Research Summary of

Jacinth Naidoo
University of Texas Southwestern Medical Center, Research Assistant II

Project: Synthesis of diazonamide side chain and of new probe

Diazonamide A, 8 was first isolated in 1991 from Diazona angulata by Fenical et al., and has shown potent in
vitro cytotoxicity to transformed human cell line HCT-116. I was responsible for synthesizing the biotinylated
control and a novel probe to determine the effect of the diazonamide side chain on its activity. Synthesis of
the side chain involved a chiral copper catalyst 1 in a glyoxylate-ene reaction to afford volatile 2 in 4:6 ratio
of α: β enantiomers. I was able to avoid volatility problems during HPLC purification and handling of 2 by
carrying out the cross metathesis reaction with a CbZ protected amine 3 and the crude mixture of 2. I
performed a solvent, temperature and catalyst loading study to optimize reaction conditions to improve
conversion from 50-85%. The desired enantiomer 5 was then saponified to
H
BnO N H H
DCM, -78 0C Me benzene, 40 0C BnO N Me BnO N Me
O O 3 HPLC separation of isomers
+ OEt OEt O OEt O OEt
2+ HO 4 HO in ratio of 2:3 α:β 5 HO
O O O O A N N Ar
15 mol% O O
N N 2 SbF6- 2 Cl Ru
Cl O
O Me3C Cu CMe3 PCy3Ph K2CO3, MeOH
HO
1 OH
HN NH
H H HN Me
O control: n=1
S NC P (OCH2CH3 )2 probe: n=3 H
O 1. H 2, Pd/C, MeOH BnO N Me
NMM, THF/MeOH
n

n O
S O OH
control: n=1 7 2. DMF, DIPEA 6 HO
probe: n=3 HN Me HN N Cl N Cl H H O O
N HN N O O O
H HN NH NHH
N O Cl H2N O Cl N
HO O O O O HN O
O O
O H S
NH NH

O O O O 8

Scheme 1: Synthesis and biotinylation of diazonamide side chain(n=1) and of novel probe(n=3)

the α -hydroxy acid 6, which was subsequently deprotected in a hydrogenation palladium on carbon reaction.
The amino acid was then coupled to biotin and the biotinylated acid 7 is then coupled to the diazonamide core
in a non-traditional way and unfortunately messy way. A novel probe using a six carbon biotin side chain was
1. n-BuLi, THF,-78 0C, 1 hr
Zr
3.3 mol%Pd(OAc)2, 3.8 mol% P(o-tolyl)3, Ag3PO4
Me Me
H
N CN
BBr3, CH 2Cl 2
Me Me
H
N CN
BocHN H 2N

also synthesized via the same route.

Cp2ZrCl 2
O Cl , -78 0C-->r.t, 3 hr Cl Me Me O O
2. H , r.t, 8 hr 4
OBn O N CN
Ph BocHN

Project: Diazonamide scale-up

O O HO O
H Br Ph TBTU, DMF, I
1 3 OH
N 2 DIPEA, r.t
NHBoc
BnO

To further investigate the mode of this promising anti-cancer agent, I was solely responsible for its scale up.
Me

HN
Me
H
N NH
Me

HN
Me
H
N CN
Me Me
H
N
5

O O 3mol% [Pd2(dba)3], 6mol%2-(t-Bu2P)biphenyl, Ag3PO 4, THF, 75 0C HN CN

BocHN O BocHN
O O BocHN O
O
HO I HO
O OO Br OBn
Ph 7 OBn
C 6H 4(o-NO 2)
8 6
hν (350 nm) H
N
Ac2O
Me Me Me Me Me Me Me Me
H H N H N H N Cl
N N N N
HN NH HN hν (300 nm) HN NCS HN
O O O NH O O O O Cl
BocHN O BocHN BocHN BocHN
O O LiOAc, epichlorohydrin O O
AcO AcO AcO NH AcO NH

