Chemistry and Biochemistry

Matt A. Peterson

Matt Peterson

Office: C463 BNSN
Office Phone: 801-422-6843
Lab Room: C454A and C470 BNSN
Lab Phone: 801-422-5188
Office Hours


BS (Chemistry), Utah State University (1987)

BS (Biology), Utah State University (1987)

Ph.D., University of Arizona (1992)

NIH Postdoctoral Fellow, Colorado State University (1993-94)


Research in our group focuses on the chemical synthesis and biological evaluation of potential antitumor and/or antiviral compounds. Modification of naturally occurring nucleosides is a unifying feature in our research. Current interests can be broken down into three areas: (1) Synthesis and evaluation of nucleoside-based enediynes (e.g., uracil-fused and uracil-linked enediynes I and II; and adenosine mimic III); (2) Synthesis and evaluation of transition-state analogue inhibitors of key enzymes involved in the pyrimidine-nucleoside manifold (e.g., potential cytidine triphosphate synthetase and cytidine deaminase inhibitors typified by structure IV), and (3) Synthesis and evaluation of inhibitors of HIV integrase.

Nucleoside-Based Enediynes

research graphicNaturally occurring enediynes are among the most potent antitumor compounds currently known. Unfortunately, selectivity levels are low, and general cytotoxicities are a major problem. This significantly limits their use as clinically useful anticancer drugs, and at the present time no naturally occurring enediyne has been approved for use in chemotherapy. We have been intrigued by the possibility that nucleoside-fused or nucleoside-linked enediynes might selectively target rapidly dividing tumors due to the tumor's enhanced need for building blocks for DNA or RNA. The enhanced uptake of nucleosides by rapidly dividing tumors could potentially lead to a more selective targeting of tumor cells and thereby reduce problems associated with general cytotoxicity. We have successfully synthesized numerous analogues of compounds I""III, and a majority of the compounds tested demonstrate promising activities (IC50 values in the low μM range) against murine models of leukemia, mammary carcinoma, and several lines of human T-lymphocytes. Analogues of compound III have been shown to cleave supercoiled DNA (see slide show).

Transition Sate Analogue Inhibitors

Cytidine triphosphate synthetase (CTP synthetase; EC and cytidine deaminase (CDA; EC are two key enzymes involved in de novo synthesis and salvage pathways in pyrimidine biosynthesis. CTP synthetase catalyzes the conversion of uridine triphosphate (UTP) to CTP. This is the key step in the only de novo pathway for the biosynthesis of cytidine. CTP may be incorporated into RNA or undergo dephosphorylation to give cytidine diphosphate (CDP), a substrate for ribonucleotide reductase. The product of reduction (dCDP) is converted to dCTP which is incorporated into DNA. Salvage pathways for uridine include hydrolysis of cytidine and cytidine monophosphate. These hydrolyses are catalyzed by CDA and CMP deaminase respectively. The activity of CTP synthetase has been shown to correlate with cellular proliferation in malignant tissues and may be linked to the process of malignant transformation. High levels of CTP synthetase activity have been reported in several malignant tissues including rat hematoma, human renal cell carcinoma, Hodgkin's disease, non-Hodgkin lymphomas, and acute lymphoblastic leukemia. Efficient CTP synthetase inhibitors could act as potent antineoplastic agents in these and other forms of cancer. CDA has been implicated in the development of resistance to commonly used cytosine-based antitumor agents such as arabinosyl cytosine (araC), 5-azacytidine (AZA), and gemcitibine. Inibitors of CDA could potentiate the activities of these currently used antitumor agents by prolonging their lifetimes in vivo. Compounds IV mimic the transition states involved in the CTP synthetase-and CDA-catalyzed reactions and could act as competitive inhibitors of these important enzymes.

