Exploring the isoform selectivity of TGX-221 related pyrido[1,2-a]pyrimidinone-based Class IA PI 3-kinase inhibitors: Synthesis, biological evaluation and molecular modelling

Article abstract of DOI:10.1016/j.bmc.2015.03.073

A novel series of TGX-221 analogues was prepared and tested for their potency against the p110α, p110β, and p110δ isoforms of the PI3K enzyme, and in two cellular assays. The biological results were interpreted in terms of a p110β comparative model, in order to account for their selectivity towards this isoform. A CH₂NH type linker is proposed to allow binding into the specificity pocket proposed to accommodate the high p110β-selectivity of TGX-221, although there was limited steric tolerance for substituents on the pendant ring with the 2-position most favourable for substitution.

Full text of DOI:10.1016/j.bmc.2015.03.073

Accepted Manuscript
Exploring the isoform selectivity of TGX-221 related pyrido[1,2-a]pyrimidi-
none-based Class-Ia PI 3-kinase inhibitors: Synthesis, biological evaluation and
molecular modeling
Andrew J. Marshall, Claire L. Lill, Mindy Chao, Sharada V. Kolekar, Woo-
Jeong Lee, Elaine S. Marshall, Bruce C. Baguley, Peter R. Shepherd, William
A. Denny, Jack U. Flanagan, Gordon W. Rewcastle
PII:
S0968-0896(15)00269-2
DOI:
http://dx.doi.org/10.1016/j.bmc.2015.03.073
BMC 12199
Reference:
Bioorganic & Medicinal Chemistry
To appear in:
Received Date:
Revised Date:
Accepted Date:
8 January 2015
26 March 2015
28 March 2015
Please cite this article as: Marshall, A.J., Lill, C.L., Chao, M., Kolekar, S.V., Lee, W-J., Marshall, E.S., Baguley,
B.C., Shepherd, P.R., Denny, W.A., Flanagan, J.U., Rewcastle, G.W., Exploring the isoform selectivity of TGX-221
related pyrido[1,2-a]pyrimidinone-based Class-Ia PI 3-kinase inhibitors: Synthesis, biological evaluation and
molecular modeling, Bioorganic & Medicinal Chemistry (2015), doi: http://dx.doi.org/10.1016/j.bmc.2015.03.073
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Exploring the isoform selectivity of TGX-221 related pyrido[1,2-
a]pyrimidinone-based Class-Ia PI 3-kinase inhibitors: synthesis, biological
evaluation and molecular modeling
Andrew J. Marshall,*a Claire L. Lill,c Mindy Chao,a Sharada V. Kolekar,c Woo-Jeong Lee,c
Elaine S. Marshall,a Bruce C. Baguley,a,b Peter R. Shepherd,b,c William A. Dennya,b, Jack U.
Flanagan,*a,b and Gordon W. Rewcastle,*a,b
aAuckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The
University of Auckland, Private Bag 92019, Auckland 1142, New Zealand, b Maurice Wilkins
Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019,
Auckland 1142, New Zealand and cDepartment of Molecular Medicine and Pathology,
Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019,
Auckland 1142, New Zealand
*To whom correspondence should be addressed. E-mail: a.marshall@auckland.ac.nz,
g.rewcastle@auckland.ac.nz and j.flanagan@auckland.ac.nz
Phone: +64-9-9236147
Fax: +64-9-3737502
Keywords: Phosphatidylinositol 3-kinase, PI3K, p110β, docking, comparative modelling,
TGX-221
Abstract
A novel series of TGX-221 analogues was prepared and tested for their potency against the
p110α, p110β, and p110δ isoforms of the PI3K enzyme, and in two cellular assays. The
biological results were interpreted in terms of a p110β comparative model, in order to
account for their selectivity toward this isoform. A CH2NH type linker is proposed to allow
binding into the specificity pocket proposed to accommodate the high p110β-selectivity of
TGX-221, although there was limited steric tolerance for substituents on the pendant ring
with the 2-position most favourable for substitution.
1

1.
Introduction
Phosphatidylinositol 3-kinases (PI3Ks) are a family of enzymes that catalyse the
phosphorylation of phosphatidylinositol at the 3′-position of the inositol ring, producing
secondary messenger lipids which control cellular activities including survival, growth and
proliferation. A large proportion of cell-surface receptors, especially those linked to tyrosine
kinases, activate PI3-kinases, and an extensive range of downstream cellular functions are
influenced by the lipid products generated by these enzymes.1 These lipid kinases are
divided into three distinct classes (Class I, II and III) based on their primary structure, mode
of regulation, substrate specificity, tissue distribution and function within the cell,2,3 Class I
PI3Ks are heterodimers which consist of one of four closely related catalytic p110 subunits
(α, β, δ and γ) and an associated regulatory subunit (p85/p55), and are divided into two-
subfamilies based on sequence homology and the receptor to which they bind.4,5 Mutations
in the p110α isoform have been observed in a broad range of human cancers, including colon,
gastric, brain, ovarian and breast, while mutations of the p85 subunit have been observed in
colon and ovarian cancers.6 These mutations fall into two major clusters in the p110α
protein, including the helical domain (E542K/E545K) and the kinase domain (H1047R).7
PI3K oncogenicity is not solely restricted to the p110α isozyme; a point mutation was
recently described8a for the p110β isoform, and this isoform was also shown to be over-
expressed in colon and bladder cancers, while the p110δ is amplified in acute myeloid
leukaemia,9, and PI3K activation is also associated with up-regulation of the drug efflux
pump, multidrug resistance protein-1 (MRP-1), in prostate carcinomas.10 It should be noted
however that p110b and other isoforms apart from p110a are rarely or not at all mutated but
overexpressed in human cancers.8b
Highly selective PI3K alpha, beta, delta and gamma inhibitors have been reported,11,12 While
dual p110β/δ and p110δ/γ inhibitors are also known.11 Several different examples of p110β-
selective compounds have been reported,13-20 with the first examples being the pyrido[1,2-
a]pyrimidin-4-ones, exemplified by the racemic TGX-221 (1a), with more than 1000 fold
selectivity over the related p110α isoform.21 For this series, affinity and selectivity for the
p110β isoform was shown to be influenced by pendant C9 aryl substitutions.22-24 The (R)-
enantiomer of TGX-221 (1a) was eventually identified as the bioactive form against the
p110β-isoform (IC50 0.006 µM and 0.8 µM for the R and S stereoisomers respectively),13 and
2

the more soluble carboxylic acid derivative AZD6482/KIN-193 (1b) was developed as an
antithrombotic agent,25 and also identified as a potential anticancer agent.26 Recently, 7-
carboxamide derivatives of the pyrido[1,2-a]pyrimidin-4-ones have also been identified as
p110β/δ inhibitors for the treatment of PTEN-deficient tumours.27,28
The PI3K kinase domain has an N-terminal lobe consisting of a five stranded β-sheet flanked
by three α-helices and a larger predominately helical C-terminal lobe comprised of three
stranded β-sheet flanked by nine α-helices.29 The two lobes are connected by a loop known as
the hinge region and the active site is located within the inter-lobe cleft. The active site of
Class I PI3Ks has been divided into key regions illustrated in Figure S1.30-32 Crystallization
studies involving PI3K inhibitors occupying the adenine-binding site, have shown that they
all form one or more hydrogen bond(s) to the hinge region backbone, while limited contacts
are made to the ATP ribose region.30 The region around the ribose pocket has low sequence
identity across the class I enzymes and has been proposed to confer isoform selectivity in
some inhibitor classes (Figure S2).33-35 Although, reciprocal site directed mutagenesis studies
of isoform specific residues in this region did not alter the isoform potency and selectivity of
(1a).36
Other active site pockets include the sequence conserved affinity pocket, adjacent to the
adenine-binding site, where ligand occupation is associated with increased potency, and the
specificity pocket. The latter was observed in p110γ and δ isoforms, where Met804 and
Met752 respectively in the N-terminal lobe active site wall, was displaced by the quinazoline
moiety of PIK-39 and related compounds.31,37 Similarly, the p110β/δ-selective PIK-108 (1c)
has also been observed to bind to the specificity pocket of p110α, by the displacement of
Met772,38 and SAR260301 (2) was also shown to occupy the specificity pocket of p110β,
displacing Met773.20 PIK-108 was also shown to occupy a second, non-ATP binding site,38
although detailed discussion of this outside the scope of our current study.
While the binding mode of the pyrido[1,2-a]pyrimidin-4-one (1a) was not available at the
time of this study, the related chromen-4-one LY294002 (3) bound in p110γ was known.39
The crystal structure of (3) in the porcine p110γ enzyme (pdb:1E7V) revealed that the
morpholino group occupies the adenine binding site, with a hydrogen bond indicated between
3

the morpholino oxygen and the backbone amide of Val882.39 The chromenone core is
approximately co-planar with the adenine ring of ATP, and potentially forms hydrogen bond
contacts to the sidechains of Tyr836, Lys833, and to the backbone NH of Asp936.39 The
pendant phenyl ring is orthogonal to the chromenone core, and positioned in the ribose
binding site between conserved N-terminal residues Trp812 and Met804 and C-terminal
residue Met953.39
The close proximity of the pendant phenyl ring of (3) to sequence variant residues in the ATP
binding site suggested that substitution of the analogous C9 position of the pyrido[1,2-
a]pyrimidinone scaffold would be attractive for probing for isoform specificity. Here we
report the synthesis and evaluation of these compounds as inhibitors of PI3K, and investigate
likely binding modes that give rise to the p110β/p110δ selectivity of (1a).
2.
Results and discussion
2.1
Chemistry
Compound 1a was prepared by modifications of the reported procedures for the key
intermediates TGX-066 (6)23,24 and 823 (Scheme 1). Firstly, bis(2,4,6,-trichlorophenyl)
malonate40 was used instead of either malonyl dichloride23 or diethyl malonate24 in the initial
step with 4, resulting in a cleaner product in much higher yield than that reported with diethyl
malonate.24 Secondly, Pd(OAc)2/BINAP catalyst was used in the Heck coupling step, instead
of PdCl2(dppf),22 with a significant improvement in yield (83% vs 39%). Subsequent
methylation of 1a with sodium hydride and methyl iodide gave the NMe analogue 9, for
evaluation of the importance of the NH group on enzyme interactions.
To determine the effect of ligand flexibility on p110β selectivity, a series of compounds that
contained an amide bond was first investigated (Scheme 2). The key acid 13 was prepared
from ethyl 2-aminonicotinate (10)41 by ring closure with bis(2,4,6-trichlorophenyl) malonate,
for which tetrahydrofuran proved the best solvent, affording the pyrido[1,2-a]pyrimidinone
11 without polymeric byproducts. Mesylation of 11 and displacement with morpholine gave
12, which was hydrolysed with lithium hydroxide in ethanol to give the desired acid 13.
Close analogues of 1 were prepared by activation of acid 13 with 1,1´-carbonyldiimidazole
(CDI) and reduction with sodium borohydride to give alcohol 14, which was converted to
4

