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Quizartinib in the FLT3 co-complex matches the second-ranked docking pose. (A) An overlay of quizartinib from the co-crystal structure (yellow) with the top-ranked docking pose (white) is shown. (B) An overlay of quizartinib from the co-crystal structure (yellow) with the second-ranked docking pose (white) is shown.
Source publication
More than 30% of acute myeloid leukemia (AML) patients possess activating mutations in the receptor tyrosine kinase FMS-like tyrosine kinase 3 or FLT3. A small-molecule inhibitor of FLT3 (known as quizartinib or AC220) that is currently in clinical trials appears promising for the treatment of AML. Here, we report the co-crystal structure of the ki...
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The aim of the study was to assess the role of allogeneic stem cell transplantation (SCT) in patients diagnosed with BCR-ABL1-positive acute myeloid leukemia (AML). Fifty-seven patients (median age, 48 years, range: 19-67) with BCR-ABL1 positive AML undergoing SCT were identified. The majority of the patients (70%) received a TKI before the transpl...
Citations
... Seven protein kinase inhibitors were identified as probable products of SGDD ("Prob" in Table 2) on the basis of indirect evidence, including (a) PDB housed a structure of the target protein 10 or more years prior to drug approval; and/or (b) structural biologists based in either academia or industry deposited a co-complex structure of the LMW-NME bound to its target protein to the PDB; and/or (c) the target had been prosecuted successfully using SGDD previously by another company. We classified these less clear-cut cases as probable because we think it highly likely that the sponsor company was in possession of the same or similar data given the ubiquity of expert structural biology and computational chemistry teams across the biopharmaceutical industry today [33,[46][47][48][49][50]. ...
Open access to three-dimensional atomic-level biostructure information from the Protein Data Bank (PDB) facilitated discovery/development of 100% of the 34 new low molecular weight, protein-targeted, antineoplastic agents approved by the US FDA 2019–2023. Analyses of PDB holdings, the scientific literature, and related documents for each drug-target combination revealed that the impact of structural biologists and public-domain 3D biostructure data was broad and substantial, ranging from understanding target biology (100% of all drug targets), to identifying a given target as likely druggable (100% of all targets), to structure-guided drug discovery (>80% of all new small-molecule drugs, made up of 50% confirmed and >30% probable cases). In addition to aggregate impact assessments, illustrative case studies are presented for six first-in-class small-molecule anti-cancer drugs, including a selective inhibitor of nuclear export targeting Exportin 1 (selinexor, Xpovio), an ATP-competitive CSF-1R receptor tyrosine kinase inhibitor (pexidartinib,Turalia), a non-ATP-competitive inhibitor of the BCR-Abl fusion protein targeting the myristoyl binding pocket within the kinase catalytic domain of Abl (asciminib, Scemblix), a covalently-acting G12C KRAS inhibitor (sotorasib, Lumakras or Lumykras), an EZH2 methyltransferase inhibitor (tazemostat, Tazverik), and an agent targeting the basic-Helix-Loop-Helix transcription factor HIF-2α (belzutifan, Welireg).
... Quizartinib is a benzothiazole phenylurea derivative (Fig. 4C) that is FDA-approved for the combination treatment with standard cytarabine and anthracycline induction and cytarabine consolidation and as maintenance monotherapy following consolidation chemotherapy for the treatment of adult patients with newly diagnosed acute myeloid leukemia (AML) that is FLT3 internal tandem duplication-positive as detected by an FDA-approved test as described in the FDA label. Zorn et al. determined the X-ray crystal structure of quizartinib bound to Flt3 [81]. They observed that the urea N-H groups hydrogen bonded with the αC-E661 and the urea oxygen hydrogen-bonded with the backbone N-H group of DFG-D829 (Fig. 5C). ...
... The native structure of the FLT3 protein, with a resolution of 3.20 Å, determined through X-ray diffraction was obtained from the Protein Data Bank (PDB) [25]. The PDB ID for the dimeric FLT3 structure is 4XUF [26]. In the structural configuration of FLT3, the fundamental kinase fold comprises a compact N-terminal lobe (N lobe) and an α-helical Cterminal lobe (C lobe) connected through a hinge segment. ...
