TAS-120 cancer target binding; defining reactivity and revealing the first FGFR1 irreversible structure
Authors: Maria Kalyukina, Yuliana Yosaatmadja, Martin J. Middleditch, Adam V. Patterson, Jeff B. Smaill, and Christopher Squire
This manuscript has been accepted after peer review and appears as an Accepted Article online prior to editing, proofing, and formal publication of the final Version of Record (VoR). This work is currently citable by using the Digital Object Identifier (DOI) given below. The VoR will be published online in Early View as soon as possible and may be different to this Accepted Article as a result of editing. Readers should obtain the VoR from the journal website shown below when it is published to ensure accuracy of information. The authors are responsible for the content of this Accepted Article.
To be cited as: ChemMedChem 10.1002/cmdc.201800719
Link to VoR: http://dx.doi.org/10.1002/cmdc.201800719
A Journal of
TAS-120 cancer target binding; defining reactivity and revealing the first FGFR1 irreversible structure.
Maria Kalyukina,[a,c] Yuliana Yosaatmadja,[a] Martin J. Middleditch,[a] Adam V. Patterson,[b,c] Jeff B. Smaill,[b,c] and Christopher J. Squire,*[a,c]
[a] M. Kalyukina (ORCID: 0000-0001-7907-6662), Dr. Y. Yosaatmadja (0000-0003-2875-5993), M.J. Middleditch (0000-0001-7077-5897), Dr. C.J. Squire (0000-0001-9212-0461)
School of Biological Sciences The University of Auckland
Private Bag 92019, Auckland 1142, New Zealand E-mail: [email protected]
[b] Dr. A.V. Patterson (0000-0001-5138-1227), Dr. J.B. Smaill (0000-0003-2954-6093)
Auckland Cancer Society Research Centre
Faculty of Medicine and Health Sciences, The University of Auckland Private Bag 92019, Auckland 1142, New Zealand
[c] M. Kalyukina, Dr. A.V. Patterson, Dr. J.B. Smaill, Dr. C.J. Squire Maurice Wilkins Centre for Molecular Biodiscovery
c/o the University of Auckland
Private Bag 92019, Auckland 1142, New Zealand
Supporting information for this article is given via a link at the end of the document.
Abstract: TAS-120 is an irreversible inhibitor of the fibroblast growth factor receptor (FGFR) family that is currently under phase I/II clinical trials in patients with confirmed advanced metastatic solid tumours harbouring FGFR aberrations. This inhibitor specifically targets the P- loop of the FGFR tyrosine kinase domain, forming a covalent adduct with a cysteine side chain of the protein. Our mass spectrometry experiments characterise an exceptionally fast chemical reaction in forming the covalent complex. The structural basis of this reactivity is revealed by a sequence of three X-ray crystal structures, a free ligand structure, a reversible FGFR1 structure, and the first reported irreversible FGFR1-adduct structure. We hypothesise that the most significant reactivity feature of TAS-120 is its inherent ability to undertake conformational sampling of the FGFR P-loop. In designing novel covalent FGFR inhibitors, such a phenomenon presents an attractive strategy requiring appropriate positioning of an acrylamide group similarly to that of TAS-120.
Lung cancer is a leading cause of death worldwide accounting for 19% of all cancer-related mortalities (http://www.who.int/mediacentre/factsheets/fs297/en/). Non- small cell lung cancer (NSCLC) accounts for 80-85% of cases with smoking-related squamous cell carcinoma, a subtype of NSCLC, linked to amplification of fibroblast growth factor receptor
1 (FGFR1) in approximately 20% of patients. FGFR1 amplifications can also occur in a wide range of other cancers, including; prostate, oesophageal, SCC head and neck, bladder, colorectal and osteosarcoma, being considered a targetable oncogenic alteration. FGFR1 is a receptor tyrosine kinase; somatic mutations in this group of receptors and aberrant activation of their signalling pathways is seen in tumours, contributing to proliferation, angiogenesis, migration, and survival. Understanding the details of receptor tyrosine kinase signalling in
the genesis and maintenance of disease is critical in delivering effective treatments to the clinic.
The fibroblast growth factor receptor (FGFR) family comprises four family members FGFR1, 2, 3, and 4 that display different tissue distribution and roles in disease. Each of these receptors has a unique and highly conserved glycosylated extracellular ligand-binding domain, a transmembrane segment, and a cytoplasmic tyrosine kinase domain.[3,4] In mammalian signalling, FGFR activation is triggered by the binding of one of 18 different fibroblast growth factors (FGFs; FGF1–FGF10 and FGF16– FGF23) to the extracellular receptor domain. This in turn leads to dimerisation of both extracellular and cytoplasmic domains; dimerised tyrosine kinase domains cross-phosphorylate each other at conserved tyrosine locations within their activation loops (A-loop) in a sequential cascade leading to signalling. Downstream signalling molecules bind to the phosphorylated sites, propagating cell signalling through different pathways.[6,7] Important roles in the regulation of many key biological processes make FGFRs attractive molecular targets for drug development with FGFR1 in particular already targeted for inhibitor design for some years.
