A 2.13 angstrom structure of E-coli dihydrofolate reductase bound to a novel competitive inhibitor reveals a new binding surface involving the M20 loop region

• Published in: Journal of medicinal chemistry Vol. 49; no. 24; pp. 6977 - 6986
• Main Authors: Summerfield, Rachael L., Daigle, Denis M., Mayer, Stanislas, Mallik, Debasis, Hughes, Donald W., Jackson, Sean G., Sulek, Margaret, Organ, Michael G., Brown, Eric D., Junop, Murray S.
• Format: Journal Article
• Language: English
• Published: WASHINGTON Amer Chemical Soc 30.11.2006
• Subjects: Chemistry, Medicinal; Life Sciences & Biomedicine; Pharmacology & Pharmacy; Science & Technology; MECHANISM; AFFINITY
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/jm060570v

Dihydrofolate reductase (DHFR) is a vital metabolic enzyme and thus a clinically prominent target in the design of antimetabolites. In this work, we identify 1,4-bis-{[N-(1-imino-1-guanidino-methyl)]sulfanylmethyl}-3,6-dimethyl-benzene (compound 1) as the correct structure of the previously reported DHFR inhibitor 1,4bis-{(iminothioureidomethyl)aminomethyl}-3,6-dimethyl-benzene (compound 2). The fact that compound 1 has an uncharacteristic structure for DHFR inhibitors, and an affinity (K-I of 11.5 nM) comparable to potent inhibitors such as methotrexate and trimethoprim, made this inhibitor of interest for further analysis. We have conducted a characterization of the primary interactions of compound 1 and DHFR using a combination of X-ray structure and SAR analysis. The crystal structure of E. coli DHFR in complex with compound 1 and NADPH reveals that one portion of this inhibitor exploits a unique binding surface, the M20 loop. The importance of this interface was further confirmed by SAR analysis and additional structural characterization.