bromide 15 with phosphorus tribromide. Reaction of 15 with anilines under standard
conditions was unsuccessful, but was successful under microwave heating in a microwave
reactor with NaI catalyst at 120 ºC for 10 min, to give compounds 17-21 (Scheme 2).42
Compounds were also accessed by reductive amination.43 Oxidation of alcohol 14 with MnO2
gave aldehyde 16, which was reacted with sodium cyanoborohydride and 4-chloro- or 4-
methoxyaniline and acetic acid in methanol, to give compounds 22 and 23 respectively.
Several other compounds bearing side chains off the C-9 carbon were also prepared from
bromide 15 (Scheme 3). Reaction with the known Boc-protected 4-methyl
benzenesulfonamide,44 in refluxing acetonitrile with potassium carbonate, followed by
deprotection with trifluoroacetic acid, gave sulfonamide 24. Similar reaction of 15 with the
sodium salts of phenylsulfinic acid and thiophenol gave the sulfone 25 and sulfide 26
respectively. Finally, the substituted benzyl ethers 27-30 were prepared by reaction of 15
with the appropriate substituted phenols with sodium hydride in tetrahydrofuran.
The Buchwald-Hartwig coupling of 6 with a variety of substituted anilines was unsuccessful
using Pd(OAc)2 and potassium tert-butoxide or cesium carbonate, even with the most
rigorous drying, presumably due the poor nucleophilicity of the anilines (Scheme 4).
Compounds 31, 33-36 were finally prepared in low to moderate yields (4–50%), using the
highly activated catalyst system Pd(OAc)2/BINAP in the presence of potassium tert-butoxide
in refluxing dioxane (Scheme 4), after separation from varying amounts of the undesired des-
bromo byproduct compound. Compound 32 was prepared by methylation of compound
31.The benzylamine analogues 37-45, including the known enantiomers 44 and 45,22 were
prepared similarly to the aniline analogues in isolated yields of about 10%, after separation of
closely-eluting impurities by recrystallization from diisopropyl ether.
The substituted phenylcarboxamides 48-51 and 52-54 were prepared by activating acid 13
with diethyl cyanophosphonate (DEPC) in dimethylformamide using 2,6-lutidine as base, and
coupling with the required amines (Scheme 5). Acid 13 was also converted to the amine 47
by a modified Curtius rearrangement, via the carbamate 46, followed by deprotection with
neat trifluoroacetic acid. Reaction of 47 with aryl acid chlorides gave amides 55-58 (Scheme
5). Sulfonamide 59 was similarly obtained by reaction of 47 with benzenesulfonyl chloride in
pyridine, and urea 60 by reaction of 47 with phenyl isocyanate. Carbamate 61 was prepared
5

by the reaction of phenyl chloroformate with 47 in dioxane without base (to avoid bis-
acylation).
2.2
Enzyme and Cellular Data
Compounds in Table 1, containing a wide variety of C-9 side chains, were tested for their
inhibitory activity against the p110α, p110β, and p110δ isoforms of the PI3K enzyme and the
results are given in Table 1. Compounds that exhibited potency < 1.0 µM are the average of
2-3 independent experiments with a variation between experiments of less than 30%. The
compounds were also evaluated in cellular assays against two early passage human cancer
cell lines. These were NZB5, a brain (medulloblastoma) cell line which contains the wild-
type gene for p110α, and NZOV9, a poorly differentiated ovarian (endometrioid)
adenocarcinoma that has wild-type for expression of p53 protein but contains a mutant p110α
enzyme with a single amino acid substitution (Y1021C) in the kinase domain leading to
activation of the PI3K enzyme.
Compounds 9, 17-23, with benzylic side chains, are close analogues of TGX-221 (1a) and
were used to explore the role of the chiral centre at the C-9 position and steric effects around
the pendant phenyl group on PI3K inhibition and selectivity. These compounds generally
showed lesser inhibitory potencies than (1a) for all three isoforms, but especially for p110β,
where decreases were from 5- to 1000-fold (compounds 19 and 21 respectively). Both the
chiral methyl group and a free NH group (cf. compounds 1a, 9 and 17) seem important for
both potency and selectivity for p110β over other isoforms. Within the achiral benzylic
series 17-23, loss of the N-bond donor had little effect on enzyme activity (cf. compounds 17
and 18). Substituents around the pendant phenyl ring indicate a negative steric effect on
p110β activity for the 4-position (compound 21) but less so for substitution at the 2- and 3-
positions (compounds 19 and 20). The 4-methoxy derivative 23 had reduced p110β
selectivity compared to (1a), and was also the most p110α-potent compound, suggesting the
possibility of a common interaction across the isoforms. Activity in the two cell lines
reflected the enzyme data, with most compounds tested exhibiting poorer IC50 potencies than
(1a). The main standout was compound 23 which confirmed its high p110α enzyme potency
with good activity against the NZB5 (p110α wild type) cell line.
6

Compounds 25-30 investigated the use of heteroatoms other than NH in the β-position of the
C-9 substituent, and with compounds 27-30 that possessed a CH2O linker, also explored
steric and electronic effects through substitution at the 4-position of the pendant aromatic
group. The sulfonamide 24, despite maintenance of an H-bond donor, only showed activity
toward the p110δ isoform, albeit with reduced potency, while the sulfone 25 was a poor
inhibitor of all three enzymes. Both the thioether 26 and ether 27 retained p110α and p110δ
activity, but lost much p110β activity, and this was not rescued by phenyl group modification
in the latter (compounds 28-30). These results, taken together with the data for the benzylic
series 17-23 indicate that an amine is required in the β-position of the pendant group for
p110β selectivity. By contrast p110δ is least affected by substitutions at this position. For
this set of compounds, the potencies in both the NZB5 and NZOV9 cell lines reflected the
trends observed for the isolated enzyme data, with all being less potent than (1a).
Compounds 31-36 studied the utility of substituted anilines at the C-9 position. Comparison
of 31 with 17 showed a substantial negative impact on potency towards p110β, but with little
impact on p110α and p110δ. Methylation of the exocyclic nitrogen (compound 32) caused a
larger change in selectivity, with a greater decrease in potency against all three isoforms.
Within the substituted anilines, methyl groups at the 2- and 3- positions (compounds 33 and
34) caused little change in potency towards any isoform. In contrast, a decrease in potency
was observed in p110β and p110α inhibition by methyl substitution at the 4-position
(compound 35), along with a 2,6-dimethylphenyl substitution pattern (compound 36),
whereas the effects on p110δ potency were less pronounced in both cases. The loss of p110β
potency seen with this aniline series is consistent with results previously reported for
compound 33.24 Despite the loss in potency towards purified enzyme compared to (1a),
potencies towards both cell lines were little affected.
The benzylamine series 37-55 explored the effect of adding a methylene spacer into the
previous aniline series. Overall this change did not improve on activity relative to (1a), but
tended to generate more potent compounds than in the aniline series. Consistent with an
earlier report,24 the most potent compound with respect to p110β inhibition was the 2-methyl
analogue 38, being only 5-fold less active than (1a), while showing unchanged potency
toward p110α and p110δ. In contrast, the 4-methyl derivative 40 was 90-fold less active than
38 against p110β, with only small effects on p110α and p110δ potency, suggesting isoform-
7

invariant bulk intolerances. All of the pyridyl analogues 41-43 were much less effective than
the unsubstituted 37, arguing against a charge-transfer binding contribution from the pendant
phenyl ring. Compounds 44 and 45 show the effect of chirality at the β-position of the C-9
side chain; the (S)-enantiomer (44) was preferred over the (R)-enantiomer (45) by all three
isoforms, although potency against p110β was affected more than the other isoforms
compared to (1a). Comparison of the results for benzylamine series with those of the aniline
series suggest that moving the phenyl ring further from the bicyclic core is necessary for
good p110β activity.
Exploring this idea further, a series of compounds with more rigid amide-type linkers (amide,
sulfonamide, urea and carbamate), and possessing a range of hydrogen-bond donor/acceptor
patterns were studied. The amides 48-51 show substantially reduced p110β inhibitory activity
compared to (1a), while activity towards p110α and p110δ was largely unaffected, changing
the selectivity profile. These compounds are actually best described as being p110δ selective.
PI3K inhibitory activity was reduced substantially when a pyridine isomer pattern extended
by a methylene spacer was introduced (compounds 52-54).
A series of carboxamide analogues 55-58 reversed the previous hydrogen-bond
donor/acceptor geometry, with the functionality and substitution pattern being less tolerated
by p110β and p110α than p110δ, so again these compounds are best described as being
p110δ selective. Incorporating a urea group (60) rescued p110β activity to some extent, while
a sulfonamide (59) or carbamate (61) did not.
Overall, in the cell proliferation assays the IC50 values for the two cell lines were in general
highly correlated with each other (r = 0.69; p = 0.00000020). The IC50 data for both cell lines
tested showed a weak but significant correlation (r = 0.39; p < 0.02; Spearman rank order)
with the enzyme inhibition data for PI3K p110δ data; the data for the NZB5 cell line data
were also correlated (r = 0.39; p < 0.02) with the PI3K p110alpha data. The most active
compounds had imino (NH), or substituted imino linkages to the C-9 sidechain; these
compounds also tended to show greater activity against the NZB5 line than the NZOV9 line.
2.3
Molecular docking
8