One modality of RTK inhibition is the use of small molecule compounds that target the kinase domain and block cross- phosphorylation. Most small molecular inhibitors are ATP- competitive, binding in place of the natural ligand, hydrogen bonding to the so-called hinge segment (between the two kinase lobes) and mimicking the interactions made by the adenine ring of ATP.[8-10] Van der Waals interactions are also formed extensively and include sandwiching interactions from below (C- terminal lobe) and from above to the ATP-binding loop, often also called the P-loop, which wraps down over both ATP and inhibitor molecules. An adjacent hydrophobic pocket is also targeted by specific substituted aromatic moieties and provides greatly increased binding affinity.
The ATP site however, is conserved across all kinases, which number greater than 500 in the human proteome; these ATP- competitive compounds are often poorly selective for one kinase over another. Poor selectivity, in kinase inhibition, as in any drugging strategy, is undesirable and “hitting” multiple kinases in addition to their main intended target is generally problematic.[11,12] Despite some advantages in multikinase inhibition, for example in cancers showing deregulation of multiple signalling pathways, major difficulties with these multi-target inhibitors include toxic side-effects such as fatigue, proteinuria, thrombosis, and strong immunological responses.[14,15] Such problems have shifted research focus towards the development of new classes of selective compounds including non-ATP- competitive inhibitors and so-called irreversible inhibitors that covalently modify very specific and potentially unique amino acid targets in the kinase.[9,10,16]
Irreversible inhibitors have the potential to be highly selective because they target a unique residue of a specific kinase by design.[17-19] This specific and irreversible behaviour allows inhibition even at high levels of intracellular ATP, which provides a lower dosing requirement and a lesser likelihood of off-target toxic side effects. However, irreversible inhibitors were avoided for some time, as a result of toxicities potentially linked to undesirable immunological responses and indiscriminate modification of random cellular targets by the highly reactive electrophilic groups involved. More recently, second- generation inhibitors have found favour following greater rationality in design using an X-ray crystal structure-guided approach, and renewing interest in irreversible inhibitor design.[20,21]
Irreversible inhibitors have most often employed a reactive acrylamide group to target an unpaired cysteine residue in the kinase active site by forming a covalent bond through a Michael addition reaction. In the FGFRs, a cysteine residue at the tip of the P-loop can be targeted (numbered Cys488 in FGFR1), and is conserved across all four receptors (FGFR1, 2, 3, and 4).[17,22] In FGFR4, an alternative active site cysteine (numbered Cys552 in FGFR4) is modified by a series of recently synthesized and highly-selective compounds. FIIN-1 (1) was the first reported irreversible FGFR inhibitor developed using a structure-guided approach using reversible inhibitor PD173074 as a lead pharmacophore.[24,25] The FIIN-1 exemplar was used as a template for the design of other irreversible inhibitors sharing the pyrimido[4,5-d]pyrimidinone core, including FIIN-2 (2), and a recently reported series (exemplified by compound 3) from our laboratories. A similar design strategy utilising the related pyrido[2,3-d]pyrimidin-7(8H)-one core has led to the clinical-stage irreversible FGFR inhibitor PRN1371 (4). Another recent example of an irreversible inhibitor is the potent and FGFR- selective molecule TAS-120 (5, Figure 1) that inhibits all four family subtypes. TAS-120 is currently under phase I/II clinical trial (ClinicalTrials.gov identifier NCT02052778) to evaluate safety, maximum tolerated dosage (MTD), and recommended phase 2 dose (RP2D) in patients with confirmed advanced metastatic solid tumours with or without FGF/FGFR abnormalities who have failed standard therapies.[30,31] TAS-120 is structurally distinct from most FGFR inhibitors described to date, yet is reported to potently target the P-loop active site cysteine of the FGFR family. A
detailed knowledge of TAS-120 and its interactions with the target kinases might benefit the development of the next generation of irreversible FGFR inhibitors.
Figure 1. Molecular structures of known irreversible FGFR inhibitors including TAS-120 (5) or 1-[(3S)-3-[4-amino-3-[2-(3,5- dimethoxyphenyl)ethynyl]-1H-pyrazolo[3,4-d]pyrimidin-1-yl]-1-pyrrolidinyl]-2- propen-1-one.
In this work, we describe the binding and covalent modification of FGFR1 by TAS-120 using a mass spectrometry assay and X-ray crystallography. We reveal a small molecule crystal structure of the free ligand, and both reversible and irreversible binding in FGFR1, providing coverage of the full range of drug conformations and binding interactions, and the features that afford high reactivity and selectivity towards the FGFR family.
Results and Discussion
TAS-120 is a pan-FGFR inhibitor with reported IC50 values of 3.9, 1.3, 1.6, and 8.3 nM towards FGFR1, FGFR2, FGFR3, and FGFR4 respectively.[30,32,33] These measurements, carried out in cell biology experiments, quantify all aspects of cellular inhibition including solubility, transport, binding, and the covalent- modification potential of the drug. In our efforts to understand the inherent reactivity of TAS-120 towards the P-loop cysteine of the FGFRs, we used mass spectrometry and a mixture of the four recombinant FGFR isoforms incubated simultaneously with TAS-
120 over a two-hour period. Liquid chromatography mass spectrometry (LC-MS) is a robust technique to monitor irreversible/covalent binding between acrylamide-containing ligands and nucleophilic amino acid side chains such as cysteines.[34-36] In the TAS-120 system, the addition of ~419 g/mol in the protein mass indicates covalent modification and the relative amounts of modified and unmodified protein can be derived from mass spectra readily.
