Dihydrofolate active site

Figure 1.4 Left panel Space filing model of the structure of bacterial dihydrofolate reductase with methotrexate bound to the active site. Right panel Close-up view of the active site, illustrating the structural complementarity between the ligand (methotrexate) and the binding pocket. See color insert. Source Courtesy of Nesya Nevins.

Figure 1.5 Interactions of the dihydrofolate reductase active site with the inhibitor methotrexate (left) and the substrate dihydrofolate (right).

In a collaboration between the Abelson and Hecht labs [56b], a series of noncoded amino acids were introduced into dihydrofolate reductase (DHFR) to probe substrate binding and the requirement of an aspartic acid residue for catalytic competence. When aspartic acid analogs mono- or disubstituted at the )0-carbon were substituted for the active site aspartic acid residue, the mutant DHFRs were still able to catalyze the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate at 74 - 86 % of the wild-type rate. While hydride transfer from NADPH is not the rate-limiting step for the wild-type enzyme at physiological pH, a kinetic isotope experiment with NADPD indicated that hydride transfer had likely become the rate-limiting step for the mutant containing the )0,)0-dimethylaspartic acid. 

The carbon-donating cofactor for this reaction is N, N methylenetetrahydrofolate, which is converted to dihydrofolate. The reduced folate cofactor occupies an allosteric site on thymidylate synthetase, which allows for the covalent binding of 5-FdUMP to the active site of the enzyme. 

The expansion in the power of computers and theoretical methods has made it possible to investigate the mechanism of action of enzymes by combinations of quantum-mechanical and molecular-mechanical calculations. A study of two possible mechanisms for dihydrofolate reductase catalysis was consistent with indirect proton transfer from aspartate to N-5 of the pterin as has been suggested for many years by crystallographic evidence <2003PCB14036>. This conclusion is also consistent with the outcome of a study that directly measured the of the active site aspartate in the Lactobacillus casei enzyme <1999B8038>. Observations of chemical shifts of... 

BH4 is essential for the AAHs to carry out their respective catalytic reactions and, at least for PAH, the prereductive activation, which appears to produce dihydrobiopterin quinonoid (g-BH2) directly (20). After the PAH catalytic cycle an oxygen atom is incorporated into the cofactor, providing 4a-OH-BH4 which dissociates from the active site. In order to regenerate the functional tetrahydro form of BH4 pterin carbinolamine dehydratase catalyzes the dehydration of 4-OH-BH4 to g-BH2, which is reduced back to by dihydropteridine reductase (Scheme 2). g-BH2 can also be converted to 7,8-dihydropterin (BH2) which can be regenerated to BH4 by dihydrofolate reductase (DHFR). 

Fig, 1. Schematic drawing showing some of the interactions between the inhibitor, methotrexate, and the active site of dihydrofolate reductase from E. coli. 

Certain therapeutic effects can be attributed to the inhibition of specific enzymic reactions. The inhibition of cholinesterase (Section 1.06.3), orotidylate pyrophosphorylase (Section 1.06.5) and of dihydrofolate reductase (Section 1.06.6.3) have already been discussed. They illustrate two modes of action, chemical alteration of the enzyme and competition with a substrate for the active site. 

Figure 15-19 Drawings of the active site of E. coli dihydrofolate reductase showing the hound ligands NADP+ and tetrahydrofolate. Several key amino acid side chains are shown in the stereoscopic views on the right. The complete ribbon structures are on the left. (A) Closed form. (B) Open form into which substrates can enter and products can escape. From Sawaya and Kraut.381 Courtesy of Joseph Kraut. Molscript drawings (Kraulis, 1991).

Some of the structural properties which have been ascribed to DA receptors appear to deserve attention for their heuristic value, but painfully few should engender much confidence in their reality. A sobering lesson is available from analysis of complexes of dihydrofolate reductase (], 8). Methotrexate is a very close analog of folic acid and is a potent inhibitor of the enzyme, but it is now almost certain that these ligands bind in the enzyme active site in aspects differing by a rota-... 

The active-site-directed inhibition of enzymes has been an important research topic in pharmaceutical drug design (Sandler, 1980). An early development of anti-cancer agents involved inhibitions of dihydrofolate reductase and thymidylate synthetase. Search enzyme resource sites for kinetic data (turnover number, Km and Kt) of these two enzymes. 

As shown in Figure 10.10, tetrahydrobiopterin activates molecular oxygen by forming a peroxypterin that reacts with an iron atom in the active site, yielding Fe=0 that reacts with the amino acid substrate, and hydroxypterin, which then undergoes dehydration to yield dihydrobiopterin. Dihydrobiopterin is reduced back to tetrahydrobiopterin by dihydrobiopterin reductase dihydrofolate reductase (Section 10.3.3) does not have any significant activity toward dihydrobiopterin (Fitzpatrick, 1999). 

Covalent bonds are not as important in drug-receptor binding as noncovalent interactions. Alkylating agents in chemotherapy tend to react and form an immonium ion, which then alkylates proteins, preventing their normal participation in cell divisions. Baker s concept of active site directed irreversible inhibitors was well established by covalent formation of Baker s antifolate and dihydrofolate reductase (46). 

A typical run took minutes on a workstation and the predicted conformations agreed with those observed crystallographicallyin all cases. Meadows and Hajduk (102) used experimental constraints with a GA algorithm to dock biotin to stepavidin. Judson et al. (101) also reported docking of flexible molecules into the active sites of thermolysin, car-boxypeptidase, and dihydrofolate reductase. In 9 of the 10 cases examined, the GA found conformations within 1.6 A root-mean-square (rms) of the relaxed crystal conformation. 

Folate analogs such as trimethoprim have potent antibacterial and antiprotozoal activity. Trimethoprim binds lO -fold less tightly to mammalian dihydrofolate reductase than it does to reductases of susceptible microorganisms. Small differences in the active-site clefts of these enzymes account for its highly selective antimicrobial action. The combination of trimethoprim and sulfamethoxazole (an inhibitor of folate synthesis) is widely used to treat infections. 

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