The high affinity and selectivity for p110β exhibited by TGX-221(1a) and close analogues
has been attributed to the inhibitor binding an active site conformation that includes the
specificity pocket,31 and this pocket was used in the development of models for TGX-221 and
related compounds bound to p110β.13,17,19,27 Occupation of the specificity pocket was also
used to explain the selectivity of some p110δ inhibitors.34 This has been further characterised
in the context of p110β with Tyr778 identified as a residue involved in binding p110β
selective inhibitors by influencing specificity pocket formation.27 IC50 data against p110β for
the enantiomers of TGX-221 (R-1a 0.0006 µM ; S-1a 0.8 µM)13 and AZD6482 (R-1b 0.01
µM ; S-1b 0.23 µM)25 illustrate that the (R)-forms are more potent, and may better fit the
specificity pocket. As direct observation of the p110β specificity pocket was only recently
reported with the pyrimidone SAR260301 bound in p110β active site (pdb: 4BFR),20 we had
developed comparative models of the p110β kinase domain in the absence of any p110β
structure data to investigate the interactions between (1a) as well as the current pyrido[1,2-
a]pyrimidinone series and the p110β active site that may account for their selectivity toward
this isoform. Four models were constructed with template structures from p110γ
(pdbs:1E8Y,29 1E7V,39 and 2CHW24) and p110α (pdb:2RD045) . These explored the effect of
individual native templates (model 1), the combination of multiple native templates (model
2), an aryl morpholine bound template (model 3) as well as the presence of the specificity
pocket (model 4). Superimposition of the different models onto the p110β structures (PDB
codes 2YA3 and 4BFR) showed that the native p110β kinase domain models that included
the p110α structure (PDB code 2RD0) had the lowest RMSD, with values between 1.75 Å
and 1.95 Å. This could be reduced even further if modelled loops were excluded, or only
active site residues were used (Table S1).
To compare how the p110β kinase domain models 1, 2 and 3 performed in sampling the
binding mode observed for the aryl-morpholine scaffold of LY294002 (3) bound in the
p110γ, Ly294002 (3) was docked into p110β models 1, 2 and 3. Only predicted binding
modes with the morpholine oxygen atom within 3 Å of the backbone amide of Val854 were
considered for further analysis. The highest scoring of the three relevant binding modes
predicted with model 3 revealed that the chromone core was located between the sidechains
of N-terminal lobe Ile803, Ile851 and C-terminal Ile936 and the Cβ of Asp937. The benzene
ring was found between the side chains of N-terminal Met779 and C-terminal Thr859,
9

Met926 and Ile936, while the carbonyl was directed toward the side chain of Tyr839 and the
back bone amide of Asp937 (Figure 2a). This is consistent with the LY294002-p110γ
structure pdb: 1E7V. RMSD values between the observed binding mode of LY294002 in
p110γ and the best predicted binding mode in the models were 2.24 Å for model 1, 1.70 Å for
model 2, and 0.77 Å for model 3. The lower RMSD values for model 2 and 3 are likely
influenced by the inclusion of the p110γ template and an improved superimposition of the
protein models. Model 3 and model 4 were then used to predict TGX-221 binding in the
p110β kinase active site in the absence (model 3) and presence (model 4) of the specificity
pocket.
Enantiomers of (1a) were docked into model 3, and predicted poses that made interactions
consistent with the aryl morpholine core of LY294002 (3) were considered for further
analysis. For both enantiomers, a hydrogen bond was predicted between the morpholine
oxygen and the backbone amide NH group of the linker amino acid Val854, while the
pyrido[1,2-a]pyrimidine carbonyl was directed towards the affinity pocket and the side chain
hydroxyl group of Tyr839 and backbone amide NH group of Asp813. The preferred
orientation with the best fitness score for each enantiomer exhibited good alignment of the
aryl morpholine scaffold compared to each other, and consistent with that predicted for (3).
The pendant α-anilinoethyl group was projected towards the entrance of the ATP binding
pocket, and different interactions were predicted for the two enantiomers. In the (S)-
enantiomer it was positioned between the sidechains of the N-terminal lobe Trp787, C-
terminal lobe Met926 and the backbone amides of Ser857, Glu858 and Thr859, while in the
(R)-enantiomer, it was positioned next to the N-terminal lobe Met779 (Figure 2c). When the
specificity pocket was made accessible with model 4, some poses were also sampled for each
enantiomer where the pendant α-anilinomethyl group occupied the pocket while the aryl
morpholine binding mode was consistent with (3) bound in the p110γ active site.
We then wished to find out if the scoring functions implemented in GOLD could predict the
likely active site conformation preferred by TGX-221 as well as the most active enantiomer.
The highest scoring preferred poses generated for model 3 and 4 were rescored, and the
results presented in Table 2. These data indicate that the Astex Statistical Potential,
Chemscore and Chemscore Piecewise Linear Potential scoring functions did show a
preference for TGX-221 (1a) binding in the specificity pocket consistent with biochemical
10

and structural data,13 but they were unable to resolve a preference for the (R)-enantiomer with
these models, as was Goldscore.
Table 2
We hypothesised that the preference for p110β observed some compounds in the current
series results from occupation of the specificity pocket, and molecular docking provided
some support for this. Predicted poses for the achiral benzylic 17 and the alternative linker
heteroatom compounds 26 and 27 in model 4 sampled binding modes with the pendant
aromatic group occupying the specificity pocket, consistent with those found for the (R and
S) enantiomers of TGX-221. As our data indicates the exocyclic nitrogen is important in
conferring p110β specificity, this may result from a preferred binding model consistent with
the (R)-enantiomer of TGX-221 where the exocyclic amine is directed away from the N-
terminal lobe wall towards the active site cavity. Additonally, we showed that the α-methyl
carbon in TGX-221 is important for potency and may limit the benzylic sidechain flexibility
preorganising the inhibitor into a comformation that is condusive to accessing the specificity
pocket. Further, the (R)-enantiomer may provide better complementarily with the specificity
residues Trp787 and Met779 as it transitions from a closed conformation by packing against
Trp787 to an open conformation.34
3.
Conclusions
Isolated enzyme data combined with molecular docking suggest the CH2NH type linker
allows binding into the specificity pocket characterised by the high β-selectivity of TGX-221
(1a). Replacement of CH2NH by CH2O or CH2S decreases potency and selectivity,
suggesting nitrogen geometry is essential for activity against p110β, likely by accessing the
p110β-specificity pocket. Replacement of the flexible CH2NH linker by constraining it with
NHSO2, NHCO or CONH moieties resulted in an observed reduction of potency against the
p110β isoform. There is limited steric tolerance for substituents on the pendant ring with the
2-position most favourable for substitution. While the isolated enzyme activity of these
analogues of TGX-221 was broadly consistent with the enzyme binding model, it did not
always correlate well with the observed anti-proliferative activity in cellular assays. A
11

contributing reason for this may be the low aqueous solubility of the compounds.46 However
the cellular data did confirm the importance of amino groups in the C-9 sidechain.
4.
Experimental
4.1
Chemistry
All reactions were carried out in oven-dried glassware under a calcium chloride
drying tube or under nitrogen unless otherwise stated. The progress of reactions was
monitored by thin layer chromatography (TLC) on 0.2 mm Merck Kieselgel 60F254 silica
plates, and compounds were visualized by ultraviolet irradiation. Flash column
chromatography was conducted using 230-320 mesh silica gel obtained from APS Finechem
Ltd, or with 70-230 mesh Merck alumina oxide 90 gel (neutral) unless otherwise stated with
1
the specified solvents. H and 13C nuclear magnetic resonance (NMR) spectra were recorded
in CDCl3 containing tetramethylsilane (TMS) as reference and DMSO-d6 at 30 °C. A Bruker
Avance 400 spectrometer operating at 400.13 MHz, and 100.62 MHz was used to record 1H
and 13C NMR spectra. The NMR spectra are reported as chemical shift (δ) in part per million
1
(ppm) and J values are given in Hertz (Hz). H NMR data are reported as s, singlet; d,
doublet; t, triplet; q, quartet; m, multiplet; br, broad. The 13C NMR data are quoted as
chemical shift (δ) and assignment to the atom.
Assignments were aided by DEPT135, COSY, HSQC and HMBC experiments. The
HMBC experiment was optimized for 8.33 Hz. Low resolution mass spectra were recorded
on a Thermo FinniganMSQ single quadrupole mass spectrometer. All melting points were
t
measured by Ez-Melt MPA120 (uncorrected). All optical rotations {[α]D = 100(αobs
–
α0)/l.c]} were measured by a Schmidt and Haensh NH8 polarimeter at 589 nm (sodium-D
line). High resolution mass spectra were recorded using a Bruker micrOTOF-QII operating
at a nominal accelerating voltage of 70 eV. Atmospheric Pressure Chemical Ionization
(APCI+) and Electrospray Ionization (ESI+) were employed.
For the synthesis of 1a, bis(2,4,6,-trichlorophenyl) malonate, and intermediates 4-8 see
Supplementary data.
4.1.1. 7-Methyl-9-[1-(methylanilino)ethyl]-2-(4-morpholinyl)-4H-pyrido[1,2-
a]pyrimidin-4-one (9)
12

NaH 80% (27 mg, 0.9 mmol) was added to a solution of 9-(1-anilinoethyl)-7-methyl-
2-(4-morpholinyl)-4H-pyrido[1,2-a]pyrimidin-4-one (TGX-221, 1a)23 (109 mg, 0.3 mmol) in
DMF (5 mL) under nitrogen at room, temperature. After stirring for 15 mins, MeI (93 µL,
1.5 mmol) was added and stirring was continued overnight, then MeOH (5 mL) was
cautiously added and the resulting mixture was stirred under nitrogen for 5 min. The solution
was then diluted with a 50:50 mixture of EtOAc and hexanes (100 mL) and washed 3x with
water, brine, dried (Na2SO4) and evaporated. Purification of the product by PLC (neat
1
CH2Cl2) gave 9 (20 mg, 18 %): H NMR (CDCl3) δ 8.69 (1H, s, H-6), 7.41 (1H, d, J 1.7, H-
8), 7.20 (2H, dd, J 8.82, J 7.3, H-3′, H-5′), 6.76-6.66 (3H, m, H-2′, H-4′, H-6′), 5.59 (1H, s,
H-3), 5.54 (1H, q, J 6.9, CHCH3), 3.61 (4H, t, J 5.0, J 4.4, OCH2), 3.43-3.37 (4H, t J 5.0, J
4.88, NCH2), 2.86 (3H, s, NCH3), 2.32 (3H, d, J 1.0, CH3-7), 1.62 (3H, d, J 7.0, CHCH3).
HRMS (APCI+) Found: MH+ 379.2135. C22H26N4O2 requires MH, 379.2129.
4.1.2. 9-(Anilinomethyl)-2-(4-morpholinyl)-4H-pyrido[1,2-a]pyrimidin-4-one (17)
Ethyl 2-aminonicotinate (10) (8.2 g, 49.4 mmol) was dissolved in anhydrous THF
(200 mL) and heated to reflux. Bis(2,4,6-trichlorophenyl) malonate (23.96 g, 51.9 mmol)
was added in small portions and the mixture was heated under reflux for 6 h. The yellow
solution was concentrated by 50% and placed in the freezer over night. The resulting
precipitate was collected by vacuum filtration to give ethyl 2-hydroxy-4-oxo-4H-pyrido[1,2-
a]pyrimidine-9-carboxylate (11) (10.25 g, 88%) as a yellow solid: mp 192-194 ºC; 1H NMR
(CDCl3) δ 11.54 (1H, s, OH), 9.43 (1H, dd, J6, 7 6.78, J6, 8 1.58, H-6), 8.80 (1H, dd, J8, 7 7.52,
J8, 6 1.69, H-8), 7.37 (1H, t, J7, 6 = J7, 8 7.16, H-7), 5.23 (1H, s, H-3), 4.53 (2H, q, JCH2, CH3 7.1,
CH2), 1.47 (3H, t, JCH3, CH2 7.1, CH3). Anal. Calcd. for C11H10N2O4: C, 56.41; H, 4.3; N,
1.96. Found: C, 56.70; H, 4.4; N, 11.96;
Triethylamine (10.3 mL, 74.6 mmol) was added to a stirred suspension of 11 (8.75 g, 37.3
mmol) in CH2Cl2 (200 mL). The resulting yellow solution was cooled in an ice bath and
MsCl (4.0 mL, 52.2 mmol) was added in one portion. The resulting white suspension was
warmed to room temperature over 30 mins, then morpholine (9.77 mL, 74.6 mmol) was
added and the solution refluxed for 24 h. The red solution was concentrated under reduced
pressure and stirred as a suspension in ice cold water (300 mL) for 30 min. The precipitate
was collected by filtration and dried in an oven at 110 °C to give ethyl 2-(4-morpholinyl)-4-
oxo-4H-pyrido[1,2-a]pyrimidine-9-carboxylate (12) (21.5g, 90%) as a fluffy white solid: mp
13