Mass spectrometry shows that TAS-120 reacts rapidly with each of the FGFRs with the covalent modification complete within ~one
minute in each case (Figure 2). By this assay, TAS-120 displays little selectivity for any FGFR isoform, but appears most active towards FGFR4, less active towards FGFR1 and FGFR2, and least reactive towards FGFR3 under these conditions. We note that our experiments are not well suited to time course measurements of such extremely reactive covalent modifiers. The location of covalent modification was confirmed after trypsin proteolytic digestion of TAS-120/FGFR1 followed by LC-MS/MS fragmentation experiments. The digest and mass analysis provided >96% coverage of the protein as small polypeptide chains and confirmation of the covalent modification site as Cys488 (Supporting Information Figure 1).
To better understand the extreme kinetics of TAS-120 reactivity we carried out X-ray crystallography experiments on the isolated compound and as a complex with both a mutant (C488A/ C584S) unreactive form of FGFR1 and a reactive (C584S) FGFR1 protein possessing the target Cys488. The combination of these three structures affords a full picture of the binding and reaction of TAS-
120 with FGFR1, providing a small molecule (free ligand) structure, non-covalently bound protein-liganded structure, and a covalently modified protein structure.
The small molecule crystal structure of TAS-120 was solved at a resolution of 1.08 Å (Supporting Information Table 1 and Supporting Information Figure 2) and provided exceptional parameters for compound modelling into the subsequently determined protein crystal structures. In this free ligand structure, the interplane angle between pendant dimethoxyphenyl group and the core pyrazolopyrimidine rings is ~15° and the pyrrolidine ring is rotated to present the acrylamide substituent close to perpendicular to the central pyrazolopyrimidine ring system (Supporting Information Figure 2).
Figure 2. Mass spectrometry analysis of TAS-120 covalent modification of FGFR1-4. Samples prior to incubation with TAS-120 are shown in the plots by grey lines and those reacted with TAS-120 for ~1 min, are shown as bold black lines; the FGFR isoform is indicated above each plot. TAS-120 shows little selectivity and can be described as a pan-FGFR inhibitor. The reactivity order by this data is FGFR4>FGFR1,2>FGFR3.
The crystal structure of C488A/ C584S FGFR1 in complex with TAS-120 was determined using molecular replacement and
refined to a resolution of 2.0 Å (Supporting Information Table 1). This protein construct is unreactive towards covalent modification by TAS-120 and is a standard protein variant used almost exclusively for X-ray crystallography experiments of FGFR1 to minimize unwanted intermolecular disulphide-linked dimer formation. Thus, this structure affords a snapshot of the TAS-120 binding mode in the FGFR family within a cellular context that must occur immediately prior to the Michael reaction between acrylamide and Cys488 of wild type protein.
The crystals belong to monoclinic space group C2 and display two monomers in the asymmetric unit – complex crystals were afforded by compound soaking experiments. Each protein shows the canonical FGFR1 protein kinase, bi-lobed domain structure in an active DFG-in conformation, and with a molecule of TAS-120 located unambiguously and refined within each inter-lobe cleft (ATP binding pocket) as illustrated in Supporting Information Figure 3. The dimethoxyphenyl ring, similarly to other FGFR1- selective inhibitors, binds into a conserved hydrophobic pocket and is stabilised by extensive van der Waals contacts and a single hydrogen bond to Asp 641; this ring has now rotated by ~57° relative to the central pyrazolopyrimidine (Figure 3A and B). The core pyrazolopyrimidine scaffold as expected, hydrogen bonds to the hinge region (specifically to Ala564 N and Glu562 O) and is sandwiched from above by the non-polar side chains of Leu484, Val492, and Ala512, and from below by Leu630. The pyrrolidine ring has rotated ~76° relative to free ligand to fit the binding site and minimize steric clash from above with the P-loop. The acrylamide functionality appears disordered in electron density maps suggesting a low energy barrier to conversion between cis and trans amide configurations.
Figure 3. X-ray crystallography of TAS-120 in complex with FGFR1. A. Binding interactions between FGFR1 and TAS-120 in a reversible binding mode. Hydrogen bonds are shown as dashed lines and van der Waal contacts as green lines with associated side chains as labelled. B. TAS-120 conformational change on reversible binding with torsional angle changes indicated. C. TAS-
120 irreversible (covalent) binding to FGFR1. The pyrrolidine ring rotates upwards to meet the P-loop. The acrylamide group is disordered in electron density maps of the reversible complex – we have displayed above the free ligand-like trans configuration (cyan) while this same groups appears exclusively in a cis configuration in the irreversible complex (yellow). D. The “bulge” conformation of the P-loop in the TAS-120 irreversible structure. The
locations of equivalent amino acid residues are indicated as sequence numbers in bold font.