... We utilized the MM-PBSA method to compute thermodynamic binding free energies for both native and mutant FLT3 structures interacting with various drug molecules. The native FLT3 protein structure was sourced from the PDB database [26]. We introduced point mutations at position Y842 to create models of the Y842C and Y842F mutant structures. ...
Simple Summary
In this study, we investigated FLT3, a protein that plays a vital role in the development of early blood cells. FLT3 often undergoes changes that contribute to the onset of a blood cancer known as acute myeloid leukemia (AML). We employed sophisticated computational techniques to examine how various mutations in the FLT3 protein affect its function and its interaction with therapeutic drugs. Our analysis covered numerous combinations of potential FLT3 mutations and drugs to identify the most effective treatments. Specifically, we concentrated on the impact of a mutation at the Y842 site within FLT3 on the efficacy of drug treatments. Furthermore, we introduced a novel scoring system designed to enhance the prediction of drug effectiveness. Our findings highlight the significance of customized medical approaches, considering that individual mutations can markedly alter a patient’s reaction to AML treatments.
Abstract
The type III receptor tyrosine kinase FLT3 is a pivotal kinase for hematopoietic progenitor cell regulation, with significant implications in acute myeloid leukemia (AML) through mutations like internal tandem duplication (ITD). This study delves into the structural intricacies of FLT3, the roles of activation loop mutants, and their interaction with tyrosine kinase inhibitors. Coupled with this, the research leverages molecular contrastive learning and protein language modeling to examine interactions between small molecule inhibitors and FLT3 activation loop mutants. Utilizing the ConPLex platform, over 5.7 million unique FLT3 activation loop mutants—small molecule pairs were analyzed. The binding free energies of three inhibitors were assessed, and cellular apoptotic responses were evaluated under drug treatments. Notably, the introduction of the Xepto50 scoring system provides a nuanced metric for drug efficacy. The findings underscore the modulation of molecular interactions and cellular responses by Y842 mutations in FLT3-KD, highlighting the need for tailored therapeutic approaches in FLT3-ITD-related malignancies.
... On the other hand, type II FLT3 hampering agent Quizartinib binds to the inactive conformation (DFGout) of the TKD as a non-competitive ATP FLT3 inhibitor (PDB: 4XUF). It forms two main hydrogen bonds with Asp829 and Glu661 amino acids and many other hydrophobic interactions within the TKD (Fig. 3) [51]. Therefore, Quizartinib preserves its activity towards FLT3-ITD mutations within the juxtamembrane region but does not have the same activity towards FLT3-TKD mutations within the tyrosine kinase region (Fig. 3) [52]. ...
Fms-like tyrosine kinase 3 (FLT3) mutation mechanisms are among the most common genetic abnormalities detected in about 30% of acute myeloid leukemia (AML) patients. These mutations are accompanied by poor clinical response, although all these progressions in identifying and interpreting biological AML bio-targets. Several small structured FLT3 inhibitors have been ameliorated to struggle against AML. Despite all these developments regarding these inhibitors, the Overall survival rate is about five years or more in less than one-third of diagnosed AML patients. Midostaurin was the first FDA-approved FLT3 inhibitor in 2017 in the United States and Europe for AML remedy. Next, Gilteritinib was an FDA-approved FLT3 inhibitor in 2018 and in the next year, Quizartinib was approved an as FLT3 inhibitor in Japan. Interestingly, indole-based motifs had risen as advantaged scaffolds with unusual multiple kinase inhibitory activity. This review summarises indole-based FLT3 inhibitors and related scaffolds, including FDA-approved drugs, clinical candidates, and other bioactive compounds. Furthermore, their chemotypes, mechanism of action, and interaction mode over both wild and mutated FLT3 target proteins had been judgmentally discussed. Therefore, this review could offer inspiring future perspectives into the finding of new FLT3-related AML therapies.