180-182 ºC (MeOH); 1H NMR (CDCl3) δ 9.02 (1H, dd, J6, 7 7.1, J6, 8 1.72, H-6), 8.02 (1H, dd,
J8, 7 7.0, J8, 6 1.7, H-8), 6.88 (1H, t, J7, 6 = J7, 8 7.0, H-7), 5.60 (1H, s, H-3), 4.42 (2H, q, JCH2,
CH3 7.1, CH2), 3.82-3.75 (4H, t, J 5.2, J 4.68, OCH2), 3.72-3.65 (4H, t, J 5.2, J 4.7, NCH2),
1.40 (3H, t, JCH3, CH2 7.1, CH3); 13C NMR δ (CDCl3) δ 164.8 (q, CO), 160.4 (q, (C-2), 158.2
(q, C-4), 147.8 (q, C-10), 138.8 (CH, C-8), 130.6 (CH, C-6), 126.6 (q, C-9), 111.1 (CH, C-6),
81.0 (CH, C-3), 66.6 (CH2, OCH2), 61.8 (CH2), 44.6 (CH2, NCH2), 14.3 (CH3). Anal. Calcd.
for C15H17N3O2: C, 59.40; H, 5.65; N, 13.85. Found: C, 59.58.7; H, 5.73; N, 13.83.
A stirred suspension of 12 (912 mg, 3 mmol) in EtOH (30 mL) was treated at room
temperature with 1N LiOH (4.5 mL, 4.5 mmol). After 30 min the solid had dissolved and a
clear yellow solution was obtained. The solution was cooled to 0 °C, acidified to pH 5 with
AcOH (white precipitate) and evaporated. The product was taken up in water, filtered, and
the precipitate was oven dried at 110 °C to obtain 2-(4-morpholinyl)-4-oxo-4H-pyrido[1,2-
a]pyrimidine-9-carboxylic acid (13) (784 mg, 95%): mp 288-291 ºC; 1H NMR (d6-DMSO) δ
8.96 (1H, dd, J6, 7 7.0, J6, 8 1.66, H-6), 8.39 (1H, dd, J8, 7 7.1, J8, 6 1.58, H-8), 7.24 (1H, t, J7, 6
= J7, 8 7.0, H-7), 5.71 (1H, s, H-3), 3.74-3.69 (4H, t, J 5.2, J 4.6 OCH2), 3.59-3.53 (4H, t, J
5.2, J 4.6, NCH2), 3.30 (1H, br, CO2H). LCMS (APCI+) 276.1, (MH+, 100%). Anal. Calcd.
for C13H13N3O4: C, 59.40; H, 5.65; N, 13.85. Found: C, 59.58; H, 5.73; N, 13.83.
A suspension of 13 (1.93 g, 7 mmol) in anhydrous DMF (150 mL) was stirred rapidly at 44
°C until homogeneous, then 1,1´-carbonyldiimidazole (1.98 g, 110.9 mmol) was added. The
reaction was stirred for 30 min, cooled to 0 °C, then treated with NaBH4 (0.54 g, 14 mmol) in
ice cold water (50 mL) and stirred for 5 min at 0 °C and a further 2 h at room temperature.
The mixture was then cooled in an ice bath, acidified to pH 5 with AcOH, and evaporated to
give 9-(hydroxymethyl)-2-(4-morpholinyl)-4H-pyrido[1,2-a]pyrimidin-4-one (14) (1.64 g, 90
1
%): mp 206-209 ºC (MeCN); H NMR (d6-DMSO) δ 8.64 (1H, dd, J6, 7 7.1, J6, 8 1.4, H-6),
7.80 (1H, dd, J8, 7 6.9, J8, 6 1.5, H-8), 7.08 (1H, t, J7, 6 = J7, 8 7.0, H-7), 5.59 (1H, s, H-3), 4.69
(2H, s, CH2) 3.72-3.64 (4H, t, J 5.1, J 4.3, OCH2), 3.62-3.55 (4H, t, J 5.0, J 4.3, NCH2).
LCMS (APCI+) 262.1, (MH+, 100%). Anal. Calcd. for C13H15N3O3: C, 59.76; H, 5.79; N,
16.08. Found: C, 59.19, H, 5.80, N, 16.06.
Phosphorous tribromide (0.46, 4.88 mmol) was added to a stirred suspension of 14
(0.64 mg, 2.44 mmol) in CH2Cl2 (50 mL). The reaction was stirred at room temperature
overnight and neutralized with aqueous Na2CO3. The organic layer was washed with brine,
14

and evaporated to give 9-(bromomethyl)-2-(4-morpholinyl)-4H-pyrido[1,2-a]pyrimidin-4-
one (15) (487 mg, 62 %): mp >320 ºC (MeOH); 1H NMR (CDCl3) δ 8.89 (1H, dd, J6, 7 7.1, J6,
8 1.6, H-6), 7.74 (1H, dd, J8, 7 6.9, J8, 6 1.6, H-8), 6.85 (1H, t, J7,6=7,8 7.0, H-7), 5.59 (1H, s, H-
3), 4.70 (2H, s,CH2), 3.84-3.78 (4H, t, J 5.3 J 4.5, OCH2), 3.73-3.68 (4H, t, J 5.1, J 4.5,
NCH2). Anal Calcd for C13H14BrN3O2: C, 48.17; H, 4.35; N, 12.96. Found: C, 48.28; H,
4.38; N, 12.91.
A mixture of 15 (48.6 mg, 0.15 mmol), aniline (47.6µL, 0.45 mmol) and NaI (2 mg,
0.015 mmol) in acetonitrile (7 mL) in a microwave chamber were subjected to the following
heating profile; ramp (25 °C to 110 °C, 30s), hold (110 °C, 10 mins), cool down (10 mins).
The solids were then removed by filtration and washed twice with CH2Cl2 (5 mL). The
combined organic extracts were evaporated to afford a yellow oil that was purified by flash
column chromatography (EtOAc/CH2Cl2, 15:75) to give 17 (30 mg, 57 %): mp 185-188 °C
1
(MeOH); H NMR (CDCl3) δ 8.84 (1H, dd, J6, 7 7.1, J6, 8 1.4, H-6), 7.64 (1H, dd, J8, 7 6.9, J8,
6 1.4, H-8), 7.21-7.13 (2H, td, J3′, 5′,= J3′, 2′ 7.4, J 2.2, H-3′, H-5′ ), 6.84 (1H, t, J7, 6= J7, 8 7.0,
H-7), 6.73 (1H, t, J4′, 3′ 7.3, H-4′), 6.61 (2H, dd, J2′, 3′ 8.6, J2′, 4′ 0.9, H-2′, H-6′), 5.64 (1H, s,
H-3), 4.59 (2H, d, J 5.0, CH2), 4.42 (NH), 3.88-3.74 (4H, t, J 5.2, J 4.6, OCH2), 3.71-3.61
(4H, t, J 5.2, J 4.6, NCH2); 13C NMR (CDCl3) δ 160.3 (q, C-2), 158.9 (q, C-4), 148.9 (q, C-
10), 147.7 (q, C-1′), 133.9 (CH, C-8), 132.6 (q, C-9′), 129.4 (CH, C-3′, C-5′), 126.3 (CH, C-
6), 118.1 (CH, C-4′), 113.1 (CH, C-2′, C-6′), 112.2 (CH, C-7), 81.3 (CH, C-3), 66.6 (CH2,
OCH2), 44.8 (CH2, CH2), 44.6 (CH2, NCH2). Anal. Calcd for C19H20N4O2.0.2 H2O: C, 67.12;
H, 6.05; N, 16.48. Found: C, 67.03; H, 5.71; N, 16.56.
For similar synthesis of 18-21 see Supplementary data
4.1.3. 9-[(4-Chloroanilino)methyl]-2-(4-morpholinyl)-4H-pyrido[1,2-a]pyrimidin-4-one
(22)
A mixture of 14 (1 g, 3.83 mmol) and MnO2 (3.32 g, 38.3 mmol) were refluxed in
CH2Cl2 (100 mL) overnight, then cooled to room temperature and filtered through a plug of
celite®. The filtrate was evaporated and purified by filtration through a plug of alumina (neat
CH2Cl2 to EtOH/CH2Cl2 5:95) to give 2-(4-morpholinyl)-4-oxo-4H-pyrido[1,2-a]pyrimidine-
9-carbaldehyde (16) (6.91g, 70 %) as a bright yellow solid: mp 231-234 ºC; 1H NMR
(CDCl3) δ 10.81 (1H, s, CHO), 9.11 (1H, dd, J6,7 7.0 J6,8 7.0, H-6), 8.23 (1H, dd, J8,7 7.0, H-
15

