X-ray Crystallographic Studies of Candida albicans Dihydrofolate Reductase

Whitlow, Marc; Howard, Andrew; Stewart, David B.; Hardman, Karl D.; Kuyper, Lee F.; Baccanari, David P.; Fling, Mary E.; Tansik, Robert L.

doi:10.1074/jbc.272.48.30289

Cited by 58 publications

(27 citation statements)

References 43 publications

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“…The overall pattern of interactions of the diaminopyrimidine moiety of all antifolates with invariant residues in DHFR complexes reported in the PDB is preserved. As observed in DHFR complexes with tight binding ligands [35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50], a hydrogen bonding network that involves structural water, the conserved residues (hDHFR numbering) Thr-136, Glu-30, Trp-24, and N1, N2-amine and N8 of inhibitors is maintained ( figure 5). Similarly, the inhibitor 4-amino group makes hydrogen bonding contacts with the conserved residues Ile-7, Val113 and Tyr-121.…”

Section: Dhfr Structures Reported In Pdbmentioning

confidence: 78%

Structural characteristics of antifolate dihydrofolate reductase enzyme interactions

Cody¹,

Schwalbe²

2006

Crystallography Reviews

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The ubiquitous enzyme dihydrofolate reductase (DHFR) is responsible for the reduction of 5,6-dihydrofolate to 5,6,7,8-tetrahydrofolate in an NADPH-dependent manner. It is also a key pharmacological target for the treatment of cancer, as well as bacterial and opportunistic pathogenic infections. Interest in the design of potent and selective antifolate inhibitors has made DHFR one of the most studied enzymes, in particular its structural and biochemical properties. This review surveys more than 129 DHFR solution and crystal structures currently (02/07) reported in the Protein Data Bank representing 15 species of enzyme. Comparison of these DHFR sequences shows that while there is a high sequence homology among vertebrate species (75-95%), there is only about 30% homology between vertebrate and bacterial species. Despite the highly conserved nature of the ligand and cofactor binding sites, DHFR can bind a wide range of compounds that can have a high degree of flexibility. The enzyme itself can also undergo ligand-induced conformational changes that reflect its catalytic mechanism of action. Mechanistic questions can now be addressed with the structural data available for atomic resolution enzyme complexes as well as from neutron diffraction data that have recently become available. These data provide new insight into the design of novel inhibitors that can target specific species with high selectivity of binding.

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Section: Dhfr Structures Reported In Pdbmentioning

confidence: 78%

Structural characteristics of antifolate dihydrofolate reductase enzyme interactions

Cody¹,

Schwalbe²

2006

Crystallography Reviews

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“…The reaction is NADPH-dependent [38]. Whitlow et al [39,40] studied the binding modes of several quinazolinediamines (structural type XVIII) to the dihydrofolate reductase. They are listed in Table 11.…”

Section: Example 8: Quinazolinediamine Analogs As Dihydrofolate Reducmentioning

confidence: 99%

Outliers in SAR and QSAR: Is unusual binding mode a possible source of outliers?

Kim

2007

J Comput Aided Mol Des

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A lead optimization is usually carried out by structure-activity relationship (SAR) and/or quantitative structure-activity relationship (QSAR) studies. One of the assumptions in SAR and QSAR studies is that similar analogs bind to the same binding site in a similar binding mode. One often observes that there are outliers, especially in QSAR. However, most QSAR studies are carried out focusing their attention to the development of QSAR and leave the outliers without much attention. We searched a number of ligand-bound X-ray crystal structures from the protein structure database to find evidences that could indicate a possible source of outliers in SAR or QSAR. Our results show that unusual binding mode could be a source of outliers.

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“…Diffraction data were collected at Brookhaven National Laboratory, beam line X25, and processed using the program HKL2000. The structure was determined by molecular replacement, using a structure of C. albicans DHFR (32), and refined using the program Refmac5 (19). Synthesis and characterization of compounds 1 to 3 and their analogs have been described previously (16,21).…”

Section: Cryptosporidium Hominis and T Gondii Dhfr-ts Preparation Dmentioning

confidence: 99%

Towards New Antifolates Targeting Eukaryotic Opportunistic Infections

Liu

Bolstad

et al. 2009

Eukaryot Cell

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Trimethoprim, an antifolate commonly prescribed in combination with sulfamethoxazole, potently inhibits several prokaryotic species of dihydrofolate reductase (DHFR). However, several eukaryotic pathogenic organisms are resistant to trimethoprim, preventing its effective use as a therapeutic for those infections. We have been building a program to reengineer trimethoprim to more potently and selectively inhibit eukaryotic species of DHFR as a viable strategy for new drug discovery targeting several opportunistic pathogens. We have developed a series of compounds that exhibit potent and selective inhibition of DHFR from the parasitic protozoa Cryptosporidium and Toxoplasma as well as the fungus Candida glabrata. A comparison of the structures of DHFR from the fungal species Candida glabrata and Pneumocystis suggests that the compounds may also potently inhibit Pneumocystis DHFR.Reduced folate cofactors such as tetrahydrofolate are required for critical cellular functions, such as the production of dTMP, several amino acids, and purines. Dihydrofolate reductase (DHFR), the sole source of tetrahydrofolate, is one of several enzymes in the folate biosynthetic pathway. DHFR has been a recognized and validated drug target since the 1960s, with the discovery of methotrexate (5). Fortunately, since pathogenic and human forms of DHFR exhibit several critical sequence differences, it has also been possible to develop speciesselective antifolates for several infectious diseases, including malaria, toxoplasmosis, and urinary tract infections. Trimethoprim (TMP) (Fig. 1) is a commonly administered antifolate, primarily in combination with sulfamethoxazole (TMP-SMZ), which inhibits dihydropteroate synthase (DHPS), another enzyme in the folate pathway (14). TMP-SMZ is most effective against prokaryotic pathogens. However, it is also recognized as first-line therapy in treating and preventing the common eukaryotic opportunistic pathogen Pneumocystis jirovecii, which causes life-threatening pneumonia in immunocompromised patients (20).Interestingly, while TMP inhibits bacterial species of DHFR at concentrations in the low nanomolar range, it inhibits many eukaryotic species of the enzyme at concentrations in the micromolar range, resulting in 3 orders of magnitude lower potency. Even the use of TMP-SMZ as a prophylactic agent against pneumocystis relies heavily on the sulfa component (31) and only on relatively weak binding between TMP and P. jirovecii DHFR (6,18). In fact, studies have reported that mutations conferring resistance to TMP-SMZ arise in DHPS, not in DHFR (17, 28). In contrast, when the DHFR inhibitor pyrimethamine, which is four times more potent than TMP (18), is used in combination with sulfadiazine against pneumocystis, mutations arise in DHFR as well as DHPS (20). A logical conclusion of these studies is that the low potency of TMP against P. jirovecii DHFR is preventing it from reaching its full potential as an effective therapy for this eukaryotic opportunistic pathogen. In contrast, high-affinity DHFR inhib...

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X-ray Crystallographic Studies of Candida albicans Dihydrofolate Reductase

Cited by 58 publications

References 43 publications

Structural characteristics of antifolate dihydrofolate reductase enzyme interactions

Structural characteristics of antifolate dihydrofolate reductase enzyme interactions

Outliers in SAR and QSAR: Is unusual binding mode a possible source of outliers?

Towards New Antifolates Targeting Eukaryotic Opportunistic Infections

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