This molecular conformation presents the reactive acrylamide group towards the predicted C488A position at an estimated distance of ~6 Å – not close enough for covalent bond formation to proceed. However, the combined crystallographic evidence within the Protein Data Bank shows the P-loop of FGFR1 to be flexible and able to attain conformations with the C488 location close to the acrylamide of TAS-120, just one example being the FGFR1 structure complex with inhibitor AZD4547, which displays an extreme distortion of the P-loop structure. Our preliminary molecular modelling simulations of FGFR1, provide many structures with “bent” P-loops that would approach closely enough to the TAS-120 acrylamide to allow the Michael addition to proceed (Supporting Information Figure 4).
The covalent complex between TAS-120 and FGFR1 was produced by co-crystallisation with seeding, and once again is found in monoclinic space group C2 (Supporting Information Table 1). This 2.2 Å resolution covalent liganded structure
deviates little from the reversible protein model with overlays for any pair of molecules giving ~0.22 Å rmsd over 257 Cα atoms. Two molecules of TAS-120 are located unambiguously in the
same binding mode as the reversible complex (Supporting Information Figures 5A and 5B). We observe the covalent bond between the ligand and C488 and a small rotation of the TAS-120 pyrrolidine upwards by ~14° to meet with the P-loop cysteine (Figure 3C).
Unexpectedly, the P-loop rather than being well ordered as a covalent complex shows flexibility and disorder on either side of the reactive cysteine. We have modelled into chain A of the crystal structure a single conformation of segments Glu486-Gly487 and Phe489-Gly490, but in reality, these appear disordered over multiple conformations that we cannot model satisfactorily (Supporting Information Figure 5C). The P-loop in chain B is even more poorly defined (Supporting Information Figure 5D). These results contrast with our in-house experiments visualising other irreversible ligands (unpublished) where covalent complexes with FGFR proteins display well-ordered and unambiguous conformations of the P-loop. Crystal structures of FIIN-2 covalently complexed with FGFR4 (PDB 4QQ5 and 4QQC) also provide full models of the P-loop structure.[26,38] In contrast to the TAS-120 covalent structure, the reactive acrylamide of FIIN-2 presents much closer to the tip of the P-loop and the site of covalent modification is ~5 Å distant from our own (Supporting Information Figure 6). However, while the reactive groups in the FIIN-2 system are closer, the inhibitory effect as measured by IC50 are very similar, for TAS-120 towards FGFR1, 3.9 nM, and for FIIN-2, 3.1 nM.
A view of the P-loop in the TAS-120 structure from above shows an unusual bulge (Figure 3D and Supporting Information Figure 6C). This bulge results from the TAS-120 anchoring or pulling the tip of the P-loop closer into the ATP-binding pocket; the TAS-120 pyrrolidine ring and the now reacted acrylamide substituent, fill the space in between the two halves of the P-loop.
To confirm the presence of a covalent bond in the crystal structure, the co-crystallisation solution that produced the crystals was
subjected to trypsin digest and LC-MS/MS mass spectrometry analysis; a covalent bond between ligand and protein at the C488 location is present (data not shown). The crystallographic data was also checked extensively for any signs of radiation damage and free radical formation that might have broken the C-S ligand/cysteine bond and produced disorder in crystallo during data collection – carbon-sulphur bonds can be broken readily by X-radiation.[40,41] The data displays no signs of radiation damage.
The presence of both a covalent bond and a disordered P-loop is a significant observation and we propose that P-loop conformational flexibility is a critical determinant of the high-level TAS-120 reactivity. We conclude that the TAS-120 molecule in solution samples multiple conformations of the P-loop and traps these different loop structures within the crystal form. We further note that in our standard crystal form in space group C2 that the P-loop is mobile and unencumbered by crystal packing interactions. This loop is often found disordered and unmodelled in both unliganded and liganded structures – it is able to wrap over a ligand and become ordered on crystal soaking with specific inhibitors. We propose that multiple P-loop conformations have been trapped in the TAS-120/FGFR1 crystal at the point of crystal freezing to produce the disorder we observe with our preliminary molecular modelling of P-loop conformational flexibility supporting this hypothesis. A full treatment using molecular dynamics and in the presence of TAS-120 ligand, is beyond the scope of this work but will be pursued.
We have produced the first covalent inhibitor-bound crystal structure of FGFR1 highlighting the binding of the clinical trial compound TAS-120, a pan-FGFR inhibitor. We propose the extreme reactivity of TAS-120 towards all FGFRs derives from several factors. High-affinity reversible binding is important, as is the rotational freedom of TAS-120 between pyrazolopyrimidine and pyrrolidine rings. However, the most significant reactivity potential of TAS-120 in presenting the acrylamide group to the reactive P-loop cysteine may be its inherent ability to undertake conformational sampling of the FGFR kinases in solution, and to “trap” multiple FGFR P-loop conformations in the protein-ligand complex. In designing novel FGFR inhibitors, such a phenomenon might be targeted as a unique inhibitory mechanism simply by the appropriate placement of the acrylamide group similarly to that of TAS-120.