8), 7.00 (1H, t, J7,6=7,8 7.0, H-7), 5.60 (1H, s, H-3), 3.82-3.75 (4H, t, J 5.2, J 4.6 OCH2), 3.72-
3.65 (4H, t, J 5.2, J 4.6 NCH2). LCMS (APCI+) 260, (MH+, 100%). Anal. Calcd. for
C13H13N3O3: C, 60.22, H, 5.05; N, 16.21. Found: C, 60.43; H, 5.12; N, 16.36.
Sodium cyanoborohydride (25 mg, 0.4 mmol) was added to a suspension of 16 (51.8
mg, 0.2 mmol), 4-chloroaniline (714 mg, 5.6 mmol) and AcOH (600 µL, 10.6 mmol) in
MeOH (20 mL). The solution was refluxed for 4 h, cooled to room temperature and the
solvent removed under reduced pressure. Purification of the product by alumina column
chromatography (EtOAc/CH2Cl2; 5:95, 10:95, 15:85, 20:80, 25:75, 30:70) gave 22 (30 mg,
42 %); mp 216-219 °C (hexanes); 1H NMR (CDCl3) δ 8.84 (1H, dd, J6, 7 7.1, J6, 8 1.36, H-6),
7.59 (1H, dd, J8, 7 6.7, J8, 6 1.2, H-8) 7.10 (2H, d, J3′,2′= J5,6′ 8.9, H-3′, H-5′ ), 6.83 (1H, t, J7,
6= J7, 8 7.0, H-7), 6.53 (2H, d, J2′, 3′= J6, 5 8.9, H-2′, H-6′), 5.63 (1H, s, H-3), 4.55 (2H, s,
CH2), 4.47 (1H, br, NH), 3.83-3.76 (4H, t, J 5.2, J 4.60), 3.68-3.61 (4H, t, J 5.2, J 4.6); 13C
NMR (CDCl3) δ 159.8 (q, C-2), 158.4 (q, C-4), 148.4 (q, C-10), 145.7 (q, C-1′) 133.4 (CH,
C-8), 131.6 (q, C-9), 128.7 (CH, C-3′, C-5′), 125.9 (CH, C-6), 122.2 (q, C-4′), 113.7 (C-2′, C-
6′), 111.6 (CH, C-7), 80.8 (CH, C-3), 66.0 (CH2, OCH2), 44.5 (CH2), 44.0 (CH2, NCH2).
Anal. Calcd for C19H19ClN4O2: C, 61.54; H, 5.16; N, 15.11. Found: C, 61.27; H, 5.22; N,
14.84.
For similar synthesis of 23 see Supplementary data
4.1.4. 4-Methyl-N-{[2-(4-morpholinyl)-4-oxo-4H-pyrido[1,2-a]pyrimidin-9-
yl]methyl}benzenesulfonamide (24)
A solution of 15 (97.2 mg, 0.3 mmol), tert-butyl tosylcarbamate (124 mg, 0.6 mmol) and
K2CO3 (89.2 mg, 0.6 mmol) in CH3CN (10 mL) were heated at reflux for 24 h. The reaction
was cooled to room temperature, diluted with CH2Cl2 (100 mL), washed with water and dried
over Na2SO4 to give a white solid that was dissolved in CH2Cl2 (5 mL) and treated with 95%
TFA (5 mL) with stirring overnight. The reaction was then cooled to 0 °C and basified to pH
8 by dropwise addition of conc. NH3(aq), diluted with CH2Cl2 (90 mL), washed with water,
brine and dried (Na2SO4). Purification by alumna column chromatography (EtOAc/CH2Cl2;
5:95, 10:90, 15:85, 20:80, 25:75) gave 24 (60 mg, 48 %) as an oil, that solidified on standing:
1
mp 156-159 °C; H NMR (CDCl3) δ 8.75 (1H, dd, J6, 7 7.1, J6, 8 1.56, H-6), 7.58 (2H, d,
J2,3=6,5 8.0, H-2′, H-6′), 7.43 (1H, dd, J 6.8, J 1.5, H-8), 7.16 (2H, d, 2,3=6,5 8.0, H-3′, H-5′),
16

6.73 (1H, t, J7, 6= J7, 8 6.98, H-7), 5.77 (1H, t, JNH, CH2 6.6, NH), 5.57 (1H, s, H-3), 4.37 (2H,
d, J CH2,NH J 6.6, CH2), 3.85-3.74 (4H, t, J 5.2, J 4.8, OCH2), 3.61-3.51 (4H, t, J 5.2, 4.8,
NCH2), 2.37 (3H, s, CH3); 13C NMR (CDCl3) δ 159.7 (q, C-2), 157.8 (q, C-4), 148.3 (q, C-
10), 143.1 (q, C-1′), 136.7 (q, C-4′), 135.6 (q, C-9), 128.9 (CH, C-3′, C-5′), 128.8 (CH, C-8),
126.9 (CH, C-6), 126.3 (CH, C-2′, C-6′), 111.5 (CH, C-7), 80.8 (CH, C-3), 65.9 (CH2,
OCH2), 44.2 (CH2), 44.1 (CH2, NCH2), 20.9 (CH3). Anal. Calcd for C20H22N4O4S; C, 57.96;
H, 5.35; N, 13.52. Found: C, 57.99; H, 5.52; N, 13.64.
4.1.5. 2-(4-Morpholinyl)-9-[(phenylsulfonyl)methyl]-4H-pyrido[1,2-a]pyrimidin-4-one
(25)
A solution of 15 (52 mg, 0.2 mmol) and sodium benzenesulfinate (65 mg, 0.4 mmol)
was heated under reflux in EtOH (10 mL) for 1 h, then cooled to room temperature and
poured on to cracked ice. The resulting precipitate was isolated by filtration and washed
several times with ice cold water to give 25 (40 mg, 52 %): mp 230-233 ºC; 1H NMR
(CDCl3) δ 8.88 (1H, dd, J6, 7 7.1, J6, 8 1.6, H-6), 7.77 (1H, dd, J8, 7 6.9, J8, 6 1.59, H-8), 7.62
(2H, dd, J 8.4, J 1.2, H-2′, H-6′), 7.52 (1H, dt, J 7.5, 1.2, H-4′ ), 7.38 (2H, t, J 7.8, H-3′, H-
5′), 6.90 (1H, t, J7, 6= J7, 8 7.0, H-7), 5.43 (1H, s, H-3), 4.78 (2H, s, CH2), 3.79-3.70 (4H, t, J
5.1, J 4.8, OCH2), 3.54-3.38 (4H, t, J 5.1, J 4.7, NCH2); 13C NMR (CDCl3) δ 159.4 (q, C-2),
157.8 (q, C-4), 148.5 (q, C-10), 138.8 (CH, C-8), 138.0 (q, C-1′), 133.3 (CH, C-4′), 128.3 (C-
3′, C-5′), 128.1 (CH, C-6), 127.9 (CH, C-2′, C-6′), 122.5 (q, C-9), 111.4 (CH, C-7), 80.3 (CH,
C-3), 65.9 (CH2, OCH2), 56.0 (CH2), 44.0 (CH2, NCH2). Anal. Calcd for C19H19N3O4S: C,
59.21; H, 4.97; N, 10.90. Found: C, 59.07; H, 5.22; N, 10.9.
4.1.6. 2-(4-Morpholinyl)-9-[(phenylsulfanyl)methyl]-4H-pyrido[1,2-a]pyrimidin-4-one
(26)
Thiophenol (0.102 µL, 0.24 mmol) was added to a solution of 2N NaOH (0.12 mL, 0.24
mmol) and stirred for 5 h until the oily starting material had dissolved. The solution was
concentrated in vacuo, and azeotroped with acetonitrile three times to give sodium thiophenol
(0.24 mmol). A solution of this and 15 (52 mg, 0.160 mmol) was refluxed in EtOH (10 mL)
for 1 h, cooled to room temperature, then poured onto cracked ice and the precipitate was
collected by filtration and dried at 110 °C to give 26 (30 mg, 53%): mp 121-123 °C
1
(hexanes); H NMR (CDCl3) δ 8.83 (1H, dd, J6, 7 7.1, J6, 8 1.5, H-6), 7.45 (1H, dd, J8, 7 6.9, J8,
6 1.36, H-8), 7.37-7.17 (5H, m, H-Ar), 6.76 (1H, t, J7, 6= J7, 8 7.0, H-7), 5.62 (1H, s, H-3), 4.33
17

(2H, s, CH2), 3.87-3.74 (4H, t, J 5.2, J 4.58, OCH2), 3.65 (4H, t, J 5.2, J 4.5, NCH2); 13C
NMR (CDCl3) δ 159.8 (q, C-2), 158.5 (q, C-4), 148.5 (q, C-10), 135.6 (q, C-1′), 134.6 (CH,
C-8), 131.2 (q, C-9), 129.9 (CH, C-3′, C-5′), 128.5 (CH, C-2′, C-6′), 126.3 (CH, C-4′), 126.2
(CH, C-6), 111.4 (CH, C-7), 80.7 (CH, C-3), 66.1 (CH2, OCH2), 44.2 (CH2, NCH2) 34.5
(CH2). Anal. Calcd for C19H19N3O2S.0.1 H2O: C, 64.24; H, 5.45; N, 11.83. Found: C,
64.04; H, 5.57; N, 11.98.
4.1.7. 2-(4-Morpholinyl)-9-(phenoxymethyl)-4H-pyrido[1,2-a]pyrimidin-4-one (27)
NaH 80% (18 mg, 0.6 mmol) was added to a solution of phenol (31 mg, 0.33 mmol) in
THF (5 mL) under nitrogen at room temperature. The solution was stirred for 1 h, then 15
(97 mg, 0.3 mmol) and DMF (5 drops) were added and stirring was continued for an
additional 1 h. The reaction was then poured onto cracked ice, and the resulting precipitate
collected and purified by filtration through a plug of alumina (neat EtOAc) to give 27 (30 mg,
1
30%): mp 170-173 °C (hexane); H NMR (CDCl3) δ 8.88 (1H, dd, J6,7 7.1, J6,8 1.43, H-6),
7.82 (1H, dd, J8,7 7.1, J8,6 1.4, H-8), 7.31 (2H, ddd, J 9.8, J 6.46, J 2.2, H-3′, H-5′), 7.04-6.97
(3H, m, H-2′, H-6′, H-4′), 6.92 (1H, t, J7,6=7,8 7.0, H-7), 5.64 (1H, s, H-3), 5.34 (2H, s, CH2),
3.83-3.75 (4H, t, J 5.2, J 4.6, OCH2), 3.69-3.55 (4H, t J 5.2, J 4.6, NCH2); 13C NMR
(CDCl3) δ 159.9 (q, C-2), 158.3 (q, C-4), 157.9 (q, C-1′), 147.5 (q, C-10), 133.1 (CH, C-8),
130.5 (q, C-9), 129.2 (CH, C-3′, C-5′) 126.0 (CH, C-6), 120.9 (CH, C-4′) 114.4 (CH, C-2′, C-
6′) 111.7 (CH, C-7), 80.8 (CH, C-3), 66.1 (CH2, OCH2), 64.8 (CH2), 44.1 (CH2, NCH2).
Anal. Calcd for C19H19N3O3: C, 67.64; H, 5.68; N, 12.46. Found: C, 67.62; H, 5.86; N,
12.49.
For similar synthesis of 28-30 see Supplementary data
4.1.8. 9-Anilino-7-methyl-2-(4-morpholinyl)-4H-pyrido[1,2-a]pyrimidin-4-one (31)
KOtBu (156 mg, 1.4 mmol) was added under a stream of nitrogen to a solution of 9-
bromo-7-methyl-2-morpholino-4H-pyrido[1,2-a]pyrimidin-4-one23 (TGX-066; 6) (162 mg, 1
mmol), PdCl2(dppf) (41.3 mg, 5 mol%) and aniline (0.11 mL, 1.2 mmol) in dioxane (30 mL).
The reaction was refluxed overnight and cooled to room temperature. Additional KOtBu
(111 mg, 1 mmol) and aniline (0.093 mL, 1 mmol) were added to the reaction under nitrogen
and reflux was continued for 8 h. The dark red solution was filtered, concentrated under
reduced pressure, taken up in EtOAc (30 mL) and washed with water 3 times and dried
18

