The structure of Pneumocystis carinii dihydrofolate reductase to 1.9 å resolution

Champness, J.N.; Achari, Aniruddha; Ballantine, Stuart P.; Bryant, P.K.; Delves, C. J.; Stammers, D.K.

doi:10.1016/s0969-2126(94)00093-x

Cited by 91 publications

(134 citation statements)

References 22 publications

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“…2). These interactions are similar to those observed in complexes of DHFR with the natural substrates FAH 2 (44), MTX (10), TMP (16,38), and B. anthracis DHFR complexed with another TMP derivative (9). The dimethoxybenzyl moiety (a trimethoxybenzyl in TMP) is enclosed in a hydrophobic channel composed of residues Asn19, Asn20, Leu21, Asn47, Ala50, and Ile51 on one side and Leu29 on the other, with Phe96 contacting the underside (Fig.…”

Section: Structure Of B Anthracis Dhfr-rab1 Complexsupporting

confidence: 72%

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Crystal Structure of Bacillus anthracis Dihydrofolate Reductase with the Dihydrophthalazine-Based Trimethoprim Derivative RAB1 Provides a Structural Explanation of Potency and Selectivity

Bunce

Bourne²,

Berlin

et al. 2009

Antimicrob Agents Chemother

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Bacillus anthracis possesses an innate resistance to the antibiotic trimethoprim due to poor binding to dihydrofolate reductase (DHFR); currently, there are no commercial antibacterials that target this enzyme in B. anthracis. We have previously reported a series of dihydrophthalazine-based trimethoprim derivatives that are inhibitors for this target. In the present work, we have synthesized one compound (RAB1) displaying favorable 50% inhibitory concentration (54 nM) and MIC (<12.8 g/ml) values. RAB1 was cocrystallized with the B. anthracis DHFR in the space group P2 1 2 1 2 1 , and X-ray diffraction data were collected to a 2.3-Å resolution. Binding of RAB1 causes a conformational change of the side chain of Arg58 and Met37 to accommodate the dihydrophthalazine moiety. Unlike the natural substrate or trimethoprim, the dihydrophthalazine group provides a large hydrophobic anchor that embeds within the DHFR active site and accounts for its selective inhibitory activity against B. anthracis.

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Section: Structure Of B Anthracis Dhfr-rab1 Complexsupporting

confidence: 72%

“…This class includes the gram-positive organism B. anthracis (6), as well as Mycobacterium species (8). One proposal is that selectivity arises from the volume of the binding site (16,49). This is directly related to TMP resistance and generally correlates with more favorable K m values for FAH 2 (3,12,39,45), thus making it harder to displace.…”

mentioning

confidence: 99%

Crystal Structure of Bacillus anthracis Dihydrofolate Reductase with the Dihydrophthalazine-Based Trimethoprim Derivative RAB1 Provides a Structural Explanation of Potency and Selectivity

Bunce

Bourne²,

Berlin

et al. 2009

Antimicrob Agents Chemother

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“…The bridging angles for the two molecules of TMP observed in the binary complexes with the Q35S/N64F and the Q35K/N64F double variants of hDHFR differ significantly from each other and have torsion angles near the extremes of the cluster at 270°and either 50°or 120°(see Table S3b in the supplemental material) (17). These conformations also differ from those reported for the structure of the pcDHFR ternary complex with TMP and NADPH (18) and the binary TMP complex with native hDHFR (16).…”

Section: Resultsmentioning

confidence: 73%

“…The structures of the hDHFR complexes were solved by molecular replacement methods using the coordinates for human DHFR (PDB 1U72) (22) in the program Molref (23), while those for pcDHFR used the coordinates for pcDHFR (PDB 1DYR) (18). Inspection of the resulting difference electron density maps was performed using the program COOT (24) running on a Mac G5 workstation and revealed binary inhibitor complexes for hDHFR-OAAG324 and the Q35S/N64F double variant-OAAG324 and a ternary complex for the Q35K single variant hDHFR complex with NADPH and OAAG324, as well as an inhibitor complex for pcDHFR-TMP (see Table S1 in the supplemental material).…”

Section: Methodsmentioning

confidence: 99%

“…Additionally, the structure of the K37S/ F69N variant of pcDHFR as a ternary complex with TMP and NADPH is also reported. These data are compared with hDHFR TMP complexes (PDB 2w3a) (16) and with the TMP complexes with the Q35K/N64F and Q35S/N64F variants of hDHFR (17), as well as the previously determined structure of the pcDHFR ternary complex with NADPH and TMP (18).…”

