DNA polymerase mechanisms of base selection and catalysis are explored using a tool-kit of dNTP analogs that have bisphosphonates in place of the , ? -bridge oxygen. These analogs are Pol substrates that have leaving groups with widely dispirate electronic properties, pKa4 values ranging from 7.8 to 12.3, enabling us to use presteady state kinetic measurements to determine the selection of right and wrong deoxynucleotides occuring at the chemical transition state. Especially important members of the toolkit include all four individually synthesized (R)- and (S)- , ? -CHF and , ? -CHCI diastereomers. Our recent observation of a pronounced stereoselection for (R)-CHF in Pol , involving an electrostatic interaction of F with Arg183, unique to family X pols such as Pol , serves as the impetus for a """"""""scaffold"""""""" strategy for the selective inhibition of Pol relative to the cellular replication Pols ?, ?, ?, and mitochondrial Pol ?.
In Aim 1, Study """"""""a"""""""" explores stereoselection in the cellular and mitochondrial pols. Studies """"""""b"""""""" and """"""""c"""""""" make use of the entire toolkit to explore chemistry vs. conformational change as a rate-limiting step In the transition-state of family X Pol ?, family Y error-prone Pol r , and for a series of cancer-associated Pol variants. In Study """"""""d"""""""", newly synthesized bisphosphonate PPI analog leaving groups are used to reverse the polymerase reaction to attain a free energy reaction profile for Pol . Study """"""""e"""""""" addresses an entirely new area of polymerase mechanistics, namely the use of EPR and ENDOR to elucidate the structure of the metal coordination site and Its role in fidelity.
Aim 2, containing three interrelated studies, spells out a detailed scaffold strategy for the design and synthesis of selective Inhibitors of Pol and BER by the dual targeting of the dNTP binding site and active site Arg183 (Study """"""""a""""""""). In Study """"""""b"""""""", we develop a new approach, using pamoic acid analogs, to inhibit BER by selectively interfering with the Pol -assocated lyase. In Study """"""""c"""""""", we take an important step along the path toward translation, by evaluating the ability of cell permeabilized scaffold compounds to inhibit cultured cancer cells.

Public Health Relevance

The proposed research will apply innovative experimental strategies to elucidate the mechanisms of fidelity occurring in the active site of DNA polymerase. We will focus on studies of human DNA polymerase p, an exceptionally important repair enzyme. Mutants of Pol have been associated with numerous different human cancers. We have devised a logical strategy using a new class of polymerase substrate analogs to selectively inhibit Pol in cell free systems and in cultured cancer cells.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Program--Cooperative Agreements (U19)
Project #
5U19CA177547-02
Application #
8754983
Study Section
Special Emphasis Panel (ZCA1)
Project Start
Project End
Budget Start
2014-09-01
Budget End
2015-08-31
Support Year
2
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of Southern California
Department
Type
DUNS #
City
Los Angeles
State
CA
Country
United States
Zip Code
90089
Oertell, Keriann; Kashemirov, Boris A; Negahbani, Amirsoheil et al. (2018) Probing DNA Base-Dependent Leaving Group Kinetic Effects on the DNA Polymerase Transition State. Biochemistry 57:3925-3933
Alnajjar, Khadijeh S; Garcia-Barboza, Beatriz; Negahbani, Amirsoheil et al. (2017) A Change in the Rate-Determining Step of Polymerization by the K289M DNA Polymerase ? Cancer-Associated Variant. Biochemistry 56:2096-2105
Alnajjar, Khadijeh S; Negahbani, Amirsoheil; Nakhjiri, Maryam et al. (2017) DNA Polymerase ? Cancer-Associated Variant I260M Exhibits Nonspecific Selectivity toward the ?-? Bridging Group of the Incoming dNTP. Biochemistry 56:5449-5456
Ni, Feng; Kung, Alvin; Duan, Yankun et al. (2017) Remarkably Stereospecific Utilization of ATP ?,?-Halomethylene Analogues by Protein Kinases. J Am Chem Soc 139:7701-7704
Petruska, John; Goodman, Myron F (2017) Relating DNA base-pairing in aqueous media to DNA polymerase fidelity. Nat Rev Chem 1:
Yoon, Hanwool; Warshel, Arieh (2017) Simulating the fidelity and the three Mg mechanism of pol ? and clarifying the validity of transition state theory in enzyme catalysis. Proteins 85:1446-1453
Maximoff, Sergey N; Kamerlin, Shina Caroline Lynn; Florián, Jan (2017) DNA Polymerase ? Active Site Favors a Mutagenic Mispair between the Enol Form of Deoxyguanosine Triphosphate Substrate and the Keto Form of Thymidine Template: A Free Energy Perturbation Study. J Phys Chem B 121:7813-7822
Je?ábek, Petr; Florián, Jan; Martínek, Václav (2016) Lipid molecules can induce an opening of membrane-facing tunnels in cytochrome P450 1A2. Phys Chem Chem Phys 18:30344-30356
Oertell, Keriann; Harcourt, Emily M; Mohsen, Michael G et al. (2016) Kinetic selection vs. free energy of DNA base pairing in control of polymerase fidelity. Proc Natl Acad Sci U S A 113:E2277-85
Yoon, Hanwool; Warshel, Arieh (2016) The control of the discrimination between dNTP and rNTP in DNA and RNA polymerase. Proteins 84:1616-1624

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