Stereoselective synthesis of rapamycin fragment to build a macrocyclic toolbox

Article abstract of DOI:10.1021/ol5034833

A stereoselective synthesis of a rapamycin fragment is developed and further utilized toward building a macrocyclic chemical toolbox. The amino alcohol moiety embedded in the 22-membered macrocyclic ring allowed for the addition of a variation in the chir

Full text of DOI:10.1021/ol5034833

Letter
pubs.acs.org/OrgLett
Stereoselective Synthesis of Rapamycin Fragment To Build a
Macrocyclic Toolbox
Shiva Krishna Reddy Guduru,† Ravikumar Jimmidi,† Girdhar Singh Deora,‡ and Prabhat Arya*,†
†Dr. Reddy’s Institute of Life Sciences (DRILS), University of Hyderabad Campus, Hyderabad 500046, India
‡School of Pharmacy, The University of Queensland, Brisbane, QLD 4072, Australia
S
* Supporting Information
ABSTRACT: A stereoselective synthesis of a rapamycin fragment is developed and further utilized toward building a
macrocyclic chemical toolbox. The amino alcohol moiety embedded in the 22-membered macrocyclic ring allowed for the
addition of a variation in the chiral side chain. The key reactions leading to the synthesis of the rapamycin-derived pyran fragment
include the following: (i) Paterson aldol, (ii) stereoselective β-OH carbonyl reduction, and (iii) regio- and stereoselective
intramolecular oxy-Michael reaction. The other piece needed for building the macrocyclic diversity was obtained from the
coupling of various amino alcohol moieties with S-pipecolic acid.
apamycin (also known as sirolimus, 1, Figure 1), a
secondary metabolite, was first isolated from soil
treatment of cardiovascular diseases by the US Food and
Drug Administration (FDA).3 Rapamycin inhibits the activity
of the mammalian target of rapamycin (mTOR) and interacts
in the mammalian cells with the immunophilin FKBP12, and
the FKBP12−rapamycin complex allosterically inhibits
mTORC1 kinase activity by an unknown mechanism.4
mTOR is an intracellular serine/threonine protein kinase that
has a central role in various cellular processes, including cell
growth and proliferation, protein synthesis, and autophagy.5 In
addition to this, the proliferative properties of rapamycin and its
analogues are being extensively studied to search for promising
anticancer agents.6 Multiple studies have also shown that
rapamycin can provide therapeutic benefits in experimental
models of several age-related neurodegenerative diseases,
including Alzheimer’s disease, Parkinson’s disease, and
Huntington’s disease.7 Several studies have demonstrated that
rapamycin is able to extend the lifespan in various species,
including mice.8 Because of the multiplicity of the mTOR
downstream signaling pathway, different molecular mechanisms
have been proposed for obtaining a better understanding of
various biological functions of rapamycin.9
R
Figure 1. Our plan to build macrocyclic diversity based on the
rapamycin fragment.
bacterium Streptomyces hygroscopicus at Easter Island (Rapa
Nui) in the 1970s.1 The pharmaceutical potential of rapamycin
was originally discovered in a screen for novel antifungal agents.
Later, it was found to be an antibiotic and immunosuppressant
and has been used for several years to prevent rejection in
organ transplantation.2 Currently, it is approved for the
Received: December 3, 2014
© XXXX American Chemical Society
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DOI: 10.1021/ol5034833
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Letter
Because of these extensive biological properties, serious
attention of the scientific community has been captured toward
developing synthesis methods to obtain various rapamycin
analogues and rapamycin-derived hybrid molecules.10 In many
cases, these analogues as well as hybrid compounds have shown
promising results toward the binding to FKBP12 and its impact
on cancer and neurodegenerative diseases.3a,11 The remarkable
biological properties of rapamycin and rapamycin-derived
hybrid compounds also attracted our attention in developing
the diversity-based synthesis of a new family of hybrid
macrocyclic compounds. Shown in Figure 1 is our generic
macrocyclic structure 2 that utilizes a rapamycin fragment
having a stereodefined pyran moiety. In our diversity-based
design strategy, we decided to keep the simplified version of the
pyran ring of rapamycin lacking the −OH group at C-10
(replaced by C10−H) and the carbonyl moiety at the C-10 side
chain. These two changes were planned to simplify our
synthetic approach reaching the target. Our first goal was to
develop a short and practical synthesis of this subunit shown in
2 and then to utilize this to building the macrocyclic diversity.
Our precise synthesis target (3) is shown in Scheme 1. In our
design and synthesis approach, we divided 3 into two sections,
Scheme 2. Synthesis of the Keto Fragment 9
Scheme 3. Synthesis of the Key Intermediate 20
Scheme 1. Our Plan to Build Macrocycles Based on the
Rapamycin Fragment
provide 17. The tert-butyl ester was subjected to reduction with
LAH to give 18, which was then oxidized with DMP to yield
aldehyde 8 (P1 = TBS).14 With freshly prepared aldehyde, we
then subjected this to a diastereoselective aldol reaction with the
keto fragment 9 using (−)-DIPCl-based Paterson aldol
protocol.15 This reaction worked very well and provided the
β-hydroxyl carbonyl compound 19 in good yield as the single
diastereomer (HPLC purity >94%). The β-hydroxyl carbonyl
compound 19 was then treated with NaBH4 in the presence of
Et2BOMe for a 1,3-syn-stereoselective β-hydroxyl carbonyl
reduction16 yielding syn-1,3-diol which was then protected with
2,2-dimethoxypropane. Finally, it was then treated with TBAF
to yield the primary alcohol as the key intermediate 20. At this