Recombinant protein production. Recombinant protein production was carried out as described previously . In brief, DNA encoding the FGFR1 kinase domain harbouring C488A/C584S or C584S mutations were cloned into the pETDuet vector (Merck) along with the complete gene for human PTP1B phosphatase. Plasmids were transformed into E. coli BL21(DE3) and protein produced by incubation in Terrific Broth medium supplemented with ampicillin at 18°C, and with IPTG induction. Protein was purified by immobilised metal affinity chromatography followed by anion exchange chromatography. Proteins were concentrated to ~40 mg/ml in a buffer comprising 20 mM Tris-HCl pH 7.8, 20 mM NaCl, 5 mM EDTA, 2mM TCEP,
and were flash-cooled after supplementing with 50% glycerol, and subsequently stored at -20°C.
X-ray crystallography. Protein aliquots were thawed and buffer exchanged to remove glycerol. A TAS-120 reversible complex was produced by ligand-soaking preformed FGFR1 crystals. Crystals were grown by mixing 1 μL of protein solution (7.5 mg/ml) with 1 μL of crystallization buffer comprising 20% (w/v) MPEG 5000, 0.25 M ammonium sulphate, and 0.1 M sodium cacodylate. Crystallisation used a hanging drop vapour diffusion method with microseeding after an initial 18 hr incubation. After one week, crystals were glutaraldehyde cross-linked by placing crystal-containing drops over 3 μL of 25% glutaraldehyde solution for 30 min. TAS-120 was soaked into preformed and cross-linked crystals for 18 hours by placing crystals into a solution comprising the crystallization solution supplemented to 5 mM with TAS-120 in DMSO. Crystals cryoprotected in a 70:30 mixture of Paratone N and mineral oils, placed in nylon loops, and flash-cooled in liquid nitrogen. Data were collected at the Australian Synchrotron MX1 beamline using the Blu-Ice software package, and were processed using XDS and Aimless software packages.[43-45] The structure was solved by molecular replacement using PHASER and PDB model 4WUN, and refined with REFMAC.[46,47] The structure was visualised using COOT and ligand and solvent molecules included after iterative rounds of modelling and refinement. Data collection and refinement details are listed in Supporting Information Table 1. The structure and data files were deposited in the PDB with accession code 6MZQ.
Irreversible TAS-120/FGFR1 crystals were produced similarly to the reversible complex but with the inhibitor molecule pre-incubated with FGFR1 for 3 hours at 4°C before buffer exchange to remove DMSO. The TAS-120/FGFR1 complex was subjected to hanging drop vapour diffusion with microseeding in a manner and with identical crystallisation conditions as the unliganded experiments. Crystals were not glutaraldehyde cross- linked in this case and were cryoprotected in Paratone N/mineral oil for subsequent data collection as detailed in Supporting Information Table 1. The structure and data files were deposited in the PDB with accession code 6MZW.
TAS-120 ligand crystallised by itself serendipitously within protein crystallisation drops where an excess of ligand had been added for co- crystallisation. These were treated as protein crystals as above until the time of data collection at the Australian Synchrotron when small molecule diffraction was apparent. Data were processed initially using XDS with no merging of equivalent reflections. Data were converted from XDS format to SHELX format using XDSCONV before structure solution with SHELXT.[44,49] Atoms of the TAS-120 molecule were identified correctly, the stereochemistry set to that indicated by the chemical supplier (Cayman Chemical) and the literature, and atoms refined by full least squares refinement with isotopic displacement parameters using SHELXL. Anisotropic displacement parameters were introduced and hydrogen atoms placed as riding models. Details of data collection and refinement are given in Supporting Information Table 1. The structure was deposited in the CCDC with accession code CCDC 1877241.
Molecular modelling of P-loop conformation. The coordinates of missing atoms in a C488A/C584S TAS-120/FGFR1 crystal structure (PDB: 6MZQ) were generated using Modeller version 9.20. Over 100 models the newly built P-loop and activation segments showed high conformational flexibility.
LC-MS mass spectrometry. Protein for mass spectrometry was produced similarly to the crystallography samples but with the addition of 10% glycerol to all buffers and a change of buffer pH to 8.5. Protein was concentrated to ~40 mg/ml, mixed 1:1 (v/v) with glycerol, and then flash
cooled in liquid nitrogen and stored at -80℃ until needed.
Protein samples were buffer exchanged to remove glycerol using a buffer comprising 20 mM Tris-HCl pH 8.5, 10% (v/v) glycerol, 20 mM NaCl, 5 mM EDTA, and 2mM TCEP. Protein at a concentration of 20 µM was mixed with TAS-120 at 1:10 protein to ligand molar ratio, and was incubated for
3 hr at 37℃. Aliquots of 10 μL volumes were removed at specific time points between 5 and 180 min. The covalent modification was stopped in
these samples by the addition of 90 µL of 0.1% formic acid, followed by flash cooling in liquid nitrogen. Samples were stored at -80℃ until needed.