Na2SO4. Purification by alumina column chromatography (EtOAc/hexanes; 2:8) gave a
yellow oil (44 mg) that crystallised on standing to give 31 (14 mg, 4 %) as white crystals: mp
209-211 °C (EtOH); 1H NMR (CDCl3) δ 8.24 (1H, t, J 1.3, H-6), 7.45-7.38 (3H, m, NH, H-
3′, H-5′), 7.32-7.25 (2H, m, obs CHCl3, H-2′, H-6′), 7.18-7.11 (2H, m, H-8, H-4′), 5.66 (1H,
s, H-3), 3.85-3.79 (4H, J 5.2, J 4.7, OCH2), 3.66-3.62 (4H, J 5.1, J 4.7, NCH2), 2.28 (3H, s,
CH3); 13C NMR (CDCl3) δ 159.9 (q, C-2), 159.2 (q, C-4), 142.2 (q, C-10), 140.4 (q, C-1),
135.7 (q, C-9), 129.7 (CH, C-3′, C-5′), 123.9 (CH, C-4′), 123.1 (q, C-7), 121.7 (CH, C-2′, C-
6′) 114.4, (CH, C-6) 112.7 (CH, C-8), 82.0 (CH, C-3), 66.6 (CH2, OCH2), 44.9 (CH2, NCH3),
18.9 (CH3). LCMS (APCI+) 337.3 (MH+, 100%). Anal. Calcd for C19H20N4O2. 0.4 H2O C,
66.42; H, 6.10; N, 16.30. Found: C, 66.32; H, 5.94; N, 16.17.
4.1.9. 7-Methyl-9-(methylanilino)-(4-morpholinyl)-4H-pyrido[1,2-a]pyrimidin-4-one (32)
NaH (6.3 mg, 0.21 mmol) was added to a solution of (31) (5.4 mg, 0.16 mmol) in
DMF (2 mL) at 0 °C. The red solution was stirred for 5 mins then MeI (20 µL, 0.3 mmol)
was added. The reaction was stirred overnight and the resulting pale yellow solution was
partitioned between EtOAc and water. The phases were separated and the organic layer was
washed 3 x with water and once with NaHCO3 and dried over Na2SO4. Purification by flash
column chromatography (EtOAc/CH2Cl2; 2:8) gave 32 (6 mg, 95 %): mp 189-191 °C
(diisopropylether); 1H NMR (CDCl3) δ 8.57 (1H, s, H-6), 7.31 (1H, d, J 1.9, H-8), 7.24-7.15
(2H, dt, J 7.4, J 2.03, J 1.2, H-3′, H-5′), 6.86 (1H, m, H-4), 6.80 (2H, td, J 8.9, J 1.7, H-2′, H-
6′ ), 5.51 (1H, s, H-3), 3.58-3.45 (4H, m, OCH2), 3.38 (3H, s, N-Me), 3.27-3.16 (4H, m,
NCH2), 2.35 (3H, d, J 1.0, 7- CH3); 13C NMR (CDCl3) δ 158.9 (q, C-2), 158.8 (q, C-4), 149.4
(q, C-1′), 145.2 (q, C-10′), 139.8 (q, C-9), 131.4 (CH, C-8), 128.2 (CH, C-3′, C-5′), 121.2 (q,
C-7), 120.3 (CH, C-6), 119.8 (CH, C-4′), 117.5 (CH, C-2′,C-6′), 80.5 (CH, C-3), 66.9 (CH2,
OCH2), 43.9 (CH2 NCH2), 40.8 (CH3, N-CH3), 17.8 (CH3, CH3-7). LCMS (APCI+) 351.3
(MH+, 100%). Anal. Calcd for C20H22N4O2: C. 68.55; H, 6.33; N, 15.99. Found: C, 68.31;
H, 6.37; N, 16.12.
4.1.10. 7-Methyl-2-(4-morpholinyl)--9-(2-methylphenyl)-4H-pyrido[1,2-a]pyrimidin-4-
one (33)
Reaction of 6 (162 mg, 0.5 mmol) in anhydrous dioxane (30 mL) with o-toluidine (64
µL, 0.6 mmol), KOtBu (28 mg, 0.7 mmol), Pd(OAc)2 (5.6 mg, 5 mol%) and BINAP (21.7
mg, 7 mol %) at reflux under N2, followed by filtration, evaporation and purification by flash
19

column chromatography (EtOAc/CH2Cl2; 3:1) gave 33 (MCA51)24 (59 mg, 34 %) as a white
solid: mp 170-171 °C (MeOH); 1H NMR (CDCl3) δ 8.21 (1H, s, H-6), 7.44-7.38 (1H, d, J
7.9, H′-6), 7.35-7.24 (2H, t, J 8.2, J 8.1, H-5′, H-3′ ), 7.12 (1H, td, J 7.4 = J 7.4, J 1.02, H-
4′), 6.77 (1H, d, J 1.7, H-8), 5.67 (1H, s, H-3), 3.82-3.77 (4H, t, J 5.2, J 4.7, OCH2), 3.71-
3.58 (4H, t, J 5.2, J 4.7, NCH2), 2.35 (3H, s, CH3-Ar) 2.19 (3H, s, CH3-7); 13C NMR
(CDCl3) δ 159.8 (q, C-2), 159.2 (q, C-4), 142.1 (q, C-10), 138.5 (q, C-1′), 136.1 (q, C-9),
131.8 (q, C-2′), 130.8 (CH, C-5′), 126.5 (CH, C-3′), 124.7 (CH, C-4′), 122.6 (q, C-7), 122.2
(CH, C-6′), 113.9 (CH, C-6), 112.2 (CH, C-8), 81.9 (CH, C-3), 66.5 (CH2, OCH2), 44.8 (CH2,
NCH2), 18.8 (CH3), 17.9 (CH3). LCMS (APCI+) 351.3 (MH+, 100%) Anal. Calcd for
C20H22N4O2: C, 68.55; H, 6.33; N, 15.99. Found: C, 68.25; H, 6.32, N, 15.91.
For similar synthesis of 34-36 see Supplementary data
4.1.11. 9-(Benzylamino)-7-methyl-2-(4-morpholinyl)-4H-pyrido[1,2-a]pyrimidin-4-one
(37)
Similar reaction of 6 (162 mg, 0.5 mmol) in dioxane (5 mL) with benzylamine (65.5 µL,
0.6 mmol), KOtBu (78 mg, 0.7 mmol), Pd(OAc)2 (5.6 mg, 5 mol%) and BINAP (21.8 mg, 7
mol%) at reflux overnight under N2, followed by workup as above and purification by flash
column chromatography (EtOAc/hexanes, 2:1) gave 37 (TGX-126)21-24 (20 mg, 11.4 %): mp
1
202-205 °C (MeOH); H NMR (CDCl3) δ 8.12 (1 H, s, H-6), 7.40-7.28 (5H, m, H-Ar), 6.36
(1H, d, J 1.61, H-8), 5.97 (1H, s, NH), 5.63 (1H, s, H-3), 4.48 (2H, d, J 5.9, CH2), 3.82-3.75
(4H, t, J 5.1, J 4.7, OCH2), 3.59 (4H, t, J 5.2, J 4.7, NCH2), 2.23 (3H, d, J 1.0, CH3); 13C
NMR (CDCl3) δ 160.1 (q, C-2,), 159.5 (q, C-4), 142.0 (q, C-10), 139.0 (q, C-1′), 138.3 (q, C-
9), 129.0 (CH, C-3′, C-5′), 127.7 (CH, C-4), 127.2 (CH, C-2′, C-6′), 123.6 (q, C-7), 112.8
(CH, C-6), 110.6 (CH,C-8), 82.1 (CH, C-3), 66.7, (OCH2), 47.7 (CH2), 44.9 (CH2, NCH2),
19.1 (CH3). LCMS (APCI+) 351.3 (MH+, 100%).
For similar synthesis of 38-45 see Supplementary data
4.1.12. 2-(4-Morpholinyl)-4-oxo-N-phenyl-4H-pyrido[1,2-a]pyrimidine-9-carboxamide
(48)
2,6-Lutidine (46.9 mg, 0.438 mmol) and aniline (47.2 mg, 0.507 mmol) were added to
a stirred suspension of 2-(4-morpholinyl)-4-oxo-4H-pyrido[1,2-a]pyrimidine-9-carboxylic
20