... Among the first molecular markers identified were internal tandem duplications (ITDs) in the gene encoding fms-like tyrosine kinase-3 (FLT3). The receptor tyrosine kinase FLT3 is composed of an extracellular module with five immunoglobulin-like domains, a transmembrane domain, and an intracellular module consisting of a juxtamembrane domain (JMD) and two tyrosine kinase subdomains (TKD1 and TKD2) connected by a kinase insert domain (Figure 1) [2]. In 1996, Nakao et al. detected in-frame ITDs of varying lengths in the JMD of the FLT3 gene in a small cohort of AML patients [3]. ...
Simple Summary
FLT3 gene mutations are among the most common genetic aberrations detected in AML and occur with a frequency of approximately 30%, mainly as internal tandem duplications (FLT3-ITD). As a novel finding, it has been reported that the specific insertion sites (IS) of FLT3-ITD exhibit marked heterogeneity in both biological and clinical features. Thus, the so-called non-juxtamembrane domain (non-JMD) FLT3-ITD insertions have been shown to be associated with worse clinical outcomes and resistance to both chemotherapy and tyrosine kinase inhibition. This present review summarizes our current knowledge of the biological and clinical impact of FLT3-ITD inserting at the non-JMD level. Recent evidence suggests that conformational changes depending on FLT3-ITD localization affect downstream signaling networks and the oncogenic potential. We propose that refined risk stratification guidelines integrating the negative prognostic impact of non-JMD FLT3-ITD are warranted. Overcoming therapy resistance in non-JMD-inserting FLT3-ITD-mutated AML may lead to promising treatment approaches.
Abstract
Mutations of the FLT3 gene are among the most common genetic aberrations detected in AML and occur mainly as internal tandem duplications (FLT3-ITD). However, the specific sites of FLT3-ITD insertion within FLT3 show marked heterogeneity regarding both biological and clinical features. In contrast to the common assumption that ITD insertion sites (IS) are restricted to the juxtamembrane domain (JMD) of FLT3, 30% of FLT3-ITD mutations insert at the non-JMD level, thereby integrating into various segments of the tyrosine kinase subdomain 1 (TKD1). ITDs inserted within TKD1 have been shown to be associated with inferior complete remission rates as well as shorter relapse-free and overall survival. Furthermore, resistance to chemotherapy and tyrosine kinase inhibition (TKI) is linked to non-JMD IS. Although FLT3-ITD mutations in general are already recognized as a negative prognostic marker in currently used risk stratification guidelines, the even worse prognostic impact of non-JMD-inserting FLT3-ITD has not yet been particularly considered. Recently, the molecular and biological assessment of TKI resistance highlighted the pivotal role of activated WEE1 kinase in non-JMD-inserting ITDs. Overcoming therapy resistance in non-JMD FLT3-ITD-mutated AML may lead to more effective genotype- and patient-specific treatment approaches.
... FMS-like tyrosine kinase 3 (FLT3), a class III receptor tyrosine kinase (RTK), generates between the normal and ferocious lymphohematopoietic cells [11]. This receptor plays a crucial part in the proliferation of stem cells and the activation of immune responses [12]. The deregulation of FLT3 activity owing to overexpression or mutation is associated with acute myeloid leukemia (AML) growth and poor prognosis [12,13]. ...
... This receptor plays a crucial part in the proliferation of stem cells and the activation of immune responses [12]. The deregulation of FLT3 activity owing to overexpression or mutation is associated with acute myeloid leukemia (AML) growth and poor prognosis [12,13]. Two groups of mutations occur in FLT3: an internal tandem duplication (ITD) located in the juxtamembrane domain and a point mutation in the kinase activation loop [14]. ...
Background:
Cancer is the second leading cause of death in the world. Leukemia is a type of cancer that accounts for 31.5% of all cancers in children under the age of 15 in industrialized countries and 15.7% in developing countries. The inhibition of FMS-like tyrosine kinase 3 (FLT3) is a suitable approach for acute myeloid leukemia (AML) therapy as it is overexpressed in AML.