Samples were subjected to liquid chromatography mass spectrometry (LC-MS) in triplicate to show mass changes attributable to irreversible inhibition. Mass spectrometry experiments were performed at the University of Auckland Mass Spectrometry Center using an electrospray QSTAR® XL ESI quadrupole Time-of-Flight (QToF) MS system (Applied Biosystems) operated in positive ionization mode. The instrument was calibrated using Renin Substrate Standard (SCIEX), over the m/z range 100–2000. Protein/inhibitor samples were thawed and 2 μL volumes injected into a liquid chromatography (LC) BIOshell™ A400 Protein C4 HPLC column (10 cm × 2.1 mm, 3.4 μm) attached to the mass spectrometer. A linear solvent gradient from 25% to 65% mobile phase buffer B was applied over 21 min (mobile phase A: 0.1% formic acid in water; mobile phase B: 0.1% formic acid in acetonitrile) with the flow rate set at 0.006 mL/min. The buffer B concentration was raised to 98% from 21 to 25 min, then returned to 25% for re-equilibration for 5 minutes. The column effluent was directed into the ion spray source of the mass spectrometer for mass analysis over the m/z range 330-1600. Mass spectrometry data were processed and analysed using the PeakView™
2.1 software and the Bio Tool Kit plug-in (SCIEX). Deconvolution calculations allowed visualisation of intact mass protein peaks and allowed peak area measurement to assess the percentage of protein covalently modified by each inhibitor at each time point. Data were plotted using GraphPad Prism 7 (GraphPad).
Proteolytic Digest and LC-MS/MS analysis. Protein samples were reacted with TAS-120 at 1:10 molar ratio with a final protein concentration of 1 mg/ml and were run on SDS-PAGE. Gel bands were cut from the gel with a clean razor blade, transferred to a micro Eppendorf tube, and cut into smaller pieces. Gel samples were incubated with 200 μL of the mixture of
50 mM ammonium bicarbonate and acetonitrile (1:1) for 10 min with shaking at 1400 rpm and at a temperature of 56°C. All supernatant was removed and gel samples were dehydrated with 200 μL of 100% acetonitrile followed by treatment with 50 μL of 10 mM DTT in 50 mm ammonium bicarbonate to reduce all cysteine residues. Supernatant was again removed and gel samples treated further with 50 μL of 50 mM iodoacetamide in 50 mM ammonium bicarbonate for 30 min at RT and in the dark. A final dehydration treatment was carried out with gel samples treated with 200 μL of 100% acetonitrile. Supernatant was removed and gel samples treated with 20-50 μL of freshly prepared 12.5 ng/μl trypsin (Promega) in 50 mM ammonium bicarbonate followed by incubation at 37°C overnight (or microwave treatment at 45°C for 60 min at 15 W power in a chilled microwave digester).
The trypsin digest solution was diluted 10× with 0.1% formic acid before injection onto a reversed phase trap column (C18 PepMap 0.3x5mm 300 Å, ThermoFisher) at 0.030 ml/min for 3 minutes. Desalted peptides were then separated on a 0.3x100mm Zorbax 300SB C18 column (Agilent Technologies) using a 24 min linear gradient from 10 to 35% mobile phase B at 0.006 ml/min (mobile phase A: 0.1% formic acid in water; mobile phase B: 0.1% formic acid in acetonitrile). The column effluent was ionised in the electrospray source of the QSTAR® XL mass spectrometer (Applied Biosystems) for Information Dependent Analysis with MS/MS performed on the three most abundant multiply-charged species detected in each cycle. Raw data files were processed with PEAKS Studio (Bioinformatics Solutions Inc.) software. PEAKS Studio was used for the initial de novo sequencing of the observed peptide ion chromatogram peaks and further screening of calculated tryptic peptide masses against a protein sequence database to identify ligand-modified residues.
The authors acknowledge the Mass Spectrometry Centre, Auckland Science Analytical Services, the University of Auckland for equipment access and assistance. This research was undertaken in part using the MX2 beamline at the Australian Synchrotron, part of ANSTO, and made use of the Australian Cancer Research Foundation (ACRF) detector. We greatly acknowledge funding from the Health Research Council of New Zealand (13-196), the Maurice Wilkins Centre for Molecular Biodiscovery (M.K.), The University of Auckland Doctoral Scholarship Programme (M.K.), and Cancer Society Auckland and Northland. We thank Xiaojing (Sean) Lin for providing FGFR2 and 3 plasmids.
Conflict of interest
The authors declare no conflict of interest.
Keywords: fibroblast growth factor receptor • irreversible inhibitor • drug discovery • TAS-120 • conformational sampling
⦁ J. Weiss, M. L. Sos, D. Seidel, M. Peifer, T. Zander, J. M. Heuckmann, R. T. Ullrich, R. Menon, S. Maier, A. Soltermann,
H. Moch, P. Wagener, F. Fischer, S. Heynck, M. Koker, J. Schöttle, F. Leenders, F. Gabler, I. Dabow, S. Querings, L. C. Heukamp, H. Balke-Want, S. Ansén, D. Rauh, I. Baessmann,
J. Altmüller, Z. Wainer, M. Conron, G. Wright, P. Russell, B. Solomon, E. Brambilla, C. Brambilla, P. Lorimier, S. Sollberg,
O. T. Brustugun, W. Engel-Riedel, C. Ludwig, I. Petersen, J. Sänger, J. Clement, H. Groen, W. Timens, H. Sietsma, E. Thunnissen, E. Smit, D. Heideman, F. Cappuzzo, C. Ligorio,
S. Damiani, M. Hallek, R. Beroukhim, W. Pao, B. Klebl, M. Baumann, R. Buettner, K. Ernestus, E. Stoelben, J. Wolf, P. Nürnberg, S. Perner, R. K. Thomas, Sci. Transl. Med. 2010, 62, 62ra93.
