Scaffold-Focused Virtual Screening: Prospective Application to the Discovery of TTK Inhibitors

We describe and apply a scaffold-focused virtual screen based upon scaffold trees to the mitotic kinase TTK (MPS1). Using level 1 of the scaffold tree, we perform both 2D and 3D similarity searches between a query scaffold and a level 1 scaffold library derived from a 2 million compound library; 98 compounds from 27 unique top-ranked level 1 scaffolds are selected for biochemical screening. We show that this scaffold-focused virtual screen prospectively identifies eight confirmed active compounds that are structurally differentiated from the query compound. In comparison, 100 compounds were selected for biochemical screening using a virtual screen based upon whole molecule similarity resulting in 12 confirmed active compounds that are structurally similar to the query compound. We elucidated the binding mode for four of the eight confirmed scaffold hops to TTK by determining their protein–ligand crystal structures; each represents a ligand-efficient scaffold for inhibitor design

The inhibitory activity of compound 1 and its analogues.^a

a<p>The NAT activity was measured by the NAT-inhibition assay using 150 µM HLZ and 120 µM Ac-CoA as substrates. The level of enzyme inhibition was measured in the presence of 50 µM inhibitor and compared to the un-inhibited control. The antimycobacterial activity against <i>M. bovis</i> BCG and <i>M. tuberculosis</i> were determined. Inhibition curves were obtained by non-linear fitting of the % inhibition and the inhibitor concentration (µM) using the Log(inhibitor) vs. response module of GraphPad Prism 5.0. The time-dependent assay <i>k_obs</i> values were obtained from the slope of the semilogarithmic plots of the residual activity vs incubation time at 11.9 µM, except for <b>3</b> (5.9 µM). The results are presented as the mean ± S.D. of triplicate measurements at 24°C. t_1/2 is the apparent inactivation half-life calculated from <i>k_obs</i> (t_1/2 = 0.693/k_obs). ND is not determined.</p>b<p>See Methods for further experimental details.</p

The chemical dehydration of compound 1.

<p>The chemical dehydration of compound 1.</p

LC/MS analysis of the reaction of compound 1 with free cysteine.

<p>(A) The total ion current chromatogram (from liquid chromatography LC) of 100 µM cysteine, 100 µM compound <b>1</b> and 100 µM cysteine: <b>1</b> (1∶1 mixture) in 20 mM MOPS buffer, pH 8 after 16 h incubation at 24°C. All samples were treated with 6-aminoquinolyl-n-hydroxysuccinimidyl carbamate before analysis. (B) The ESI-MS spectra of fractions collected from the peaks in the chromatogram (in A) corresponding to i: cysteine (m/z = 291.9 Da), iii: cystine (m/z = 290.9) and viii: the product of the reaction of cysteine with <b>1</b> (m/z = 423.9 Da). The chemical structures of the compounds corresponding to each peak are shown. The round symbol represents the aminoquinolyl carbamate moiety.</p

Specificity of compound 1 for prokaryotic NAT enzymes.

<p>Compound <b>1</b> was tested at 30 µM against pure recombinant NAT enzymes from <i>M. smegmatis</i> (MSNAT), <i>P. aeruginosa</i> (PANAT), <i>S. typhimurium</i> (STNAT), MMNAT and TBNAT, and also against two eukaryotic enzymes, hamster NAT2 (shNAT2) and human NAT1. The results are shown as the mean ± S.D. of triplicate determinations of the percentage inhibition of hydrolysis of Ac-CoA in the presence of 5-aminosalicylic acid (5ASA) and against TBNAT using hydralazine as a substrate. The inhibition is represented as a percentage compared to an uninhibited control from triplicate measurements. The structure of compound <b>1</b> is shown and the piperidinol nucleus is highlighted by the shaded area.</p

Reagents and conditions: (i) MeNH₂.HCl, paraformaldehyde, MeCN, cat. HCl, Δ, 16 h.

<p>Reagents and conditions: (i) MeNH₂.HCl, paraformaldehyde, MeCN, cat. HCl, Δ, 16 h.</p

Reversibility of the inhibition of TBNAT and MMNAT by compound 1.

<p>Each enzyme (MMNAT, TBNAT, 0.07 mM, 50 µL) was preincubated either alone or with 15-fold molar excess 1 at 24°C for 1 h. Each sample was then dialysed against 1 L fresh assay buffer (20 mM Tris-HCl pH 8) at 4°C for 16 h. The enzyme activities of the samples were measured before dialysis and then measured after dialysis by measuring the rate of Ac-CoA hydrolysis in the presence of HLZ as described in Methods. The mean ± S.D. of three measurements of the activity is shown. Loss of enzyme activity upon dialysis is likely to be due to the oxidation of the active site sulfhydryl group, especially since dialysis was performed in the absence of dithiothreitol.</p

The ESI mass spectrum of MMNAT in the presence of 1, 3 and 4.

<p>MMNAT was mixed with an equimolar sample (1∶1 ratio) of each inhibitor (50 µM) in 20 mM Tris-HCl, pH 8, and 5% (v/v) DMSO, and the ESI-MS was performed after 30 min of incubation. The masses correspond to each peak according to MMNAT with compound <b>3</b> chromatogram are: a = 30915 (Δm = 0 Da), b = 30955.5 (Δm = 40 Da), c = 31046.5 (Δm = 131.5 Da), and d = 31087.5 Da (Δm = 172.2 Da). The mass corresponding to the addition of a 132 Da-fragment is marked with a dashed line. Δm of +40 Da is likely to correspond to a potassium ion (38 Da). A mass spectrum of the protein in the absence of any inhibitor is shown as control in the top panel.</p

The active site electron density observed in the MMNAT-POP complex.

<p>The crystal structure of MMNAT after reaction with compound <b>1</b> showed excess electron density connected to Cys70, into which a 3-phenyl-3-oxopropyl (POP) modification was modelled with full occupancy. All three cysteine residues in the MMNAT structure and the covalent modification (in pink) are shown with the electron density shown using blue 2Fo–Fc electron density contoured at 1 σ. This observation is compatible with the MS data, since the excess inhibitor was washed out prior to crystallisation and the native state of the protein was preserved throughout the structure determination process. The figures were prepared using PyMOL <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052790#pone.0052790-Schrodinger1" target="_blank">[67]</a>.</p

The chemical transformation of 1 to the corresponding phenyl vinyl ketone (PVK) and the subsequent modification of a thiol containing residue by the PVK.

<p>(A) A proposed pathway of the formation of bis-Mannich bases from the rigid cyclic piperidinol. The bis-Mannich base can undergo a β-elimination of the amino group forming a reactive phenyl vinyl ketone (PVK). (B) The PVK reaction with thiols resulted in the addition of a 3-phenyl-3-oxopropyl moiety (POP) (when R₁ is H) or a 3-(4-chlorophenyl)-3-oxopropyl moiety (when R₁ is Cl). The expected Δm values of the added fragments are +132.07 Da and +166 Da, respectively. The shaded areas highlight the Michael acceptor moiety. Since the PVK binding species is transient, the second order rate constant cannot be determined without major assumptions being made.</p