Structure-Based Design of Lipophilic Quinazoline Inhibitors of Thymidylate Synthase

Abstract

To develop novel lipophilic thymidylate synthase (TS) inhibitors, the X-ray structure of Escherichia coli TS in ternary complex with FdUMP and the inhibitor 10-propargyl-5,8-dideazafolic acid (CB3717) was used as a basis for structure-based design. A total of 31 novel lipophilic TS inhibitors, lacking a glutamate residue, were synthesized; 26 of them had in common a N-((3,4-dihydro-2-methyl-6-quinazolinyl)methyl)-N-prop-2-ynylaniline+ ++ structure in which the aniline was appropriately substituted with simple lipophilic substituents either in position 3 or 4, or in both. Compounds were tested for their inhibition of E. coli TS and human TS and also for their inhibition of the growth in tissue culture of a murine leukemia, a human leukemia, and a thymidine kinase-deficient human adenocarcinoma. The crystal structures of five inhibitors complexed with E. coli TS were determined. Five main conclusions are drawn from this study. (i) A 3-substituent such as CF(3), iodo, or ethynyl enhances binding by up to 1 order of magnitude and in the case of CF(3) was proven to fill a nearby pocket in the enzyme. (ii) A simple strongly electron-withdrawing substituent such as NO(2) or CF(3)SO(2) in the 4-position enhances binding by 2 orders of magnitude; it is hypothesized that the transannular dipole so induced interacts favorably with the protein. (iii) Attempts to combine the enhancements of i and ii in the same molecule were generally unsuccessful (iv) A 4-C(6)H(5)SO(2) substituent provided both electron withdrawal and a van der Waal's interaction of the phenyl group with a hydrophobic surface at the mouth of the active site. The inhibition (K(is) = 12 nM) of human TS by this compound, 7n, showed that C(6)H(5)SO(2) provided virtually as much binding affinity as the CO-glutamate which it had replaced. (v) The series of compounds were poorly water soluble, and also the potent TS inhibition shown by several of them did not translate into good cytotoxicity. Compounds with large cyclic groups linked to position 4 by an SO or SO(2) group did, however, have IC(50)'s in the range 1-5 microM. Of these, 4-(N-((3,4-dihydro-2-methyl-6-quinazolinyl)methyl)-N-prop-2-ynylamino )phenyl phenyl sulfone, 7n, had IC(50)'s of about 1 microM and was chosen for further elaboration.

Testing a Flexible-receptor Docking Algorithm in a Model Binding Site

“…37,39 The conformations of three flexible parts of the enzyme (composed of residue Phe176, residues Val77 through Trp83, and residues Asp169, Tyr209, and Pro261 through Ile264, respectively), observed in three different crystal structures, were recombined to generate 18 different receptor structures. The experimental structures used were that of a binary complex with 2 0 -deoxyuridine-5 0 -monphosphate (dUMP, PDB entry 1BID), which we consider an "apo" structure, and two ternary complexes, one with the antifolate BW1843 (PDB entry 1SYN) and a second with the antifolate methotrexate (PDB entry 1AXW).…”

Synthesis and Structure–Activity Relationships of the First Ferrocenyl-Aryl-Hydantoin Derivatives of the Nonsteroidal Antiandrogen Nilutamide

“…Synthesis. Compounds 7, 8,42 and 1125 were prepared following the literature procedures.4-(4,4-Dimethyl-2,5-dioxo-3-ferrocenylmethyl-1-imidazolidinyl)-2-trifluoromethylbenzonitrile (1).Aqueous HCl solution (2 N, 3.2 mL) was added to a solution of imine 3 (0.390 g, 0.79 mmol) in methanol (20 mL). The reaction mixture was heated under reflux for 2 h. The solution was then cooled to room temperature and was poured into cold water (100 mL).…”

Coolade. A Low‐Foaming Surfactant for Organic Synthesis in Water

“…Spectroscopic data matched that reported in the literature. [15] R f = 0.30 (EtOAc/hexanes 40:60). 34,129.68,118.69,112.69,65.26,45.90,: Synthesis was performed according to the procedure described in section 4.1 (procedure B; Supporting Information) using THF cosolvent (20 vol %) and 5equiv of NaBH 4 to give 8 as at an oil.…”