Discovery and Structure–Activity Relationships of N‐Aryl 6‐Aminoquinoxalines as Potent PFKFB3 Kinase Inhibitors

Abstract

Energy and biomass production in cancer cells are largely supported by aerobic glycolysis in what is called the Warburg effect. The process is regulated by key enzymes, among which phosphofructokinase PFK‐2 plays a significant role by producing fructose‐2,6‐biphosphate; the most potent activator of the glycolysis rate‐limiting step performed by phosphofructokinase PFK‐1. Herein, the synthesis, biological evaluation and structure–activity relationship of novel inhibitors of 6‐phosphofructo‐2‐kinase/fructose‐2,6‐biphosphatase 3 (PFKFB3), which is the ubiquitous and hypoxia‐induced isoform of PFK‐2, are reported. X‐ray crystallography and docking were instrumental in the design and optimisation of a series of N‐aryl 6‐aminoquinoxalines. The most potent representative, N‐(4‐methanesulfonylpyridin‐3‐yl)‐8‐(3‐methyl‐1‐benzothiophen‐5‐yl)quinoxalin‐6‐amine, displayed an IC50 of 14 nm for the target and an IC50 of 0.49 μm for fructose‐2,6‐biphosphate production in human colon carcinoma HCT116 cells. This work provides a new entry in the field of PFKFB3 inhibitors with potential for development in oncology.

Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects

“…Based on our extensive experience with free energy calculations in our in-house projects where we unfortunately cannot publish the structures at this moment, we decided to construct a new benchmark consisting of eight challenging, recently published data sets with pharmaceutically relevant targets. − The benchmark comprises 264 ligands in total. The protein targets and the chemical space in this benchmark data set are representative of the targets in our in-house projects.…”

“…Protein cocrystal structures were downloaded from the Protein Data Bank (). Ligand structures and affinities (IC 50 ) were extracted manually from papers and patents − or extracted via ChEMBL. , Protein structures and ligand structures were prepared for free energy calculations as described above. In contrast to the in-house data sets, ligand structures were aligned by Glide core-constrained docking using the X-ray ligand as reference (standard precision settings).…”

Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects

“…Based on our extensive experience with free energy calculations, we decided to construct a new benchmark consisting of eight challenging, recently published data sets with pharmaceutically relevant targets. [53][54][55][56][57][58][59][60][61][62] The benchmark comprises 264 ligands in total. It illustrates many of the challenges we faced when using FEP+ in projects and reflects the typical type and size of chemical transformations during hit-to-lead and lead optimization.…”

“…Protein co-crystal structures were downloaded from the Protein Data Bank (www.rcsb.org). Ligand structures and affinities (IC 50 ) were extracted manually from papers and/or patents [53][54][55][56][57][58][59][60][61][62]. IC 50 values were converted into free energy values using the equation ∆G ≈ k B T log IC 50 .…”

Structural derivatization strategies of natural phenols by semi-synthesis and total-synthesis

“…However, it's not so applicable for complex polyphenols as it requires sufficient protection of active groups including phenolic hydroxyls. Furthermore, cross-coupling of arylhalide or aryltriflate with organoboron or organometal was also a potential strategy to introduce alkyl or aryl with a great diversity [31,32] (Scheme 1A-m). Introducing specific groups onto the phenolic ring may improve the bioactivity of natural phenols.…”