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Mechanism of action of rapamycin and its applications in aging, cancer therapy and metabolism
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Mechanism of action of rapamycin and its applications in aging, cancer therapy and metabolism
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Content
MECHANISM OF ACTION OF RAPAMYCIN AND ITS APPLICATIONS IN
AGING, CANCER THERAPY AND METABOLISM
by
Anuja Raut
________________________________________________________________________
A Thesis Presented to the
FACULTY OF THE USC GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
MASTER OF SCIENCE
(PHARMACEUTICAL SCIENCES)
May 2014
Copyright 2014 Anuja Raut
ii
ACKNOWLEDGEMENTS
The thesis would not have been possible without the help and guidance from Dr. Clay
Wang. I want to take this opportunity to thank Dr.Wang from the deepest corner of my
heart for his kindness and support. I also want to thank my committee members, Dr. Ian
Haworth and Dr. Bogdan Olenyuk for their supervision and direction. I thank my
colleagues and peers at University of Southern California, who have also become my
friends. They have constantly been a source of inspiration and positivity. I want to
especially mention Aida Kouhi, Saranya Sankar and Ishan Patil for their kindness in the
past two years. The willingness of students and Faculty at University of Southern
California to offer their help selflessly has touched my heart. I want to especially mention
Wade Thompson-Harper for his constant support throughout my M.S. journey. I
appreciate all the times he patiently answered the questions I may have had coming from
a foreign country. My mother, Ujwala Raut, is my core support system, without whom I
would not have been where I am today. She is the light at the end of a dark tunnel. Her
ability to make me see everything positively has sailed me through lots of perceived
storms. She is my best friend, a sister I never had, a confidante, a mentor, a guide,
everything. I want to thank my father, Bhagwat Raut, and my brother, Abhijit Raut, for
making life so much better with their presence. They are my two pillars of strength. I
want to thank my friends from outside of University of Southern California for making
me a better person every passing day. Last but not the least, I thank Dr.Sarah F. Hamm-
Alvarez for giving me the opportunity to collaborate with her and learn various aspects of
iii
molecular biology in her laboratory at University of Southern California. I thank Maria
Edman-Woolcott, Mihir Shah, Srikanth Reddy Janga, Pang-Yu Hsueh, Frances Yarber
and Zhen Meng from Dr.Hamm-Alvarez’s laboratory for their guidance during my
association with the Hamm-Alvarez laboratory. I also want to thank Dr. Andrew MacKay
for his guidance and positive feedback during my association with Dr.Hamm-Alvarez,
and Pu Shi from Dr.MacKay’s laboratory for teaching me to operate the High
Performance Liquid Chromatography instrument in their laboratory. I consider myself
very lucky to have met and associated with so many wonderful and kind people at the
University of Southern California.
iv
TABLE OF CONTENTS
ACKNOWLEDGEMENTS ii
LIST OF FIGURES v
ABSTRACT vi
CHAPTER 1: INTRODUCTION 1
CHAPTER 2: RECEPTORS FOR RAPAMYCIN WITHIN THE CELL
2.1 FK506 binding proteins (FKBPs) 4
2.1.1 Table 1: The human FKBP family 5
2.2 FKBP-Rapamycin complex in yeast 5
2.3 mTOR: Mammalian Target of Rapamycin 8
CHAPTER 3: APPLICATIONS OF RAPAMYCIN
3.1 Application of Rapamycin in Aging 10
3.2 Application of Rapamycin in Cancer therapy 11
3.3 Rapamycin and Metabolism 14
CHAPTER 4: CONCLUDING REMARKS 16
REFERENCES 18
v
LIST OF FIGURES
Figure 1: Chemical structure of Rapamycin 2
Figure 2: Members of the TOR family 7
Figure 3: Chemical structure of Temsirolimus 12
Figure 4: Chemical structure of Everolimus 12
Figure 5: Chemical structure of Ridaforolimus 13
vi
ABSTRACT
Rapamycin is a potent immunosuppressive macrolide which binds to FK506 binding
protein (FKBP12), the cytosolic receptor to rapamycin. The FKBP12-Rapamycin
complex binds to and allosterically inhibits mammalian Target of Rapamycin (mTOR),
thereby interfering with its function in a signaling pathway necessary for cell cycle
progression from the late G
1
phase to S phase. Rapamycin, because of its ability to
regulate cell growth and cell cycle progression, has been studied as a potential therapeutic
solution for diseases characterized by dysregulation of the mTOR signaling pathway.
