RUcore: Rutgers University Community Repository
Construction of the 3D structure of the mTOR kinase-domain and discovery of novel mTOR inhibitors
Descriptive
TitleInfo
Title
Construction of the 3D structure of the mTOR kinase-domain and discovery of novel mTOR inhibitors
Name
(type = personal)
NamePart
(type = family)
Tobak
NamePart
(type = given)
Anne Theresa
DisplayForm
Anne Tobak
Role
RoleTerm
(authority = RUETD)
author
Name
(type = personal)
NamePart
(type = family)
Olson
NamePart
(type = given)
Wilma
Affiliation
Advisory Committee
DisplayForm
Wilma Olson
Role
RoleTerm
(authority = RULIB)
chair
Name
(type = personal)
NamePart
(type = family)
Welsh
NamePart
(type = given)
William
Affiliation
Advisory Committee
DisplayForm
William Welsh
Role
RoleTerm
(authority = RULIB)
internal member
Name
(type = personal)
NamePart
(type = family)
Ehrlich
NamePart
(type = given)
Paul
Affiliation
Advisory Committee
DisplayForm
Paul Ehrlich
Role
RoleTerm
(authority = RULIB)
internal member
Name
(type = personal)
NamePart
(type = family)
Kong
NamePart
(type = given)
Tony
Affiliation
Advisory Committee
DisplayForm
Tony Kong
Role
RoleTerm
(authority = RULIB)
outside member
Name
(type = personal)
NamePart
(type = family)
Zheng
NamePart
(type = given)
Steven
Affiliation
Advisory Committee
DisplayForm
Steven Zheng
Role
RoleTerm
(authority = RULIB)
outside member
Name
(type = corporate)
NamePart
Rutgers University
Role
RoleTerm
(authority = RULIB)
degree grantor
Name
(type = corporate)
NamePart
Graduate School-New Brunswick
Role
RoleTerm
(authority = RULIB)
school
TypeOfResource
Text
Genre
(authority = marcgt)
theses
OriginInfo
DateCreated
(qualifier = exact)
2007
DateOther
(qualifier = exact);
(type = degree)
2007
Language
LanguageTerm
(authority = ISO 639-3:2007);
(type = text)
English
PhysicalDescription
Form
(authority = marcform)
electronic
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
xi, 95 pages
Abstract
(type = abstract)
The mammalian target of rapamycin (mTOR) is a serine/threonine kinase involved in the regulation of protein translation and cell proliferation. Based on signals received from nutrition, growth factors, and insulin, mTOR controls cell growth accordingly and is therefore a key target for anticancer therapeutics through its inhibition. Two regions of interest are the FRB domain, where mTOR's natural ligand rapamycin binds when in complex with FKBP12, and the ATP-binding site located within the kinase-domain. Because cancer cells have shown resistance to rapamycin's inhibitory effects, the kinase portion of the protein has become an attractive target for the design of novel inhibitors. Current kinase-domain inhibitors generally lack stability and specificity, mainly due to the absence of a high-resolution crystal structure for mTOR. Therefore, an urgent need exists for more insight into mTOR's three-dimensional (3D) structure as well as improved kinase-domain targeted therapeutics.
The purpose of this study was to construct a 3D structural model of the mTOR kinase-domain using homology modeling techniques, which would then facilitate the discovery of novel compounds with increased inhibitory effects. After constructing the mTOR structural model, we employed pharmaceutical drug design approaches to virtually 'dock' known mTOR kinase inhibitors into the putative ligand binding pocket of the kinase domain. Using the key structural features of mTOR inhibitors LY294002 and wortmannin, two pharmacophores were created and later employed as queries in our in silico search of commercially available compounds. This systematic procedure yielded 14 novel compounds, 7 from each pharmacophore search, which were purchased in sufficient quantities for initial biological evaluation. Western blot experimental results revealed that 4 of the 14 test compounds show mTOR inhibition in vitro at 10uM concentration.
Analysis of the lead compounds' binding interactions with mTOR identifies several active site residues potentially responsible for ligand binding affinity. In order for a small molecule to possess mTOR inhibitory activity, it it must establish interactions with Leu2186, Ile2237, and Ile2356. In addition, it must also make contact with Lys2166 and/or Val2240. Our homology model, in conjunction with these findings, will facilitate the continued rational (computer-aided) design of potent and selective mTOR kinase domain inhibitors.
The purpose of this study was to construct a 3D structural model of the mTOR kinase-domain using homology modeling techniques, which would then facilitate the discovery of novel compounds with increased inhibitory effects. After constructing the mTOR structural model, we employed pharmaceutical drug design approaches to virtually 'dock' known mTOR kinase inhibitors into the putative ligand binding pocket of the kinase domain. Using the key structural features of mTOR inhibitors LY294002 and wortmannin, two pharmacophores were created and later employed as queries in our in silico search of commercially available compounds. This systematic procedure yielded 14 novel compounds, 7 from each pharmacophore search, which were purchased in sufficient quantities for initial biological evaluation. Western blot experimental results revealed that 4 of the 14 test compounds show mTOR inhibition in vitro at 10uM concentration.
Analysis of the lead compounds' binding interactions with mTOR identifies several active site residues potentially responsible for ligand binding affinity. In order for a small molecule to possess mTOR inhibitory activity, it it must establish interactions with Leu2186, Ile2237, and Ile2356. In addition, it must also make contact with Lys2166 and/or Val2240. Our homology model, in conjunction with these findings, will facilitate the continued rational (computer-aided) design of potent and selective mTOR kinase domain inhibitors.
Note
(type = degree)
Ph.D.
Note
(type = bibliography)
Includes bibliographical references (p. 86-94).
Subject
(authority = RUETD)
Topic
Computational Biology and Molecular Biophysics
Subject
(authority = ETD-LCSH)
Topic
Rapamycin
Subject
(authority = ETD-LCSH)
Topic
Macrolide antibiotics
RelatedItem
(type = host)
TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
Identifier
(type = local)
rucore19991600001
Identifier
(type = hdl)
http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.13836
Identifier
ETD_138
Identifier
(type = doi)
doi:10.7282/T3DN45HP
Location
PhysicalLocation
(authority = marcorg);
(displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Genre
(authority = ExL-Esploro)
ETD doctoral
Back to the top
Rights
RightsDeclaration
(AUTHORITY = GS);
(ID = rulibRdec0006)
The author owns the copyright to this work.
Copyright
Status
Copyright protected
Availability
Status
Open
AssociatedEntity
(AUTHORITY = rulib);
(ID = 1)
Name
Anne Tobak
Role
Copyright holder
Affiliation
Rutgers University. Graduate School-New Brunswick
RightsEvent
(AUTHORITY = rulib);
(ID = 1)
Type
Permission or license
Detail
Non-exclusive ETD license
AssociatedObject
(AUTHORITY = rulib);
(ID = 1)
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
Back to the top
Technical
Format
(TYPE = mime);
(VERSION = )
application/x-tar
FileSize
(UNIT = bytes)
3633152
Checksum
(METHOD = SHA1)
bfb148bebce2af0cb82651a52b7ec41b9483ec4d
ContentModel
ETD
CompressionScheme
other
OperatingSystem
(VERSION = 5.1)
windows xp
Format
(TYPE = mime);
(VERSION = NULL)
application/x-tar
Back to the top
Statistical Profile