HIV Integrase Inhibitors

HIV integrase (IN) is one of three enzymes encoded for by HIV. IN is a 32 kDa protein consisting of three distinct domains (N-terminus, catalytic core, and C-terminus), and plays a key role in incorporating viral DNA into host DNA. This is accomplished via a three-step process referred to collectively as integration. The first step in integration involves cleavage of a GT dinucleotide from both 3'-ends of double stranded viral DNA and is called 3'-end processing. The 3'-end processed duplex next undergoes a concerted transesterification reaction with a phosphodiester linkage in host DNA, a process referred to as strand transfer. In the final step, the unmatched AC dinucleotides on both 5'-ends and associated gaps are repaired by a cellular enzyme. The first two steps, 3'-end processing and strand transfer, are catalyzed by IN. IN is a magnesium metalloenzyme, and an active site Mg2+ is involved in both 3'-end processing and strand transfer. Although IN was identified as a promising antiviral target over a decade ago, only recently has a viable candidate for clinical inhibition of IN been discovered (the Shionogi/GlaxoSmithKline compound S-1360 is currently undergoing phase II clinical trials). The relentless emergence of drug-resistant HIV strains demands continual addition of antiviral compounds to our arsenal of chemotherapeutic agents. We have recently embarked on a drug discovery program aimed at discovering inhibitors of HIV integrase. We utilize state-of-the-art molecular modeling software (FlexX and CombiFlexX, Sybyl 6.9, Tripos, Inc.) to perform high-throughput screening of vast (> 50,000) compound libraries in order to identify promising leads for laboratory synthesis. Vast combinatorial libraries are docked at strategic points indicated by the X-ray crystal strucure of IN. Compounds identified by the docking studies share in common a nucleoside(tide) scaffold and should bind tightly to critical residues at or near the active site of IN. We will utilize our expertise in nucleoside chemistry to synthesize the most promising compounds indicated by the in silico high-throughput screen. The IN inhibitory activities of lead compounds will be determined in collaboration with expert enzymologists.

Student Projects

Projects are currently open in each of the areas listed above. Students gain valuable hands-on experience in all aspects of modern synthetic organic chemistry. This includes: (1) working with air and moisture sensitive compounds/reagents under inert atmosphere conditions, (2) designing and executing multi-step syntheses, (3) purifying reaction products to analytical purity (Flash, radial, and preparative chromatography; HPLC, recrystallization, distillation, etc.), (4) obtaining and interpreting 1H and 13C NMR and UV spectra, and (5) writing and preparing manuscripts for publication and/or presentation at scientific meetings. For students desiring experience that will prepare them for a career as a medicinal chemist in the pharmaceutical industry, research projects in this group provide excellent training.


J. R. Shelton, J. Balzarini, and M. A. Peterson* “Discovery of a nanomolar inhibitor of lung adenocarcinoma in vitro”  Bioorg. Med. Chem. Lett. 24, 5107–5110 (2014).

J. R. Shelton and M. A. Peterson*  “Efficient Synthesis of 5’-O-(N)-Carbamyl and Polycarbamyl Nucleosides”  Tetrahedron Lett. 54, 6882-6885 (2013).

J. Balzarini, F. Gago, W. Kulik, A. B. P. van Kuilenburg, A. Karlsson, M. A. Peterson, and M. J. Robins “Introduction of a Fluorine Atom at C3 of 3-Deazauridine Shifts Its Antimetabolic Activity from Inhibition of CTP Synthetase to Inhibition of Orotidylate Decarboxylase, an Early Event in the de Novo Pyrimidine Nucleotide Biosynthesis Pathway” J. Biol. Chem.287, 30444–30454 (2012).

J. R. Shelton, C. E. Cutler, M. S. Browning, J. Balzarini, and M. A. Peterson “Synthesis and SAR of 2ʹ,3ʹ-bis-O-substituted- N6,5'-bis-ureidoadenosine derivatives: Implications for prodrug delivery and mechanism of action.”  Bioorg. Med. Chem. Lett. 22, 6067–6071 (2012).