Aim and objective:
This study intends to explore the natural constituents from the bark of Corypha utan Lamk., and assess their cytotoxicity on murine leukemia cell lines (P388) in addition to predicting their interaction with FLT3 as a studied target by computational methods.
Methods:
Compounds 1 and 2 were isolated from Corypha utan Lamk using the stepwise radial chromatography method. These compounds were assessed for their cytotoxicity against Artemia salina using the BSLT and P388 cells and the MTT assay. The docking simulation was employed to predict the possible interaction between triterpenoid and FLT3.
Results:
Isolation from the bark of C. utan Lamk. generated two triterpenoids, cycloartanol (1) and cycloartanone (2). Based on the in vitro and in silico studies, both compounds were found to have anticancer activity. The evaluation of cytotoxicity from this study reveals that cycloartanol (1) and cycloartanone (2) could inhibit P388 cell growth (IC50 value at 102.6 and 110.0 μg/mL, respectively). The binding energy of cycloartanone was -9.94 Kcal/mol with a Ki value of 0.051 μM, while the binding energy and Ki value of cycloartanol (1) were found to be 8.76 Kcal/mol and 0.38 μM, respectively. These compounds also demonstrate a stable interaction by forming hydrogen bonds with FLT3.
Conclusion:
Cycloartanol (1) and cycloartanone (2) exhibit potency as anticancer agents by inhibiting P388 cells in vitro and the FLT3 gene in silico.
... Secondary mutation F691L develops during gilteritinib therapy as a cause of resistance and there is no applicable therapeutic option for patients with F691L mutation [34]. Structurally, gilteritinib interacted with F691 residue via van der Waals or CH − π interactions and quizartinib formed π-π interactions with F691 residue [35,36]. Unlike gilteritinib and quizartinib, the predicted binding sites of sitravatinib with FLT3 did not include F691, indicating that sitravatinib might overcome F691L resistance. ...
Background
Gilteritinib is the only drug approved as monotherapy for acute myeloid leukemia (AML) patients harboring FMS-like tyrosine kinase 3 internal tandem duplication ( FLT3 -ITD) mutation throughout the world. However, drug resistance inevitably develops in clinical. Sitravatinib is a multi-kinase inhibitor under evaluation in clinical trials of various solid tumors. In this study, we explored the antitumor activity of sitravatinib against FLT3 -ITD and clinically-relevant drug resistance in FLT3 mutant AML.
Methods
Growth inhibitory assays were performed in AML cell lines and BaF3 cells expressing various FLT3 mutants to evaluate the antitumor activity of sitravatinib in vitro. Immunoblotting was used to examine the activity of FLT3 and its downstream pathways. Molecular docking was performed to predict the binding sites of FLT3 to sitravatinib. The survival benefit of sitravatinib in vivo was assessed in MOLM13 xenograft mouse models and mouse models of transformed BaF3 cells harboring different FLT3 mutants. Primary patient samples and a patient-derived xenograft (PDX) model were also used to determine the efficacy of sitravatinib.
Results
Sitravatinib inhibited cell proliferation, induced cell cycle arrest and apoptosis in FLT3 -ITD AML cell lines. In vivo studies showed that sitravatinib exhibited a better therapeutic effect than gilteritinib in MOLM13 xenograft model and BaF3- FLT3 -ITD model. Unlike gilteritinib, the predicted binding sites of sitravatinib to FLT3 did not include F691 residue. Sitravatinib displayed a potent inhibitory effect on FLT3 -ITD-F691L mutation which conferred resistance to gilteritinib and all other FLT3 inhibitors available, both in vitro and in vivo. Compared with gilteritinib, sitravatinib retained effective activity against FLT3 mutation in the presence of cytokines through the more potent and steady inhibition of p-ERK and p-AKT. Furthermore, patient blasts harboring FLT3 -ITD were more sensitive to sitravatinib than to gilteritinib in vitro and in the PDX model.
Conclusions
Our study reveals the potential therapeutic role of sitravatinib in FLT3 mutant AML and provides an alternative inhibitor for the treatment of AML patients who are resistant to current FLT3 inhibitors.