 M. Katoh, Nat. Rev. Clin. Oncol. 2018, doi: 10.1038/s41571- 018-0115-y.
⦁ S. K. Hanks, A. M. Quinn, T. Hunter, Science 1988, 241, 42– 52.
⦁ A. Bennasroune, A. Gardin, D. Aunis, G. Crémel, P. Hubert,
Crit. Rev. Oncol. Hematol. 2004, 50, 23–38.
⦁ F. C. Kelleher, H. O’Sullivan, E. Smyth, R. McDermott, A. Viterbo, Carcinogenesis 2013, 34, 2198–2205.
⦁ M. J. Cross, L. Lingge, P. Magnusson, D. N. Nyqvist, K. Holmqvist, M. Welsh, L. Claesson-Welsh, Mol. Biol. Cell 2002, 13, 2881–2893.
⦁ M. Tsang, I. B. Dawid, Sci. STKE 2004, 2004, pe17.
⦁ M. I. Davis, J. P. Hunt, S. Herrgard, P. Ciceri, L. M. Wodicka,
G. Pallares, M. Hocker, D. K. Treiber, P. P. Zarrinkar, Nat. Biotechnol. 2011, 29, 1046–1051.
⦁ S. Müller, A. Chaikuad, N. S. Gray, S. Knapp, Nat. Chem. Biol.
2015, 11, 818–821.
⦁ J. Zhang, P. L. Yang, N. S. Gray, Nat Rev Cancer 2009, 9,
⦁ F. Broekman, E. Giovannetti, G. J. Peters, World J. Clin. Oncol. 2011, 2, 80–93.
⦁ L. K. Shawver, D. Slamon, A. Ullrich, Cancer Cell 2002, 1, 117–123.
⦁ J. Bain, L. Plater, M. Elliott, N. Shpiro, C. J. Hastie, H. Mclauchlan, I. Klevernic, J. S. C. Arthur, D. R. Alessi, P. Cohen, Biochem. J. 2007, 408, 297–315.
⦁ M. S. Khodadoust, B. Luo, B. C. Medeiros, R. C. Johnson, M.
D. Ewalt, S. Schalkwyk, C. D. Bangs, M. Cherry, S. Arai, D. Arber, J. L. Zehnder, J. Gotlib, Leukemia 2015, 1–4.
⦁ H. Huynh, R. W. Ong, P. Y. Li, S. S. Lee, S. Yang, L. W. Chong, D. A. Luu, C. T. Jong, I. W. Lam, Anticancer Agents Med Chem. 2011, 11, 560–575.
⦁ R. Lonsdale, R. A. Ward, Chemical Society Reviews 2018, 47, 3816-3830.
⦁ Y. Wang, L. Li, J. Fan, Y. Dai, A. Jiang, M. Geng, J. Ai, W. Duan, J. Med. Chem. 2018, 61, 9085-9104.
⦁ T. A. Baillie, Angew. Chemie – Int. Ed. 2016, 55, 13408– 13421.
⦁ M. S. Cohen, C. Zhang, K. M. Shokat, J. Taunton, Science
2005, 308, 1318–1322.
⦁ Q. Liu, Y. Sabnis, Z. Zhao, T. Zhang, S. J. Buhrlage, L. H. Jones, N. S. Gray, Chem. Biol. 2013, 20, 146–159.
 T. Barf, A. Kaptein, J. Med. Chem. 2012, 55, 6243-6262.
⦁ G. Liang, Z. Liu, J. Wu, Y. Cai, X. Li, Trends in Pharmacological Sciences 2012, 33, 531-541.
⦁ M. Hagel, C. Miduturu, M. Sheets, N. Rubin, W. Weng, N. Stransky, N. Bifulco, J. L. Kim, B. Hodous, N. Brooijmans, A. Shutes, C. Winter, C. Lengauer, N. E. Kohl, T. Guzi, Cancer Discov. 2015, 5, 424-437.
⦁ N. Kammasud, C. Boonyarat, S. Tsunoda, H. Sakurai, I. Saiki,
D. S. Grierson, O. Vajragupta, Bioorganic Med. Chem. Lett.
2007, 17, 4812–4818.
⦁ Y. Zhou, W. Luo, L. Zheng, M. Li, Y. Zhang, Plasmid 2010,
⦁ L. Tan, J. Wang, J. Tanizaki, Z. Huang, A. R. Aref, M. Rusan, S.-J. Zhu, Y. Zhang, D. Ercan, R. G. Liao, M. Capelletti, W. Zhou, W. Hur, N. Kim, T. Sim, S. Gaudet, D. a. Barbie, J.-R. J. Yeh, C.-H. Yun, P. S. Hammerman, M. Mohammadi, P. A. Jänne, N. S. Gray, Proc. Natl. Acad. Sci. 2014, 111, E4869– E4877.