Here we discuss the pharmacology of rapamycin and highlight findings of recent studies
exploring its applications in aging, cancer therapy and metabolism.
1
CHAPTER 1
INTRODUCTION
Rapamycin is a lipophilic macrocyclic lactone produced by a strain of Streptomyces
hygroscopicus that was first recovered from a soil sample obtained from the Vai Atore
region of Eastern Island (Rapa Nui) (Vezina et al., 1975). A white, crystalline solid with
a melting point range of 183-185
o
C, it is poorly soluble in water but readily soluble in
ethanol, methanol, dimethylsulfoxide and other organic solvents. While being a strong
inhibitor of yeast growth, rapamycin inhibits filamentous fungi growth only moderately
(Sehgal et al., 1975). Being most active against various species of Candida,
predominantly C.albicans, it prevents systemic and vaginal candidosis in mice with no
acute toxic side effects (intraperitoneal LD50: 597 mg/kg in mice) (Baker et al., 1978).
Rapamycin prevents incorporation of [
32
P] phosphate into DNA and RNA, as
demonstrated by labeling studies in C.albicans (Singh et al., 1979). Early mechanistic
studies demonstrated that a rapamycin concentration of 1.0 µg/ml did not inhibit the
growth of C.albicans during the first hour after addition to growth media, whereas, a
lower rapamycin concentration of 5.0 ng/ml completely prevented growth after addition
to growth media for 90 minutes. Structural characterization of rapamycin shows the
molecule to be a mixture of two conformational isomers because of the cis-trans rotation
about an amidic bond in the 31-membered macrolidic lactone ring. Total organic
synthesis of rapamycin (Hayward et al., 1993; Nicolaou et al., 1993; Romo et al., 1993;
Smith et al., 1995) helped confirm its proposed chemical structure (Findlay et al., 1980).
2
Figure 1: Chemical structure of Rapamycin.
Although initially discovered as an antifungal metabolite, later studies indicating the
inhibitory effects of rapamycin against production of humoral IgE first demonstrated its
immunosuppressive activity. These studies also revealed the preventive effects of
rapamycin in animal models of two human autoimmune diseases: experimental
autoimmune encephalitis and adjuvant arthritis (Martel et al., 1977). A later study
showed prolongation of survival and prevention of the progression of glomerulonephritis
3
associated with the disease in the MLR/lpr mouse model of human systemic lupus
erythematosus after rapamycin treatment (Kahan et al., 1991). This study also revealed
inhibitory effects of rapamycin against development-stage and established adjuvant-
induced arthritis in rats.
4
CHAPTER 2
RECEPTORS FOR RAPAMYCIN WITHIN THE CELL
2.1 FK506 binding proteins (FKBPs)
Rapamycin binds to intracellular receptors called FK506 binding proteins (FKBPs). The
most important FK506 binding protein is the 12-kDa FKBP12 present in the cytosol.
FKBP12 belongs to the enzyme family peptidyl-prolyl isomerases (PPIs), which cause
the isomerization of peptidyl-prolyl bonds within proteins and peptides (Harding et al.,
1989; Siekierka et al., 1989).
Rapamycin has two structural domains: a) the effector domain which, along with FKBP,
forms a composite surface that binds to the cognate human receptor for rapamycin
(mTOR- the mammalian Target of Rapamycin), and b) the binding domain that facilitates
the binding of rapamycin to FKBP (Bierer et al., 1990; Dumont et al., 1990).
Because the conformation of rapamycin in a free crystalline form is identical to its three-
dimensional conformation in a complexed form with FKBP12, the conformation of
rapamycin is believed to be energetically favorable for FKBP12 binding (Van Duyne et
al., 1991). Table 1 (Abraham and Wiederrecht, 1996) summarizes some of the
characteristics of seven members of the human FKBP family.