J. R. Shelton, M. Oliveira, C. E. Cutler, J. Balzarini, and M. A. Peterson  "Synthesis, SAR, and preliminary mechanistic evaluation of novel antiproliferative N6,5'-bis-ureido- and 5'-carbamoyl-N6-ureidoadenosine derivatives"  Bioorg. Med. Chem.  20, 1008–1019 (2012).

J. R. Shelton, Scott R. Burt, and M. A. Peterson "A Broad Spectrum Anticancer Nucleoside with Selective Toxicity Against Human Colon Cancer Cells in Vitro" Bioorg. Med. Chem. Lett.  21, 1484–1487 (2011).

M. A. Peterson, M. Oliveira, M. A. Christiansen, and C. E. Cutler “Preliminary SAR Analysis of Novel AntiproliferativeN6,5'-Bis-ureidoadenosine Derivatives” Bioorg. Med. Chem. Lett. 19, 6775–6779 (2009).

M. J. Robins, H. Yang, K. Miranda, M. A. Peterson, E. DeClercq, and J. Balzarini “Synthesis and Biological Evaluation of 3,3-Difluoropyridine-2,4(1H,3H)-dione and 3-Deaza-3-fluorouracil Base and Nucleoside Derivatives,”  J. Med. Chem. 523018–3027 (2009).

M. A. Peterson, M. Oliveira, M. A. Christiansen “Antiproliferative and Protein Kinase Binding Activities of Some N6,5'-Bis-ureido 5'-Amino-5'-deoxyadenosine Derivatives” Nucleos. Nucleot. Nucl. 28, 394–407 (2009).

M. J. Robins, V. K. Rajwanshi, K. Miranda, M. A Peterson, E. DeClercq, and J.  Balzarini, "Synthesis and Antiviral Evaluation of 6-[Alkyl-heteroaryl)furo[2,3-d]pyrimidin-2(3H)-one  Nucleosides and Analogues with Ethynyl, Ethenyl, and Ethyl Spacers at C6 of the Furopyrimidine Core" J. Med. Chem. 50, 3897–3905 (2007).

M. A. Peterson, P. Ke, H. Shi, B. R. McDougal, and E. W. Robinson, Jr. "Design, Synthesis, and Antiviral Evaluation of Some 3'-Carboxymethyl-3'-deoxyadenosine Derivatives" Nucleos. Nucleot. Nucl. 26, 499–519 (2007).

M. A Peterson, H. Shi,  P. Ke "A Simple and Efficient Biphasic Method for the Preparation of 4-Nitrophenyl N-Methyl- and N-Alkylcarbamates" Tetrahedron Lett.  47, 3405–3407 (2006).

M. J. Robins, K. Miranda, V. K.  Rajwanshi, M. A Peterson, G. Andrei, R. Snoeck,  E. De Clercq, and J.  Balzarini, "Synthesis and Biological Evaluation of 6-(Alkyn-1-yl) furo[2,3-d]pyrimidin-2(3H)-one Base and Nucleoside Derivatives" J. Med. Chem. 49, 391–398 (2006).

Z. Zhao, D. Gubler, J. Peacock, and M. A. Peterson, "Photoinduced Bergman Cycloaromatization of Imidazole-Fused Enediynes"Tetrahedron Lett. 46, 1373–1375 (2005).

Z. Zhao, Y. Peng, N.K. Dalley, J.F. Cannon, and M.A. Peterson, “Bergman Cycloaromatization of Imidazole-Fused Enediynes:  The Remarkable Effect of N-Aryl Substitution,” Tetrahedron Lett.  45, 3621-3624 (2004).

E. S. Kumarasinghe, M. A. Peterson, and M. J. Robins, “Synthesis of 5, 6-bis (alkyn-1-yl) Pyrimidines and Related Nucleosides,” Tetrahedron Lett.41, 8741-8745 (2000).