acid (13) (100 mg, 0.362 mmol) in DMF (20 mL), then the solution was cooled to 0 °C and
diethyl cyanophosphonate (DEPC) (87.7 mg, 0.507 mmol) was added. The mixture was
stirred at 0 °C for 5 min, allowed to warm to room temperature overnight, then diluted with
EtOAc, and the organic layer was washed with 5% HCl, water, and brine. The organic layer
was dried (Na2SO4) and evaporated, and the crude product was purified by alumina column
chromatography (EtOAc/CH2Cl2; 0:1, 5:95, 10:90, 15:85, 20:80, 25:75, 30:70) to give 48 (60
1
mg, 47 %): mp 229-231 °C (MeOH); H NMR (CDCl3) δ 12.12 (1H, br s, NH), 9.16 (1H,
dd, J6, 7 6.9, J6, 8 1.86, H-6), 8.94 (1H, dd, J8, 7 7.23, J8, 6 1.85, H-8), 7.66 (2H, dd, J2′, 3′= J6′, 5′
8.6, J2′, 4′= J6′, 4′ 1.11, H-2′, H-6′), 7.39 (2H, t, 7.6, H-3′, H-5′), 7.22 (2H, m, H-7, H-4′), 5.68
(1H, s, H-3), 3.93-3.79 (4H, t, J 5.2, J 4.7, OCH2), 3.76 (4H, t, J 5.2, 4.7); 13C NMR (CDCl3)
δ 160.2 (q, CO), 159.4 (q, C-2), 157.2 (q, C-4), 148.4 (q, C-10), 142.4 (CH, C-8), 137.4 (q,
C-1′), 130.8 (CH, C-6), 128.8 (CH, C-3′, C-5′), 124.5 (CH, C-4′), 123.3 (q, C-9), 120.1 (CH,
C-2′, C-6′), 112.3 (CH, C-7), 81.00 (CH, C-3), 65.8 (CH2, OCH2), 44.8 (CH2, NCH2). LCMS
(APCI+) 351.2 (MH+, 100%) Anal. Calcd for C19H18N4O3.0.1 H2O: C, 64.80; H, 5.21; N,
15.91. Found: C, 64.77; H, 5.45; N, 16.15.
For similar synthesis of 49-51 see Supplementary data
4.1.13. 2-(4-Morpholinyl)-4-oxo-N-(2-pyridinylmethyl)-4H-pyrido[1,2-a]pyrimidine-9-
carboxamide (52)
DIPEA (42 µL, 0.24 mmol) was added to suspension of 13 (55 mg, 0.2 mmol) in
anhydrous DMF (10 mL), and 2-(aminomethyl)pyridine (25 mg, 0.22 mmol) and DEPC (42
µL, 0.28 mmol) were then added to the resulting solution, which was stirred overnight at
room temperature. The reaction was quenched with aqueous NaHCO3, and the solvents were
removed under reduced pressure. The residue was taken up in CH2Cl2 (50 mL) and washed
three times with water, dried (Na2SO4) and evaporated, and the product was filtered through a
1
plug of alumina (EtOAc) to give the 52 (60 mg, 82%): mp 248-250 °C (MeOH); H NMR
(CDCl3) δ 10.72 (1H, br, NH), 9.12 (1H, dd, J6,8 7.0, J6,8 1.9, H-6), 8.87 (1H, dd, J8,7 7.2, J8,6
1.86, H-8), 8.56 (1H, dd, H-3′), 7.68 (1H, td, J5',4'=5',6' 7.7, J5,4 1.8, H-5′), 7.38 (1H, d, J6',5' 7.8,
H-6′), 7.24 (1H, dq, H-4′), 7.08 (1H, t, J 7.1, H-7), 5.63 (1H, s, H-3), 4.85 (2H, d, J 5.4,
CH2), 3.75-3.65 (4H, t, J 5.8, J 5.2, OCH2), 3.55 (4H, t, 5.2, 4.7 NCH2); 13C NMR (CDCl3) δ
162.8 (q, CO), 160.1 (q, C-1′), 157.9 (q, C-2), 157.2 (q, C-4), 149.4 (CH, C-3′), 148.9 (q, C-
10 ), 142.4 (CH, C-8), 136.9 (CH, C-5′), 131.0 (CH, C-6), 124.8 (q, C-9), 122.7 (CH, C-4′),
21

122.6 (CH, C-6′), 112.5 (CH, C-7), 81.3 (CH, C-3), 66.4 (CH2, OCH2), 45.8 (CH2, NCH2),
45.1 (CH2). Anal. Calcd for C19H19N5O3: C, 62.46; H, 5.24; N, 19.17. Found: C, 62.19; H,
5.25; N, 19.13.
For similar synthesis of 53 and 54 see Supplementary data
4.1.14. N-[2-(4-Morpholinyl)-4-oxo-4H-pyrido[1,2-a]pyrimidin-9-yl]benzamide (55)
Triethylamine (7.5 mL, 54.3 mmol) was added to a suspension of 13 (5 g, 18.1 mmol)
in anhydrous 2-methyl-2-propanol. The suspension was heated until the solid had mostly
dissolved, then DPPA (4.7 mL, 21.7 mmol) was added and the reaction was refluxed
overnight (precipitate). The solution was concentrated and purified by alumina column
chromatography (EtOH/CH2Cl, 5:95) to give a crude product (4 g) that was separated by
flash column chromatography (CH2Cl2/EtOAc: 70:30). Early elutes gave tert-butyl 2-(4-
morpholinyl)-4-oxo-4H-pyrido[1,2-a]pyrimidin-9-ylcarbamate (46) (3.0 g, 48%): mp 180-
182 ºC (EtOAc); 1H NMR (CDCl3) δ 8.56 (1H, dd, J6, 7 7.1, J6, 8 1.4, H-6), 8.35 (1H, d, J8, 7
7.4, H-8), 8.12 (1H, s, NH), 6.91 (1H, t, J7, 6= J7, 8 7.4, H-7), 5.63 (1H, s, H-3), 3.86-3.79 (4H,
t, J 5.2, J 4.71), 3.66-3.60 (4H, t, J 5.2, J 4.68), 1.57 (9H, s, (CH3)3). Anal. Calcd. for
C17H22N4O4: C, 58.95, H, 6.4, N, 16.17. Found: C, 59.00, H, 6.18, N, 16.29.
Further elution gave 9-amino-2-(4-morpholinyl)-4H-pyrido[1,2-a]pyrimidin-4-one
(47) (2.0 g, 22%) as an orange solid: mp 202-204 ºC; 1H NMR (CDCl3) δ 8.07 (1H, dd, J6, 7
6.6 , J6, 8 1.8, H-6), 6.83 (1H, t, J7, 6= J7, 8 7.4 , H-7,), 6.81 (1H, dd, J8, 7 7.4 J7, 8 1.8 H-8), 5.95
(2H, br, NH2), 5.56 (1H, s, H-3), 3.68-3.61 (8H, m, morpholine),. LCMS (APCI+) 247.1
(MH+, 100%). Anal. Calcd. for C12H14N4O2: C, 58.53, H, 5.73; N, 22.75. Found: C, 58.28,
H, 5.58, N, 22.68.
Trifluoroacetic acid (17.7 mL, 0.24 mol) was added to a stirred solution of 46 (3.0 g,
8.7 mmol) at 0 °C. The reaction was allowed to stir overnight at room temperature and then
concentrated in vacuo to give an orange solid. The solid was diluted with ice cold water (100
mL), basified with aqueous ammonia and extracted twice with dichloromethane (100 mL).
The combined organic extracts were washed with water twice, dried over sodium sulfate and
concentrated in vacuo to give 47 (1.44 g, 70%), identical to above. A solution of benzoyl
chloride (84 mg, 0.60 mmol) in CH2Cl2 (2 mL) was added to an ice cold solution of 47 (123
mg, 0.50 mmol) and Et3N (75 mg, 0.75 mmol) in CH2Cl2 (10 mL). The reaction mixture was
22

stirred overnight, water was added, and the layers were separated. After drying (Na2SO4) the
solvent was removed and residue was recrystallized from EtOH to give 55 (130 mg, 74 %):
mp 230-231 °C; 1H NMR (CDCl3) δ 9.40 (1H, s, NH), 8.85 (1H, dd, J6,7 7.6, J6,8 1.4, H-6),
8.64 (1H, dd, J8,7 7.11, J8,6 1.4, H-8), 7.94 (2H, dt, J 7.1, J 1.7, H-2', H-6'), 7.61 (1H, td, J
7.4, J 1.3, H-4′), 7.54 (2H, tt, J 7.4, J 1.30, H-3′, H-5′), 6.99 (1H, t, J7,6=7,8, 7.4, H-7), 5.65
(1H, s, H-3), 3.85-3.82 (4H, m, OCH2), 3.68-3.65 (4H, m, NCH2); 13C NMR (CDCl3) δ 165.3
(q, CO), 159.7 (q, C-2), 158.4 (q, C-4), 143.3 (q, C-10), 134.3 (q, C-1′), 132.4 (CH, C-4′),
129.9 (q, C-9), 129.9 (CH, C-3′, C-5′), 126.9 (CH, C-2′, C-6′), 121.1 and 120.0 (CH, C-6, C-
8), 113.0 (CH, C-7), 81.6 (CH, C-3), 66.3 (CH2, OCH2), 44.7 (CH2, NCH2). Anal. Calcd for
C19H18N4O3: C, 65.31; H, 5.68; N, 15.04. Found: C, 65.57; H, 5.61; N, 15.10.
For similar synthesis of 56-59 see Supplementary data
4.1.15. N-[2-(4-Morpholinyl)-4-oxo-4H-pyrido[1,2-a]pyrimidin-9-yl]-N'-phenylurea (60)
Phenyl isocyanate (29 µL, 0.26 mmol) was added to a stirred solution of 47 (60 mg, 0.24
mmol) in CH2Cl2 (20 mL) at room temperature. The reaction was stirred overnight and the
resulting precipitate was collected by filtration and washed five times with ice cold CH2Cl2 to
1
give 60 (50 mg, 57%): mp > 310 °C (MeOH); H NMR (d6-DMSO) δ 9.84 (1H, s, NH), 8.71
(1H, s, NH), 8.47 (1H, dd, J6, 7 7.7, J 6, 8 1.41, H-6), 8.43 (1H, dd, J8, 7 7.0, J8, 6 1.4, H-8),
7.50 (2H, dd, J 8.6, J 1.0, H-2′, H-6′), 7.32 (2H, t, J 7.5, H-3′, H-5′), 7.13-6.98 ( 2H, m, H-7,
H-4′), 5.66 (1H, s, H-3), 3.83-3.58 (8H, m, CH2); 13C NMR (d6-DMSO) δ 159.6 (q, C-2),
157.3 (q, C-4), 152.0 (q, CO), 142.9, (q, C-10), 139.1 (q, C-1′), 131.0 (q, C-9), 128.9 (CH, C-
3′, C-5′), 122.6, (CH, C-4′), 119.0 (CH, C-2′, C-6′), 119.5 (CH, C-6), 118.8 (CH, C-8), 113.0
(CH, C-7), 80.4 (CH, C-3), 65.9 (CH2, OCH2), 44.5 (CH2, NCH2). Anal. Calcd for
C19H19N5O3.0.1 H2O: C, 62.15; H, 5.27; N, 19.07. Found: C, 62.05; H, 5.23; N, 19.24
4.1.16. Phenyl 2-(4-morpholinyl)-4-oxo-4H-pyrido[1,2-a]pyrimidin-9-ylcarbamate (61)
Phenyl chloroformate (70 µL, 0.45 mmol) was added to stirred solution 47 (107 mg,
0.41 mmol) in pyridine (8 mL). The reaction was stirred overnight, and then diluted with ice
cold water (50 mL), and the resulting precipitate was eluted through a plug of alumina
1
(EtOAc/CH2Cl2; 2:8) to give 61 (120 mg, 80%): mp 196-200 °C (EtOH); H NMR (CDCl3)
δ 8.65 (1H, br, NH) 8.64 (1H, dd, J6, 7 7.1, J6, 8 1.4, H-6) 8.36 (1H, d, J8, 7 7.4, H-8), 7.43 (2H,
t, J 8.3, H-3′, H-5′) 7.28 (1H, td, J 7.4, J 1.0, H-4′), 7.23 (2H, dd, J 8.7, J 1.2, H-2′, H-6′),
23