5
FKBP MW
(kDa)
% IDENTITY TO
FKBP12
AFFINITY (nM)
TO RAPAMYCIN
FKBP12 11.8 100 0.2 (K
d
)
FKBP12.6
a
11.6 83 0.2 (K
d
)
d
FKBP13 13.3 50 ND
e
FKBP25 25.0 40 0.9 (K
i
)
FKBPr38
n
38.3 33 No binding
FKBP51
b
51.2 50 29 (IC
50
)
f
FKBP52
c
51.8 53 8 (K
i
)
Table 1: The human FKBP family. a, an alternative splice product of the FKBP12.6
mRNA which encodes an 8.8 kDa FKBP-related protein (Arakawa et al., 1994). b, a
human cDNA which was cloned (Baughman G et al, unpublished results). c, also known
as hsp56, FKBP59, p59, hsp59. d, value based upon the K
d
for FK-506 and adjusted for
the greater capability of rapamycin to inhibit PPIase activity (Lam et al., 1995). e, Not
Determined. f, these values are for murine FKBP51 (Baughman et al., 1995). [The table
has been reconstructed from the corresponding table in (Abraham and Wiederrecht, 1996)
so as to only include information relevant to this review]
Rapamycin inhibits the PPIase activity of all FKBPs. Since the drug binding domain of
FKBPs overlaps with the PPIase active site, PPIase activity inhibition by rapamycin may
serve as a good measure of affinity of a particular FKBP for rapamycin (Galat et al.,
1992).
2.1 FKBP-Rapamycin complex in yeast
Because of the strong inhibitory effect of rapamycin on S.cerevisiae growth, studies were
conducted that allowed identification of mutants resistant to rapamycin inhibitory action
6
and genes conferring sensitivity to rapamycin. Resistance to rapamycin was found to be
granted by mutant alleles of three genes: FKB1, TOR1 and TOR2 (Cafferkey et al., 1993;
Heitman et al., 1991; Helliwell et al., 1994; Koltin et al., 1991; Kunz et al., 1993).
Studies indicated the mutations in FKB1 to be recessive, while those in TOR1 and TOR2
were dominant or semi-dominant (Cafferkey et al., 1993; Helliwell et al., 1994; Kunz et
al., 1993). The growth of S.cerevisiae strains with disrupted TOR1 was 15% slower than
that of the wild-type strains (Helliwell et al., 1994). Strains with TOR1 mutation when
grown in the presence of rapamycin showed cell cycle arrest in the early G
1
phase within
one generation. Strains mutated in TOR2 showed cell cycle arrest randomly through the
cell cycle. Strains with disrupted TOR1 and TOR2 stopped growing in G
1
during the first
generation, thereby indicating that rapamycin has an inhibitory effect on both TOR1 and
TOR2 proteins (Helliwell et al., 1994). It was therefore concluded that either TOR1 or
TOR2 was capable of allowing the yeast cells to grow beyond the G
1
phase by
performing the required G
1
function.
TOR1 and TOR2 proteins, devoid of transmembrane domains or sequences facilitating
signaling, contain 2470 and 2474 amino acid residues respectively (Cafferkey et al.,
1993; Kunz et al., 1993).
7
Figure 2: Members of the TOR family. Important serine residues Ser
1972
, Ser
1975
and
Ser
2035
in TOR1, TOR2 and mTOR, respectively, are highlighted in red. [Amino acid
sequence obtained from (Sturgill and Hall, 2009)].
Because functional interchangeability of lipid kinase domains in TOR1 and TOR2 was
observed (Helliwell et al., 1994), it is believed that the amino-terminal regions of both
proteins are functionally different in yeast with mutated TOR1 and TOR2. Any mutation
in Ser
1975
of TOR2 inhibits binding of the FKBP-Rapamycin complex to TOR2 (Stan et
al., 1994). Similarly, mutation of any amino acid residue except alanine within the
binding domain of TOR1, which is located around its Ser
1972
residue, prevents binding of
FKBP-Rapamycin complex to TOR1 (Zheng et al., 1995).