stage, the relative stereochemistry of cis-1,3-diol (20) was
assigned by 2D-NOESY experiments (see Scheme 3).
Our approach to regio- and stereocontrolled intramolecular
oxy-Michael reaction is shown in Scheme 4.17 Compound 20
was oxidized to aldehyde with DMP and then subjected to
Horner−Wittig reaction to obtain α,β-unsaturated ethyl ester
21 in good yield.18 The 1,3-diol was deprotected with PPTS
and further treated with potassium tert-butoxide, which afforded
a smooth intramolecular oxy-Michael cyclization giving 22 in
72% yield as a single diastereomer. The stereochemistry of the
2,6-cis-tetrahydropyran moiety (22) was assigned through the
coupling constant of proton at C-10 and 2D-NOESY
experiments. The details of the synthesis and the structural
assignments are provided in the Supporting Information.
4 and 5. Fragment 5 has a diversity site (R1), and it can be
easily obtained from S-pipecolic acid coupled to various amino
alcohols having a terminal olefin. Following the coupling of 5
and 4 through an amide bond, we rely upon the ring-closing
metathesis as the key 22-membered macrocyclic stitching
reaction. The crucial pyran fragment 4 can be obtained from 6
by a regio- and stereocontrolled intramolecular oxy-Michael
reaction. The 1,3-syn-dihydroxyl groups can be accessed by a
stereoselective reduction of the β-OH keto derivative 7. Finally,
we envisioned the synthesis of 7 using Paterson’s facial-selective
aldol reaction giving us the starting materials 8 and 9.
Our synthesis plan to obtain the keto fragment 9 is shown in
Scheme 2. (E)-Ethyl 3-methyl-4-oxopent-2-enoate12 10 was
subjected to keto protection (11) and ethylene glycol and then
subjected to carboxyl ester reduction to give 12. This upon
allylation followed by the keto deprotection produced 9 in
good yields.
The chiral aldehyde moiety 8 (P1 = TBS) needed for the
aldol reaction was obtained using Evans’ Michael addition-
based approach using tert-butyl acrylate 15 with oxazolidinone,
14 (Scheme 3).13 The removal of an auxiliary led the synthesis
of a primary alcohol which was then protected with TBS to
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Scheme 4. Synthesis of 2,6-cis-Tetrahydropyran Scaffold 22
The enantiopure 2,6-cis-tetrahydropyran moiety (22) was
hydrolyzed with LiOH to obtain the carboxylic acid, which was
then coupled with four secondary amines 24 (Scheme 5) using
Figure 2. (A) 3d at the binding pocket of human immunophilin
FKBP-12. (B) Binding of 3d with human immunophilin FKBP-12 and
FKBP12-rapamycin associated protein complex. (C) Interactions of 3d
with the rapamycin binding site of human immunophilin FKBP-12.
(D) Interactions of 3d with human immunophilin FKBP-12 and
FKBP12-rapamycin associated protein complex.
Scheme 5. Synthesis of Rapamycin Fragment-Derived
Macrocycles 3a−d
binding with both protein targets. It interacts with Ile-56 (H-
Bond), His-87 (π−π interaction), and A:Ile-56, A:Gln-53 (H-
bond) with human immunophilin FKBP-12 and FRAP-human
immunophilin complex, respectively (Figure 2C,D). In the case
of human immunophilin FKBP-12 and FKBP12-rapamycin
associated protein complex, Ile-56 is a common hydrogen-
bonding residue except in the case of 3b. Detailed information
on the binding interactions, glide score, and contributing XP
parameters of macrocycles (3a−d) docking with the human
immunophilin FKBP-12 and human immunophilin FKBP12-
FRAP complexes is provided in the Supporting Information.
In summary, we developed a practical, stereoselective
synthesis of rapamycin fragment-derived pyran moiety which
was further utilized in building 22-membered macrocycles. The
biological studies with these compounds are in progress and
will be reported in due course.
EDC·HCl and HOBT as the coupling reagents to obtain 23.19
The synthesis details (with R1 as the first diversity site) are
provided in the Supporting Information. This was then treated
with acid chloride (as the second diversity site) to obtain the
ring-closing metathesis precursor. Finally, the stage was set to
try a crucial ring-closing metathesis stitching reaction for
obtaining 22-membered ring macrolides. To our delight, the
RCM approach gave the macrocyclic product (3) in all four
cases in good yields and with only E-olefin geometry across the
double bond.20 The synthesis details and full characterization
are provided in the Supporting Information.
As a test study, the molecular docking studies were
performed to predict the key binding interactions of our
rapamycin fragment-derived hybrid macrocycles with human
immunophilin FKBP-12 and FKBP12-rapamycin associated
protein complexed with human immunophilin. The docking
studies predicted a good binding interactions of rapamycin
analogues with both the target proteins (see Figure 2). The
detailed information on this study is provided in the Supporting
Information.
ASSOCIATED CONTENT
* Supporting Information
■
S
Detailed experimental section and spectral data are provided.
This material is available free of charge via the Internet at
http://pubs.acs.org.
AUTHOR INFORMATION
Corresponding Author
■
*E-mail: prabhata@drils.org.
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
We thank DST and DBT (funding agencies from India) for the
financial support. S.K.R.G. and R.J. thank CSIR-India for the
award of Senior Research Fellowships. We thank the DRILS
analytical facility team for providing excellent technical support.
We offer our sincere thanks to Dr. Ben Ross, The University of
Queensland, Australia, for assistance with molecular docking
studies.
All our macrocyclic compounds occupy the binding pockets
of proteins (see Figure 2A,B). Compound 3d showed good
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