-Activated Protein Kinase and Extracellular Signal-Regulated Kinase 1/2-Mediated Phosphorylation of CCAAT/Enhancer Binding Protein β

“…elicited by CDCA was attenuated by DN-AMPK␣ transfection or compound C treatment (a chemical inhibitor of AMPK) (Machrouhi et al, 2010) (Fig. 4B), suggesting that AMPK activation by CDCA may be involved in the ERK1/2 phosphorylation.…”

Fragment-Based Drug Design: Computational and Experimental State of the Art

“…This docking strategy has also been successfully used for the discovery of dipeptidyl peptidase IV inhibitors which are potential anti-diabetic agents [111]. Machrouhi et al designed new analogs of a non-specific reference inhibitor (compound C) of the 5'-AMP-activated protein kinase (AMPK) by using a modeling workflow [112]. They first built a homology model of this enzyme which was subsequently used to sample, with an in-house tool and a grand canonical Monte-Carlo strategy, three fragments obtained from the breaking of the reference ligand.…”

Computer-Aided Drug Design for AMP-Activated Protein Kinase Activators

“…One of the successful examples of fragment-based drug design was reported by Anthony et al, who identify potent inhibitors of AMPK starting from a scaffold of compound C, a non-specific inhibitor of AMPK [125]. A homology model of catalytic 2 subunit of human AMPK with the DFG-loop was generated using MOE.…”