Some studies show TOR proteins to play a role in a signaling pathway that allows cell
cycle progression if corresponding required nutrients are available to the cell cycle
machinery. Yeast cells with mutated TOR1 and TOR2 genes grown on nutrient rich
medium showed cell cycle arrest in the early G
1
phase, as seen with cells that are starved
of essential nutrients (Barbet et al., 1995). This cell cycle arrest is because of inability of
TOR depleted cells to synthesize CLN3, a cyclin protein that is essential for cells to cross
the G
1
phase of the cell cycle. CLN3 is a transcriptional activator of CLN1, CLN2,
ORFD, HCS26 and CLB5 genes which express proteins that are crucial for cell cycle
8
progression from the late G
1
phase into the S phase. CLN3 translation is initiated by the
translational factor eIF-4E such that eIF-4E-independent translation of CLN3 causes
inhibition of the rapamycin induced cell cycle arrest in G
1
phase of the cell cycle. These
results demonstrated that TOR1 and TOR2 proteins are signaling entities which facilitate
eIF-4E-dependent translation of CLN3 depending on availability of essential nutrients for
cell cycle progression beyond the G
1
phase (Barbet et al., 1995).
2.2 mTOR: Mammalian Target of Rapamycin
Purified homologous, high molecular weight mTOR proteins obtained from bovine brain
(FRAP: FKBP-Rapamycin Associated Protein) (Brown et al., 1994), rat brain
(Rapamycin And FKBP Target: RAFT; mammalian Target of Rapamycin: mTOR)
(Sabatini et al., 1994; Sabers et al., 1994) and human lymphocyte (Rapamycin Target:
RAPT; Sirolimus Effector Protein: SEP) (Chen et al., 1994; Chiu et al., 1994) weighed
more than 200kDa (Brown et al., 1994; Chen et al., 1994; Sabatini et al., 1994). 16-keto-
Rapaycin and 25, 26 iso-Rapamycin, two structural analogs of Rapamycin, bound with
higher affinity to FKBP12 as compared to rapamycin, however, inhibition of G
1
progression in MG-63 osteosarcoma cells by both analogs was 100-fold lower than that
by rapamycin. This lower inhibition of G
1
progression may be because the complexes
that these rapamycin analogs formed with FKBP12 bound poorly to mTOR or did not
bind at all (Brown et al., 1994). Another set of results showed that cell extracts obtained
from mutant murine T cell (YAC) lines isolated for resistance to rapamycin action
9
showed little or no FKBP12-Rapamycin binding to mTOR (Dumont et al., 1994; Sabers
et al., 1994). These results indicated that binding of FKBP12-Rapamycin complex to
mTOR was essential for rapamycin to exhibit inhibitory effects in mammalian cells.
The mTOR binding domain, which facilitates FKBP12-Rapamycin binding to mTOR,
has been identified to be a 90 amino acid sequence upstream of the lipid kinase motif
(Chen et al., 1995). This binding domain contains Ser
2035
which, similarly to Ser
1972
and
Ser
1975
in yeast TOR1 and TOR2, respectively, prevents FKBP12-Rapamycin binding to
mTOR when mutated to an amino acid other than alanine (Chen et al., 1995; Chiu et al.,
1994). This observation indicates that binding of mTOR and FKBP-12-Rapamycin
complex does not require Ser
2035
phosphorylation.
Though expressed extensively in human tissues, mTOR levels are significantly higher is
testis and skeletal muscle (Brown et al., 1994; Chiu et al., 1994). Human and rat mTOR
share 46% homology with the yeast TOR2, while sharing 44% identity with the yeast
TOR1. The greatest amino acid sequence similarity of 65% among all three proteins is
found in the 600 amino acids of their C-terminal region, which contains the lipid kinase
motif. This suggests that mTOR and yeast TORs may have similar enzymatic activities.
Other regions of the three proteins, including the N-terminal region, share little or no
amino acid sequence similarity.
10
CHAPTER 3
APPLICATIONS OF RAPAMYCIN
3.1 Application of Rapamycin in Aging
mTOR inhibition has been found to promote lifespan extension in yeast, nematodes and
fruit flies (Lamming et al., 2013). In mammals, rapamycin treatment from the 9
th
or 20
th
month of age (total duration of treatment: 18-24 months) in male and female mice with
distinct genetic backgrounds extended both median and maximal lifespan (Harrison et al.,
2009). It was hypothesized that rapamycin increases lifespan by preventing metabolic or
neoplastic diseases which are not exacerbated by aging effects. A study designed to test
this hypothesis utilized a genetically distinct mouse model to examine age-dependent
effects and spontaneous activity of mice treated with rapamycin from 9
th
to 21
st
month of
age (Wilkinson et al., 2012). The results indicated that age-related pathologies including
changes in liver, heart, adrenal gland, endometrium and tendon elasticity occur slower in
rapamycin treated mice. Rapamycin treatment also reduced the age-related decrease in
spontaneous activity of mice.