6.94 (1H, t, J7, 6 = J7, 8 7.36, H-7) 5.65 (1H, s, H-3), 3.86-3.81 (4H, t, J 5.2, J 4.7) 3.68-3.62 (4
H, t, J 5.2, J 4.7); 13C NMR (CDCl3) δ 159.4 (q, C-2), 157.9 (q, C-4), 150.8 (q, CO), 149.8
(q, C-1′), 142.6 (q), C-10), 129.2 (q, C-9), 129.1 (CH, C-3′, C-5′), 125.6 (CH, C-4′), 121.1
(CH, C-2′, C-6′), 120.3 (CH, C-6), 119.3 (CH, C-8), 112.2 (CH, C-7), 81.1 (CH, C-3), 65.9
(CH2, OCH2), 44.3 (CH2, NCH2). Anal. Calcd for C19H18N4O4: C, 62.29; H, 4.95; N, 15.29.
Found: C, 62.42; H, 5.04, N, 15.09.
4.2
Enzyme assays
The Class IA PI3K assays were performed using a basic thin-layer chromatography
technique. IC50 values were measured using a standard lipid kinase activity using
phosphatidylinositol as a substrate, as previously described.47 The differences were: (a) that
100 µM unlabelled ATP was used instead of 10 µM, (b) the DMSO concentration was 1%
rather than 2% and (c) γ-33P-ATP (GE Healthcare) was used instead of γ-32P-ATP. The TLC
plates were quantified using a phosphorimager screen (StormImager, Amersham). The
reported IC50 value is determined by non-linear regression analysis using (GraphPad Prism
software).
The PI 3-kinases were produced by co-expressing the catalytic subunits with the p85α
regulatory subunit. Human clones for p110α, p110β, p110δ and p85α were isolated using
PCR with an N-terminal His-tag being added to the p110 isoforms to facilitate purification.
The catalytic subunits were cloned together with p85 in an baculoviral expression vector
containing an IRES sequence and the co-expressed in Sf9 insect cells. The PI3Ks were
purified using nickel-nitrilotriacetic acid (Ni-NTA) superflow (Qiagen) affinity column. The
purity of the PI3K preparations was verified by coomasie staining of SDS-PAGE gels and the
titers of baculovirus were adjusted such that the ratio of p85:p110 was approximately 1:1.
The functional authenticity of multiple preparations of the recombinant PI3K was verified by
western blotting and also by sensitivity to previously described isoform selective PI3K
inhibitors. Nine inhibitor concentrations were used to determine the IC50. Values reported are
means of two experiments, variation between experiments is no more than 20%, unless
otherwise stated.
24

4.3
Cellular assays
The compounds were also evaluated in a cellular assay measuring inhibition of proliferation
of two early passage human cancer cell lines, using 3H-labelled thymidine incorporation as an
index of proliferation, as previously described. 35,48,49 The NZB5 cell line was developed from
a patient with medulloblastoma and was chosen because it contains the wild-type gene for
p110α. The NZOV9 cell line was developed from a patient with a poorly differentiated
ovarian (endometrioid) adenocarcinoma that was wild-type for expression of p53 protein but
contained a mutant p110α enzyme with a single amino acid substitution (Y1021C) in the
kinase domain leading to activation of the PI3K enzyme.50
Cell lines were grown in a-modified minimal essential growth medium supplemented with
insulin, transferrin, selenite and 5% foetal bovine serum. Individual wells of 96-well tissue
culture plates contained 1000 cells in a volume of 150 µL. Drugs were added at 10-fold
concentration steps to a maximum of 20 µM and plates were incubated under an atmosphere
of 5% O2, 5% CO2 and 90% N2 for five days, with 3H-thymidine (0.04 µCi per well) being
added over the last 6 h. Cells were harvested and the incorporated radioactivity was
measured. Duplicate samples were analyzed for each drug dose with multiple control
samples and data were fitted to a least-squares regression of the form y = y0 + ae-bx, where y
is the incorporated radioactivity, x is the drug concentration and y0, a and b are variables. The
IC50 value was defined as the drug concentration reducing 3H-thymidine incorporation by
50%.
4.4
Molecular modeling
All mammalian sequences for the p110α, β, δ and γ were retrieved from the Homologene
database and aligned to the p110β kinase region (706-1067) using T-COFFEE.51 The
Consensus predicted secondary structure elements within the p110β and p110δ sequences
were defined using the JPRED52 and PSIPRED53 methods, and superimposed onto the
multiple sequence alignment. The DSSP calculated secondary structure for the p110γ and
p110α structures (pdb: 1E8Y and 2RD0) were also superimposed. The secondary structure
superpositions were used to guide the positioning of insertions and deletions in p110β into
loop (Figure S2).
25

Construction of atomic models for the p110β kinase domain was performed using
MODELLER 9.354 using the default automodel class with the alignment shown in Figure S3,
and template structures obtained from the protein data bank.55 A model for the p110β apo-
form was constructed using as template structures, either the p110α apo-form (pdb: 2RD0) as
a single template (model 1) or in combination with the p110γ apo-form (pdb: 1E8Y) (model
2) to explore the effect of multiple templates. Ligand bound conformations were modelled
using the p110γ structure (pdb: 1E7V) with LY294002 (3) bound (model 3), and that with
PIK-39 bound (pdb: 2CHW) was used to model the p110β kinase active site with the
specificity pocket exposed (model 4). Loops were automatically generated in the absence of a
template and twenty models per template were built. The model with the lowest objective
function was assessed for stereochemical correctness and side chain packing using
PROCHECK, ERRAT and VERIFY3D at default settings. These data are presented in Table
S2. Hydrogens were added, and sidechain orientations of histidine, asparagine and glutamine
were checked using Molprobity56 and were flipped if clear evidence was noted using TRIPOS
SYBYL 8.0.57 Sidechain adjustments to relieve clashes were made using the Lovell rotamer
library as implemented in SYBYL8.0. Further, the active site side chains of N-terminal
residues Ile803, Ile851, Lys805 and C-terminal residues Met926, Ile936, Asp813 and Tyr839
and Asp937 adjusted to reflect the conformations of the LY294002 (3) bound p110γ structure
(pdb: 1E7V).
To see how close the models were to known p110β structures structural superposition was
carried out using jCE58,59 with scoring function defined as CA distance and angle between
sidechains, with all other options set to default. RMSD values were also obtained for
alignment of the kinase structure models with modelled loop residues omitted, and used the
p110β model residues 792-799, 866-878, 941-960, 970-980, 1008-1016, 1029-1032.
Alignment of active site residues was also performed using the same method, with the
structure truncated to the model p110β residues (775-787), (801-817), (838-862) and (919-
939).
4.5
Molecular docking
26

A single low energy conformer was generated for each ligand by OMEGA 2.2.1 (Openeye
Scientific Software, Santa Fe) using the MMFF94s force field with a dielectric constant of
80.0 and all other options set as default. Each compound was docked into a 12 Å cavity
centred on the p110β Ile803 Cδ1 atom using GOLD 4.0 with search efficiency set at 200%
and flips enabled for ring corners and planar R-NR1R2 groups. A total of 20 genetic
algorithm runs were performed with the diverse solutions option set at an RMSD cut-off of
0.8 Å, and 20 poses per ligand were kept, clustered with a cluster size of 3, and scored with
the GoldScore scoring function.60
To better model the specificity pocket for the current series of TGX-221 analogues, the
model 4 active site was energy minimised in the presence of the best TGX-221 (R) pose using
the minimize subset module of SYBYL X-1.3.1. All side chains within a 6 Å zone around
the ligand were minimized using MMFF94s force field and MMFF94 charge assignment,
with the conjugate gradient method, a distance dependent dielectric function with dielectric
constant set at 4 and non-bonding cutoff set at 12 Å, and a cutoff of 0.1 Kcal/mol. A further 6
Å zone was held rigid, and the rest of the protein was ignored during the calculation. To
improve exploration of the energy minimised specificity pocket while docking TGX-221
analogues, the position of the pyrido[1,2-a]pyrimidine core was restrained using a scaffold
restraint with weighting of 5. The scaffold was defined as the 2-morpholino-4H-pyrido[1,2-
a]pyrimidin-4-one core of the best scoring, correctly oriented, TGX-221 (R)-enantiomer
docked into model 4.
Acknowledgements
The authors would like to thank Drs Maruta Boyd and Shannon Black for NMR spectroscopy
services, Wilson Sun, Sisira Kumara, and Karin Tan for technical assistance, and the Maurice
Wilkins Centre for Molecular Biodiscovery and the Auckland Cancer Society for project
funding.
Supplementary data
27

Experimental procedures and analytical data for bis(2,4,6-trichlorophenyl) malonate and
compounds 1a, 4-8, 18-21, 23, 28-30, 34-36, 38-45, 49-51, 53, 54, and 56-59, as well as
molecular modelling studies.
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