Drug Designing: Open Access
Open Access

Abstract

An Integrated Computational and Experimental Binding Study Identifies the DNA Binding Domain as the Putative Binding Site of Novel Pyrimidinetrione Signal Transducer and Activator of Transcription 3 (STAT3) Inhibitors

Shan Sun, Peibin Yue, Mingzhu He, Xiaolei Zhang, David Paladino, Yousef Al-Abed, James Turkson and John K Buolamwini

Objective: Signal transducer and activator of transcription 3 (STAT3) is as a potential drug target for cancer and inflammation. Strategies to block STAT3 dimerization have dominated STAT3 inhibitor discovery, while inhibition of direct STAT3-DNA binding has not been much explored. This study was to identify novel STAT3 inhibitors that may be developed into probes or therapeutics, and to investigate their putative binding site.

Methods: A library of in-house compounds was screened against STAT3-DNA binding using an electrophoretic mobility shift assay (EMSA). Inhibition of DNA and STAT3:STAT3 or STAT3:STAT1 interaction and antiproliferative activity in STAT3 expressing or STAT3 knockout cells were tested. Pharmacophore modeling and 3D-QSAR; and docking with molecular mechanics generalized born surface area (MM-GBSA) refinement were also undertaken at the STAT3 SH2 and STAT3 DNA binding domains. Surface plasmon resonance (SPR) analysis was done to determine STAT3 domain interactions. Organic synthesis was also undertaken.

Results: Pyrimidinetriones derivatives were identified as novel STAT3 inhibitors, with activity in low micromolar concentrations. Application of 3D-QSAR and docking analysis with MM-GBSA refinement suggested that the compounds bind at the STAT3-DNA binding interface, and not at the SH2 domain where most current STAT3 inhibitors are thought to bind. The results were confirmed with SPR analysis, pointing to the DNA binding domain (DBD) as the putative binding site of this novel class of STAT3 inhibitors. The analysis guided the synthesis of active novel compounds.

Conclusion: Pyrimidinetrione were identified as new STAT3 inhibitors that putatively bind at the STAT3 DBD. This study is an excellent example of the use of QSAR and structure-based design to aid the identification of putative ligand binding sites on proteins. The compounds will provide new tools for studying STAT3 biology; and also serve as potential leads for the development of new therapeutics against STAT3 to fight or study diseases such as cancer and inflammation.