To study age-independent effects, rapamycin was administered to C57BL/6j mice divided
into three groups depending on treatment onsets (total duration of treatment: 12 months):
4 months of age, 13 months of age and 20 months of age (Neff et al., 2013). It was
observed that rapamycin extended lifespan in mice but had no effect on age related
pathologies. Because rapamycin treatment improved spatial learning, memory
impairments and exploratory activity in older and well as young mice, it was concluded
that rapamycin had an age-independent effect.
11
3.2 Application of Rapamycin in Cancer therapy
Any gain of function mutations in oncogenes like Ras, AKT and PI3K or loss of function
mutations in tumor suppressors like TSC1/2, PTEN and LKB1 lead to upregulation of
mTORC1. Cells with these mutations selectively grew at a faster rate as compared to
normal cells (Menon and Manning, 2008). The high nutrient uptake and energy
metabolism observed in cancer cells are processes regulated by the mTORC1 pathway.
Additionally, mTORC1 activation stimulates glycolysis, lipid biosynthesis (Yecies and
Manning, 2011) and glutamine metabolism (Csibi et al., 2013). Therefore, drugs which
exclusively inhibit mTORC1 potentially impair cancer cell metabolism, thereby proving
to be worthwhile treatment strategies for cancer.
Poor water solubility of rapamycin lead to development and Food and Drug
Administration (FDA) approval of two water-soluble rapamycin analogs (rapalogs),
temsirolimus and everolimus, in 2007 and 2009, respectively. Everolimus was approved
by the FDA for use in progressive neuroendocrine tumors of pancreatic origin (PNET) in
2011. Various clinical trials have been carried out to assess the use of temsirolimus in
advanced neuroendocrine carcinoma (NEC), endometrial cancer and relapsed mantle cell
lymphoma (MCL). Everolimus has also been examined in some trials for its use against
advanced gastric cancer and advanced hepatocellular carcinoma.
12
Figure 3: Chemical structure of Temsirolimus.
Figure 4: Chemical structure of Everolimus.
13
Another rapamycin analog, ridaforolimus, was tested clinically for its therapeutic use in
patients with advanced bone and soft tissue carcinoma (Wander et al., 2011). However,
mTORC1 regulates certain negative feedback loops which ultimately inhibit upstream
signaling pathways including receptor tyrosine kinase (RTK) activation and PI3K-Akt
signaling which can be reactivated by rapamycin. This has contributed to limited
therapeutic success of rapalogs for use in the treatment of major types of solid tumors.
Alternatively, ATP-competitive mTOR inhibitors, which target the catalytic site and
inhibit PI3K/Akt activation by feedback mechanism, have been explored recently
because of their ability to inhibit both mTORC1 and mTORC2 activity. Similarly, some
compounds initially characterized as PI3K inhibitors later showed inhibitory effects
against mTOR, possibly because of substantial sequence homology between PI3K and
mTOR (Benjamin et al., 2011).
Figure 5: Chemical structure of Ridaforolimus.