⦁ X. Li, C. P. Guise, R. Taghipouran, Y. Yosaatmadja, A. Ashoorzadeh, W. K. Paik, C. J. Squire, S. Jiang, J. Luo, Y. Xu,
Z. C. Tu, X. Lu, X. Ren, A. V. Patterson, J. B. Smaill, K. Ding,
Eur. J. Med. Chem. 2017, 135, 531–543.
⦁ K. A. Brameld, T. D. Owens, E. Verner, E. Venetsanakos, J. Michael, V. T. Phan, D. Tam, K. H. Leung, J. Shu, J. Lastant,
G. David, D. E. Karr, M. E. Gerritsen, D. M. Goldstein, J. O. Funk, J Med Chem. 2017, 60, 6516-6527.
⦁ H. Ochiiwa, H. Fujita, K. Itoh, H. Sootome, A. Hashimoto, Y. Fujioka, Y. Nakatsuru, N. Oda, K. Yonekura, H. Hirai, T. Utsugi, Mol. Cancer Ther. 2013, 12, A270–A270.
⦁ F. Meric-Bernstam, H. Arkenau, B. Tran, R. Bahleda, R. Kelley, C. Hierro, D. Ahn, A. Zhu, M. Javle, R. Winkler, H. He,
J. Huang, L. Goyal, Ann. Oncol. 2018, 29, v100–v110.
⦁ F. Biello, G. Burrafato, E. Rijavec, C. Genova, G. Barletta, A.
Truini, S. Coco, M. Giovanna, D. Bello, A. Alama, F. Boccardo,
F. Grossi, Anticancer Agents Med Chem. 2016, 16, 1142- 1154.
⦁ L. Goyal, H.-T. Arkenau, B. Tran, J.-C. Soria, R. Bahleda, G. Mak, A. Zhu, M. Javle, H. Hiroshi, F. Benedetti, J. Huang, R. Winkler, F. Meric-Bernstam, Ann. Oncol. 2017, 28, 145.
⦁ I. S. Babina, N. C. Turner, Nat. Rev. Cancer 2017, 17, 318– 332.
⦁ I. D. G. Campuzano, T. San Miguel, T. Rowe, D. Onea, V. J. Cee, T. Arvedson, J. D. McCarter, J. Biomol. Screen. 2015, 21, 136-144.
⦁ S. G. Kathman, Z. Xu, A. V Statsyuk, J Med Chem. 2014, 57, 4969-4974.
⦁ P. A. Schwartz, P. Kuzmic, J. Solowiej, S. Bergqvist, B. Bolanos, C. Almaden, A. Nagata, K. Ryan, J. Feng, D. Dalvie,
J. C. Kath, M. Xu, R. Wani, B. W. Murray, Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 173–178.
 J. S. Cottrell, J. Proteomics 2011, 74, 1842–1851.
 Z. Huang, L. Tan, H. Wang, Y. Liu, S. Blais, J. Deng, T. A. Neubert, N. S. Gray, X. Li, M. Mohammadi, ACS Chem. Biol. 2015, 10, 299-309.
 M. Katoh, Int. J. Mol. Med. 2016, 38, 3–15.
⦁ E. Garman, Curr. Opin. Struct. Biol. 2003, 13, 545–551.
⦁ R. B. Ravelli, E. F. Garman, Curr. Opin. Struct. Biol. 2006, 16, 624–629.
⦁ Y. Yosaatmadja, A. V. Patterson, J. B. Smaill, C. J. Squire,
Acta Crystallogr. Sect. D Biol. Crystallogr. 2015, 71, 525–533.
⦁ T. M. McPhillips, S. E. McPhillips, H. J. Chiu, A. E. Cohen, A.
M. Deacon, P. J. Ellis, E. Garman, A. Gonzalez, N. K. Sauter,
R. P. Phizackerley, S. M. Soltis, P. Kuhn, J. Synchrotron Radiat. 2002, 9, 401–406.
⦁ W. Kabsch, Acta Crystallogr. Sect. D Biol. Crystallogr. 2010,
⦁ P. R. Evans, G. N. Murshudov, Acta Crystallogr. Sect. D Biol. Crystallogr. 2013, 69, 1204–1214.
⦁ G. N. Murshudov, P. Skubák, A. A. Lebedev, N. S. Pannu, R.
A. Steiner, R. A. Nicholls, M. D. Winn, F. Long, A. A. Vagin,
Acta Crystallogr. Sect. D Biol. Crystallogr. 2011, 67, 355–367.
⦁ A. J. McCoy, R. W. Grosse-Kunstleve, P. D. Adams, M. D. Winn, L. C. Storoni, R. J. Read, J. Appl. Crystallogr. 2007, 40, 658–674.
⦁ P. Emsley, B. Lohkamp, W. G. Scott, K. Cowtan, Acta Crystallogr. Sect. D Biol. Crystallogr. 2010, 66, 486–501.
⦁ G. M. Sheldrick, Acta Crystallogr. Sect. A Found. Crystallogr.
2015, 71, 3–8.
⦁ G. M. Sheldrick, Acta Crystallogr. Sect. A Found. Crystallogr.
2008, 64, 112–122.