... Type 2 inhibitors stabilize FLT3 in the inactive conformation with the activation loop in a closed configuration (phenyalanine in the DFG motif protruding into the hydrophobic groove). As FLT3-TKD mutations disrupt the activation loop, maintaining an open configuration, Type 2 inhibitors are unable to bind FLT3 in this context, as demonstrated in Fig. 1C [15]. FLT3 inhibitors are further characterized based on specificity. ...
Recent advances in FLT3 and IDH targeted inhibition have improved response rates and overall survival in patients with mutations affecting these respective proteins. Despite this success, resistance mechanisms have arisen including mutations that disrupt inhibitor-target interaction, mutations impacting alternate pathways, and changes in the microenvironment. Here we review the role of these proteins in leukemogenesis, their respective inhibitors, mechanisms of resistance, and briefly ongoing studies aimed at overcoming resistance.
... 108 Quizartinib binds to the FLT3 kinase in the inactive conformation (DFG out ) as shown in Fig. 11. 111 Following preclinical studies, a phase I dose escalation trial was completed to assess safety and tolerability of quizartinib among 76 patients irrespective of FLT3-ITD status (NCT00462761). 112 The maximum tolerated dose was determined to be 200 mg per day, and QT prolongation was identified as a dose-limiting toxicity. ...
... 38 In addition to the covalent bond with C695 at the hinge region, FF-10101 interacts with E692 and K644 via hydrogen bonds. 111 Quizartinib is a type-II inhibitor that is ATP non-competitive and binds to the inactive (DFG out ) conformation of the kinase. The hinge region, αC-helix, and DFG loop are illustrated in red, orange, and blue, respectively. ...
FLT3 mutations are one of the most common genetic aberrations found in nearly 30% of acute myeloid leukemias (AML). The mutations are associated with poor prognosis despite advances in the understanding of the biological mechanisms of AML. Numerous small molecule FLT3 inhibitors have been developed in an effort to combat AML. Even with the development of these inhibitors, the five-year overall survival for newly diagnosed AML is less than 30%. In 2017, midostaurin received FDA approval to treat AML, which was the first approved FLT3 inhibitor in the U.S. and Europe. Following, gilteritinib received FDA approval in 2018 and in 2019 quizartinib received approval in Japan. This review parallels these clinical success stories along with other pre-clinical and clinical investigations of FLT3 inhibitors.
... FMS-like tyrosine kinase 3 (FLT3), a class III receptor tyrosine kinase (RTK), generates between the normal and ferocious lymphohematopoietic cells [11]. This receptor plays a crucial part in the proliferation of stem cells and the activation of immune responses [12]. The deregulation of FLT3 activity owing to overexpression or mutation is associated with acute myeloid leukemia (AML) growth and poor prognosis [12,13]. ...
... This receptor plays a crucial part in the proliferation of stem cells and the activation of immune responses [12]. The deregulation of FLT3 activity owing to overexpression or mutation is associated with acute myeloid leukemia (AML) growth and poor prognosis [12,13]. Two groups of mutations occur in FLT3: an internal tandem duplication (ITD) located in the juxtamembrane domain and a point mutation in the kinase activation loop [14]. ...
Humic acid (HA) is one of natural organic compound existed in soils which contributes to create unpleasant odor, taste and color in drinking water. Efforts have been developed to eliminate this substance, one of which is membrane technology. In this present study, we have successfully fabricated PVDF and PVDF/cellulose membranes through phase inversion method. The cellulose extracted from oil-palm empty fruit bunches was in two different dimension, namely microcrystalline- (MCC) and nanocrystalline cellulose (NCC). The physicochemical properties of the membrane were evaluated in this study. It was found that the hydrophilicity of the membrane was elevated by the presence of cellulose filler. This also led to reduce the porosity of the membrane, but on the other hand increase the pure water flux. The study revealed that by incorporating 1% of MCC (PMC1) improved the rejection performance toward HA, above 90%. In addition, PMC1 membrane has a higher Flux Recovery Ratio (FRR) value than other membranes. Thus, for further applications, especially in water treatment, PMC1 membranes are highly recommended.