14
3.3 Rapamycin and Metabolism
mTOR signaling regulates anabolic and catabolic processes of the cell depending on
availability of growth factors and nutrients. In fasting state, adipose tissue produces fatty
acids via lipolysis, and muscle and liver obtain glucose through gluconeogenesis and
glycogenolysis. Upon food intake, glycogenesis and lipid uptake are the favored
processes in liver and muscle, and adipose tissue respectively. Dysregulation of the
mTOR signaling pathway may play a role in metabolic disorders like obesity and
diabetes (Laplante and Sabatini, 2012). Rapamycin treatment improved insulin sensitivity
both in vitro and in vivo by disrupting the S6K-mediated feedback loop mechanism
(Krebs et al., 2007; Tremblay and Marette, 2001). Rapamycin also inhibited human
adipocyte differentiation in vitro (Bell et al., 2000) and protected 16 week old C57BL/6j
mice from obesity promoted by a high fat diet (Chang et al., 2009a). Some studies,
however, have also observed harmful metabolic effects of rapamycin. KK/HIJ mice on a
high fat diet showed aggravated glucose intolerance after treatment with rapamycin for
six weeks (Chang et al., 2009b). Rapamycin treatment for two weeks caused
hyperlipidemia due to increased hepatic gluconeogenesis and impaired deposition of
lipids in adipose tissue in rats (Houde et al., 2010). A later study demonstrated that
inhibition of mTORC1 activity increased lifespan while that of mTORC2 promoted
insulin resistance, thereby concluding that rapamycin may exert different effects through
its effect on different mechanisms (Lamming et al., 2012). Another study aimed to
compare effects of rapamycin on metabolism in male mice following 2, 6 and 20 weeks
15
of rapamycin treatment (Fang et al., 2013). The study group treated with rapamycin for 2
weeks showed bigger livers and smaller pancreas as compared to groups treated with
rapamycin for longer durations. Prolonged rapamycin administration decreased adipose
tissue, food consumption and body weight. Rapamycin treatment affected oxygen
consumption, ketogenesis and lipid profile in mice in proportion to the duration of the
treatment. Insulin levels were observed to be higher after 2 weeks of rapamycin
treatment, rendering the mice glucose intolerant and resistant to insulin. Better insulin
sensitivity was observed in mice treated with rapamycin for 6 weeks and 20 weeks.
16
CHAPTER 4:
CONCLUDING REMARKS
Initially discovered as an antifungal metabolite, rapamycin was later found to possess
immunosuppressive properties in mammalian cells, thereby arousing great interest in
understanding its mechanism of action. Rapamycin binds to and forms a complex with its
intracellular receptor, FKBP12. The FKBP12-Rapamycin complex thereby binds to and
allosterically inhibits mammalian Target of Rapamycin, mTOR. mTOR shares a high
degree of amino acid sequence homology with TOR1 and TOR2, its yeast homologs.
Rapamycin interferes with cell cycle progression by inducing cell cycle arrest at the late
G
1
phase, thereby inhibiting the cell from entering S phase of the cell cycle. Over the
years, many studies have aimed to determine the beneficial effects rapamycin may have
in several chronic diseases caused by dysregulation of mTOR signaling. However,
clinical success of rapamycin has been found to be limited to just a few benign and
malignant cancers. This limited success may be because of the inability of rapamycin to
completely inhibit some mTORC1 mediated processes, like autophagy (Thoreen and
Sabatini, 2009). Certain feedback mechanisms for cell survival may also play a role in
limited success of rapamycin in clinical trials. mTORC1 activates S6K1 thereby causing
degradation of insulin receptor substrate (IRS) and downregulation of PI3K signaling.
Rapamycin-induced inhibition of mTORC1 interrupts this negative feedback mechanism
and allows PI3K signaling (Laplante and Sabatini, 2012). Certain compensatory
pathways that promote cell survival and growth may also contribute to ineffectiveness of
17
rapamycin to block cell cycle progression in certain cancer cells. S6K1 inhibition can be
compensated for by other AGC kinase family members: RSK and Akt (Mendoza et al.,
2011). These factors call for development of treatment strategies which can overcome
negative feedback loops and survival pathways, thereby increasing efficacy of rapamycin
as a potential therapeutic solution to many chronic diseases.
18
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Abstract (if available)
Abstract
Rapamycin is a potent immunosuppressive macrolide which binds to FK506 binding protein (FKBP12), the cytosolic receptor to rapamycin. The FKBP12-Rapamycin complex binds to and allosterically inhibits mammalian Target of Rapamycin (mTOR), thereby interfering with its function in a signaling pathway necessary for cell cycle progression from the late G₁ phase to S phase. Rapamycin, because of its ability to regulate cell growth and cell cycle progression, has been studied as a potential therapeutic solution for diseases characterized by dysregulation of the mTOR signaling pathway. Here we discuss the pharmacology of rapamycin and highlight findings of recent studies exploring its applications in aging, cancer therapy and metabolism.
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Raut, Anuja (author)
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Mechanism of action of rapamycin and its applications in aging, cancer therapy and metabolism
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