O O Br O O Br O O O O
Ph Ph Ph Ph
9 10 11 12

Scheme 2: Scale-up synthesis of Diazonamide

1
 O HN N
O S
O O O O O
O2N S Ph3P O S TFA, CH 2Cl2, r.t S 1. toluene, SOCl 2, reflux O2N S MeO N
O 2N O2 N
H O OH N

In scheme 2, dibutylzirconocene is treated with chlorostyrene 1 and the in situ generated ZrIV species is then
Y=100 %
benzene, reflux N H
2. H O
Y=82% N toluene, reflux
1 2 3 N S 5
O O
cross coupled with bromooxazole 2 in a Negishi coupling reaction. The protecting groups of 3 are
1.CH3COH, KOH/MeOH
2. Ac2 O, heat O 2N S
O
1. NaClO2 , CH 3CN
2. NaH2PO4, H 2O2(35%)
Y=40 %
4
NH 2

simultaneously removed before condensation of the amine 4 with tyrosine derivative 5 to yield modified
3. HCl, H2O, reflux H Y=85 %
Y=75 %
6
Scheme 3: Synthetic route for SMAC sulfonamide
dipeptide 6, which then undergoes an endocyclic Heck reaction to form product 7 securing the diazonamide
core. Further along in the sequence, I acylated intermediate 8 to yield the benzofuran 9 and also carried out
the very tricky photocyclisation ring closing reaction to yield 11 in 25% yield. The cyclised product is then
chlorinated in an equally tricky reaction giving a varied mixture of mono, di and even trichlorinated product.

Project: Synergist for SMAC mimetic

The sulfonamide 5 in scheme 3 is used as a synergist with SMAC mimetic for inducing apoptosis. When
NH2
R
R=Cl, F,Br, Me, N-pyridine, NH2, OCH3, OCF3, CF3, SCH3

Cl NH
traditional peptide coupling techniques failed in condensing the commercially available acrylic acid 3 with the
NO 2
+
R DMF, heat NO 2

benzenesulfonamide 4, I synthesized the acrylic acid 3 via 2 routes. The optimized route used a phosphorane
CF 3
Cl
CF 3
Cl
O
NHBn NHBn NHBn
NO2
NHBn
NO 2
NHBn
F
N N
to convert nitrofuraldehyde 1 to t-butyl acrylate 2, which is quantitatively deprotected to give acrylic acid 3.
NH 2
N Cl Cl NHBn
X NHBn NH CF 3 CF3 CF 3 CF3 CF3
An alternate route to acrylic acid 3 is via acrylaldehyde 6, but this route was more time consuming with
Y
Z
+ or
heat or Pd-catalysis base Y
Z
and Y
Z
O O O O O O O
harsher conditions. Acrylic acid 3 was converted to the acyl chloride before nucleophilic addition to
CF3
W
O CF3
W
CF3
W
N N N N N N N

sulfonamide 4 to give sulfonamide 5. N NH NH NH NO2 NH

N N
1. X=Cl, Y=C, W=Cl, Z=NO2 NH 2 NO 2 F
N N
2. X=Br, Y=C, W=H, Z=F Cl Cl
3. X=F, Y=N, W=H, CF3 Cl CF3 Cl CF3
4. X=Cl, Y=N, W=Cl CF 3 CF 3 CF3 CF3

Project: Analogues for SAR study to optimize lead scaffold for compounds that induce necrosis.
Scheme 4: Synthetic route for new analogs

I undertook the synthesis of these analogs with 4-aminomorpholine, benzylamine and 2-substituted
benzylamines which underwent nucleophilic substitution with various dihalogenated trifluormethylbenzenes
and trifluoromethylpyridines under heat or catalytic conditions.

Project: Synthesis of Deazaneplanocin A for neurogenic study

2
 Scheme 5: Synthesis of Deazaneplanocin A

Using acetone and a catalytic amount of acid, D-(+)-Ribonolactone 1 is converted to the D-(-)-isopropylidene
ribonolactone 2, which was then benzyl protected to yield 3. Using an alternative work up I was able to
improve the literature yield of 3 by 25%. Ketone 3 is then installed with a β -hydroxy phosphonate to give
hemiketal 4, which under basic conditions undergoes ring opening to give the β -ketophosphonate 5. I found
that oxidation of 5 only worked with in situ generated PCC to give diketone 6. Oxidation with commerically
available PCC gave no product while oxidation attempts with Dess-Martin periodinane were slow with low
conversion. This oxidation step was the weakest in the sequence due to poor yield and mass recovery. The
diketone 6 was subjected to base and 18-crown-6 to yield partially racemic cyclopentenone 7 as an oil. After
isomer separation, optically pure cyclopentenone 7 is carried forward onto a Luche reduction, the
cyclopentenol product which is then mesylated to give 8. The sodium salt of the chloropurine 9 is then reacted
with the mesylate 8 to give intermediate 10, which is then deprotected by BCl3, to yield intermediate 11.
When reduction of intermediate 11 using hydrazine and Raney nickel failed, the route was abandoned due to
poor throughput and time constraints. A B C D E F G H I J
HH HH H H NO2 OCH3 H H
Cl H
H H NO2 OCF3 H H
H Cl H H

