1. Inhibition of HIV-1 (AIDS) Using Rationally Designed Drugs
2. Effects of Chemical Carcinogens on DNA

The major research interests of this laboratory are concerned with (1) chemical aspects of genetic toxicology and (2) a program of synthesis aimed at rationally designed drugs to inhibit viral enzymes associated with HIV-1 (AIDS).

Our approach to studies in genetic toxicology involves the synthesis (automated) of DNA having chemical lesions that arise physiologically from carcinogenic substances or radiation. The chief objective is to examine the mutation spectrum associated with these lesions. This is investigated both by in vitro and in vivo studies with DNA polymerases and repair enzymes. In our work, we have examined lesions associated with acrolein, carcinogenic amines, and oxidation products of both deoxyguanosine and deoxyadenosine, products that are associated with both radiation damage and asbestos-mediated transformations. In the course of this work, the oxidation chemistry of the carcinogenic amine adducts has shown that at physiological pH a slow, oxygen-induced degradation takes place, producing an array of intermediates derived from the initial adduct. The role of these secondary lesions in carcinogenesis is under investigation.

In addition, new protecting groups for the synthesis of DNA containing these lesions have had to be designed to accommodate the extreme sensitivity of a number of these adducts to the normal chemistry of DNA synthesis.

In the area of AIDS research, we have been successful in designing new substances that will interfere with the reverse transcriptase responsible for the viral DNA/RNA replication. In addition, a search to find compounds that inhibit the viral protease, an enzyme that is responsible for correctly cleaving the polyprotein from the translation step into the required viral polypeptides, has been successful. Both of these areas are under active investigation.

A third area of research involves the use of polyhalo-olefins as new synthetic agents for the synthesis of natural products. This has led to a new group of phenol-protecting agents useful in a variety of ways, including the deactivation of aromatic rings towards electrophiles and a new method for the synthesis of aromatic acetylenes.

Publications (1994-2000)

Johnson, F., Huang, C-Y., and Yu, P-L. (1994). Synthetic and oxidative studies of 8-arylamino-2'-deoxyguanosine and -guanosine derivatives. Environ. Health Perspec. 102: 143-149.

Tchou, J., Bodehupi, V., Shibutani, S., Antoshechkin, I., Miller, J., Grollman, A.P., and Johnson, F. (1994). Substrate specificity of Fpg protein. Recognition and cleavage of oxidatively damaged DNA. J. Biol. Chem. 269: 15318-15324.

Gandolfi, C.A., Beggiolin, C, Menta, E., Palumbo, M., Sissi, C., and Johnson, F. (l995). Chromophore-modified anti-tumor anthracenediones: synthesis, DNA binding, and cytotoxic activity of 1,4-Bis [(aminoalkyl) amino]benzzo [g]phthalazine-5-1 0,diones. J. Med. Chem. 38: 526-536.

Zhang, W., Rieger, R., Iden, C., and Johnson, F. (1995). Synthesis of 3,N⁴-etheno, 3,N⁴-ethano, and 3-(2-hydroxyethyl) derivatives of -2'-deoxycytidine and their incorporation into oligomeric DNA. Chem. Res. Toxicol. 8: 148-156.

Maruenda, H. and Johnson, F. (1995). Design and synthesis of novel inhibitors of HIV-1 reverse transcriptase. J. Med. Chem. 38: 2145-2151.

Gelfand, C.A., Plum G.E., Grollman, A.P., Johnson, F. and Breslauer K.J. (1996) The impact of a bistrand abasic lesion on DNA duplex properties. Biopolymers 38, 439-445.

Bulychev, N.V., Varaprasad, C.V., Dorman, G., Miller, J.H., Eisenberg, M., Grollman, A.P., and Johnson, F. (1996) Substrate specificity of Escherichia coli MutY protein. Biochemistry 35, 13147-13156.

Cullinan, D., Johnson, F., Grollman, A.P., Eisenberg, M., and de los Santos C. (1997) Solution structure of a DNA duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyguanosine. Biochemistry 36, 11933-11943.

Johnson, F., Dorman, G., Rieger, R.A., Marumoto, R., Iden, C.R., and Bonala, R. (1998) Synthesis of enzymatically noncleavable carbocyclic nucleosides for DNA-N-glycosylase studies. Chemical Research in Toxicology 11, 193-202.

Gelfand, C.A., Plum, G.E., Grollman, A.P., Johnson, F., and Breslauer K.J. (1998) Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence. Biochemistry 37, 7321-7327.

Gelfand, C.A., Plum, G.E., Grollman, A.P., Johnson, F., and Breslauer K.J. (1998) The impact of an exocyclic cytosine adduct on DNA duplex properties: significant thermodynamic consequences despite modest lesion-induced structural alterations. Biochemistry 37, 12507-12512.

Khullar, S., Varaprasad, C.V. and Johnson, F. (1999) Postsynthetic generation of a major acrolein adduct of 2'-deoxyguanosine in oligomeric DNA. J. Med. Chem. 42, 947-950.

Rieger, R.A., Iden, C.R., Gonikberg, E., and Johnson, F. (1999) 8-Amino-2'-deoxyguanosine incorporation into oligomeric DNA. Nucleosides & Nucleotides 18, 73-88.

Torres, M.C., Varaprasad, C.V., Johnson, F., and Iden, C.R. (1999) Formation of s-triazines during aerial oxidation of 8-oxo-7,8-dihydro-2'-deoxyguanosine in concentrated ammonia. Carcinogenesis 20, 167-172.

Shibutani, S., Fernandes, A., Suzuki, N., Zhou, L., Johnson, F., and Grollman A.P. (1999) Mutagenesis of the N-(deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenylimidazo[4, 5-b]pyridine DNA adduct in mammalian cells. Sequence context effects. J. Biol. Chem. 274, 27433-27438.

Tan, X., Suzuki, N., Johnson, F., Grollman, A.P., and Shibutani S. (1999) Mutagenic properties of the 8-amino-2'-deoxyguanosine DNA adduct in mammalian cells. Nucleic Acids Research 27, 2310-2314.

Bonala, R.R., Rieger, R.A., Shibutani, S., Grollman, A.P., Iden, C.R., and Johnson F. (1999) 3,N(4)-ethano-2'-deoxycytidine: chemistry of incorporation into oligomeric DNA and reassessment of miscoding potential. Nucleic Acids Research 27, 4725-4733.

Moriya, M., Pandya, G.A., Johnson, F., and Grollman, A.P. (1999) Cellular response to exocyclic DNA adducts. IARC Scientific Publications (Lyon). (150):263-270.

Miller, H., Prasad, R., Wilson, S.H., Johnson, F., and Grollman, A.P. (2000) 8-oxodGTP incorporation by DNA polymerase beta is modified by active-site residue Asn279. Biochemistry 39, 1029-1033.

Budil, D.E., Kolaczkowski, S.V., Perry, A., Varaprasad, C., Johnson, F., and Strauss, P.R. (2000) Dynamics and ordering in a spin-labeled oligonucleotide observed by 220 GHz electron paramagnetic resonance. Biophysical Journal 78, 430-438.

Cullinan, D., Johnson, F., and de los Santos, C. (2000) Solution structure of an 11-mer duplex containing the 3, N(4)-ethenocytosine adduct opposite 2'-deoxycytidine: implications for the recognition of exocyclic lesions by DNA glycosylases. J. Molec. Biol. 296, 851-861.

De Riccardis, F. and Johnson, F. (2000) Chemical synthesis of cross-linked purine nucleosides. Organic Letters 2, 293-295.