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confidence: 99%

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Kinetic and Structural Analysis for Potent Antifolate Inhibition of Pneumocystis jirovecii, Pneumocystis carinii, and Human Dihydrofolate Reductases and Their Active-Site Variants

Cody

Pace

Queener

et al. 2013

Antimicrob Agents Chemother

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A major concern of immunocompromised patients, in particular those with AIDS, is susceptibility to infection caused by opportunistic pathogens such as Pneumocystis jirovecii, which is a leading cause of pneumonia in immunocompromised patients. We report the first kinetic and structural data for 2,4-diamino-6-[(2=,5=-dichloro anilino)methyl]pyrido[2,3-d]pyrimidine (OAAG324), a potent inhibitor of dihydrofolate reductase (DHFR) from P. jirovecii (pjDHFR), and also for trimethoprim (TMP) and methotrexate (MTX) with pjDHFR, Pneumocystis carinii DHFR (pcDHFR), and human DHFR (hDHFR). OAAG324 shows a 9.0-fold selectivity for pjDHFR (K i , 2.7 nM) compared to its selectivity for hDHFR (K i , 24.4 nM), whereas there is only a 2.3-fold selectivity for pcDHFR (K i , 6.3 nM). In order to understand the determinants of inhibitory potency, active-site mutations of pj-, pc-, and hDHFR were explored to make these enzymes more like each other. The most unexpected observations were that the variant pcDHFR forms with K37Q and K37Q/F69N mutations, which made the enzyme more like the human form, also made these enzymes more sensitive to the inhibitory activity of OAAG324, with K i values of 0.26 and 0.71 nM, respectively. A similar gain in sensitivity was also observed for the hDHFR N64F variant, which showed a lower K i value (0.58 nM) than native hDHFR, pcDHFR, or pjDHFR. Structural data are reported for complexes of OAAG324 with hDHFR and its Q35K and Q35S/N64F variants and for the complex of the K37S/F69N variant of pcDHFR with TMP. These results provide useful insight into the role of these residues in the optimization of highly selective inhibitors of DHFR against the opportunistic pathogen P. jirovecii.

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QSAR Studies on a Series of 7,8‐Dialkyl‐1,3‐diaminopyrrolo‐[3,2‐f]quinazolines with Anticancer Activity

Chen¹,

Li²,

Shen³

et al. 2006

Chin. J. Chem.

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The quantitative structure-activity relationship (QSAR) studies on a series of 7,8-dialkyl-1,3-diaminopyrrolo-[3,2-f]quinazolines, dihydrofolate reductase (DHFR) inhibitors as potential anticancer agents, have been carried out by using the density functional theory (DFT) method, molecular mechanics method (MM＋) and statistical method. Some QSAR models based on their lipophilic and steric parameters were built up via a stepwise regression analysis. It is very interesting to find that the established optimal QSAR equation involves only two descriptors: lipophilicity indexes Clog P and Clog P 2 . However, such descriptors can quite well describe a significant statistic quality and have a remarkable predictive activity according to the square of adjusted correlation coefficient ( 2 A R ＝0.937) and the square of cross-validation coefficient (q 2 ＝0.911) of this equation. The results show that the lipophilicity is a main factor affecting the anticancer activity of this series of antimetastatic agents, and the obtained equation describes a parabolic correlation between pIC 50 and Clog P, and indicates a suitable range of Clog P (around 4.43) being very important for optimal pIC 50 values. These QSAR studies can offer some useful references for understanding the action mechanism and performing the molecular design or modification of this series of antimetastatic agents.

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The structure of Pneumocystis carinii dihydrofolate reductase to 1.9 å resolution

Cited by 91 publications

References 22 publications

Crystal Structure of Bacillus anthracis Dihydrofolate Reductase with the Dihydrophthalazine-Based Trimethoprim Derivative RAB1 Provides a Structural Explanation of Potency and Selectivity

Crystal Structure of Bacillus anthracis Dihydrofolate Reductase with the Dihydrophthalazine-Based Trimethoprim Derivative RAB1 Provides a Structural Explanation of Potency and Selectivity

Kinetic and Structural Analysis for Potent Antifolate Inhibition of Pneumocystis jirovecii, Pneumocystis carinii, and Human Dihydrofolate Reductases and Their Active-Site Variants

QSAR Studies on a Series of 7,8‐Dialkyl‐1,3‐diaminopyrrolo‐[3,2‐f]quinazolines with Anticancer Activity

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