Project: Benzoxadiazole library for NCI supported SAR study H

OCF3
H
H
Cl
H
H

H
H

H
H
H
NO 2
Cl
H
H
H
H
H
H
H F H H H
CF3 H H H H
H H Cl H H
B H CF 3 H H H
H F Br H H
NH 2 A C CH3 H H H H
NO 2H H CF3 Cl H H
E A DMF/DMAC N H CH 3 H H H
H H CF3 H H
N D H H CH3 H H
70-100 0C O H F H F H
D B N E H CF3 Cl H H
H NO 2 Cl H H
NO2 C NO2 H H H H H
H NO2 CH 3 H
N Cl + AND H H Cl
Br H H H Cl H H
O NH2 NO2H F Cl H
N H Br H H H F H H
J F DMF/DMAC N N G H H Br H H H Cl H H H

0C O H Cl F H H
I 70-100 N Table 1 :Analogs generated
G J H from substituted F H H F H
H I benzylamines. F F H H H

H F F H H
H F CH 3 H H
H
Scheme 6: Synthetic route for new analogues F
Cl
H
F H
H
H
H
H
H Cl H F H
H F Cl H H
F H
Some of the analogs that were generated in the benzoxadiazole SAR library are Br H H
Table 2 : Analogs generated
illustrated in tables 1 and 2. Reactions were generally rapid and clean with little or from substituted
no purification required after work up. anilines.

Project: Analogues for SAR study to investigate mitochondrial effects in the apoptotic pathway.
3
 CF3 1. DCM, BBr 3, r.t N OMe
2.BocHN OMs HO
Br Br Br Br N O NaOMe,
13 O
K 2 CO 3, DMAC, 70 0C MeOH
3. TFA, DCM, r.t N OMe Br Br
N N HO
15 O
N3 N CF3 N
HO HO H
Br 8 7 N OMe
O
Br Br Br Br Br O
14
DMF, DIPEA DMF, EDC, DIPEA
N
N N O
O O O
NHH O
N N O NH2 OH N O NH
HO H HN O N H H
O HO HO
17 S
H 16 18
NH O
O O N
N O O
O

S
H H Scheme 7: Synthetic Route for P7C3 Analogs
HN NH
O

P7C3, 2 in scheme 7, belongs to a family of compounds which have shown the ability to slow down and also
reduce the effects of neurodegenerative disorders. Compound 2 is efficiently synthesized from the
nucleophilic addition of dibromocarbazole to epibromohydrin to yield epoxide 1, which undergoes ring
opening with anisidine under lewis acid conditions. With a goal of inclusion of various anilines, pyrazines and
pyrimidines into the library, amine 4 was made from epoxide 1, which underwent ring opening with
benzenethiol and phenol to give 5 and 6 respectively, as did trifluoromethylaniline to give analog 7. I
investigated an alternate route to making amine 4 via azide 8, followed by reduction with Pearlman’s catalyst,
which interestingly gave a mixture of mono and de-brominated products. Epoxide 1 underwent ring opening
with 2-aminopyridine under typical acidic conditions to give 9. Parent 2 undergoes specific N-methylation
with methyl iodide and K2CO3 in acetone to yield 10, and selective O-methylation (3:1 O-Me: N-Me) with
NaH and DMF to give 11. I prepared formamide 12 with mixed formyl acetic anhydride reagent. Ketone 3
was prepared via a Parikh-Doering oxidation. Carbamate 14 was formed by ring closing carbonate 13 under
basic condition. Carbonate 13 was the product of treating parent 2 with an excess of methyl chloroformate and
indium powder. N-acetylation was specific in the microwave preparation of 15, using acetyl chloride and
dibutyltin oxide. Fluorinating agent diethylamino sulfurtrifluoride was used in the synthesis of 19. For a pull
down assay, biotinylated 2 was required. I was able to carry this out by first deprotecting the methyl ester
using boron tribromide and then alkylating the phenol with boc-aminopentanol mesylate under basic
conditions. This is followed by Boc-deprotection to give free amine 16, which undergoes coupling with the
biotin ester to give 17.