Homology modeling of DFG-in FMS-like tyrosine kinase 3 (FLT3) and structure-based virtual screening for inhibitor identification.

Yi-Yu Ke,John T A Hsu,Szu-Huei Wu,Mohane Selvaraj Coumar,Hsing-Pang Hsieh,Chun-Hwa Chen,Chuan Shih,Wen-Chieh Wang,Vivek Kumar Singh,Yung Chang Hsu,Wen-Hsing Lin,Jen-Shin Song

doi:10.1038/srep11702

Abstract

The inhibition of FMS-like tyrosine kinase 3 (FLT3) activity using small-molecule inhibitors has emerged as a target-based alternative to traditional chemotherapy for the treatment of acute myeloid leukemia (AML). In this study, we report the use of structure-based virtual screening (SBVS), a computer-aided drug design technique for the identification of new chemotypes for FLT3 inhibition. For this purpose, homology modeling (HM) of the DFG-in FLT3 structure was carried using two template structures, including PDB ID: 1RJB (DFG-out FLT3 kinase domain) and PDB ID: 3LCD (DFG-in CSF-1 kinase domain). The modeled structure was able to correctly identify known DFG-in (SU11248, CEP-701, and PKC-412) and DFG-out (sorafenib, ABT-869 and AC220) FLT3 inhibitors, in docking studies. The modeled structure was then used to carry out SBVS of an HTS library of 125,000 compounds. The top scoring 97 compounds were tested for FLT3 kinase inhibition, and two hits (BPR056, IC50 = 2.3 and BPR080, IC50 = 10.7 μM) were identified. Molecular dynamics simulation and density functional theory calculation suggest that BPR056 (MW: 325.32; cLogP: 2.48) interacted with FLT3 in a stable manner and could be chemically optimized to realize a drug-like lead in the future.

Highlights

Acute myeloid leukemia, which is typically referred to as AML, is a hematological malignancy characterized by the abnormal growth of white blood cells, leading to the disruption of normal blood cell production in the bone marrow
For the identification of the second template structure, an NCBI protein-BLAST search was performed against the FMS-like tyrosine kinase 3 (FLT3) kinase domain 293-amino acid target sequence
Known FLT3 inhibitors bind to the kinase domains of this enzyme in either DFG motif adopts the “in” conformation (DFG-in) or DFG-out conformation

Summary

Introduction

Acute myeloid leukemia, which is typically referred to as AML, is a hematological malignancy characterized by the abnormal growth of white blood cells, leading to the disruption of normal blood cell production in the bone marrow. A number of FLT3 inhibitors have been investigated in clinical trials for the treatment of AML8, including sunitinib (SU11248)[9], lestaurtinib (CEP-701)[10], midostaurin (PKC-412)[11], sorafenib[12], linifanib (ABT-869)[13] and AC22014 These agents competitively inhibit the activity of FLT3 by binding to the ATP binding site of this enzyme. The active kinase typically adopts the DFG-in conformation, while the inactive enzyme adopts the DFG-out conformation Based on their preferences for binding to the active or inactive kinase, the known FLT3 inhibitors SU11248, CEP-701, and PKC-412 are classified as type-I inhibitors, while sorafenib, ABT-869 and AC22014 are considered type-II inhibitors[16]. We aimed to identify type-I inhibitors through computer-aided drug design (CADD)

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Results

Conclusion