inhibitors of dihyinhibitors of dihydrodipicolinate reductase, a key enzyme of thedrodipicolinate...

Inhibitors of dihydrodipicolinate reductase, a key enzyme of thediaminopimelate pathway of Mycobacterium tuberculosis

Anthony M. Paiva a, Dana E. Vanderwall 1;a, John S. Blanchard b,John W. Kozarich a, Joanne M. Williamson a, Theresa M. Kelly a;*

a Department of Endocrinology and Chemical Biology, Merck Research Laboratories, P.O. Box 2000, Rahway, NJ 07065, USAb Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA

Received 29 August 2000; received in revised form 17 October 2000; accepted 19 October 2000

Abstract

Tuberculosis (TB) remains a leading cause of infectious disease in the world today and therapies developed over the lastforty years are becoming increasingly ineffective against resistant strains of Mycobacterium tuberculosis. In an effort toexplore new mechanisms for drug development, we have investigated the enzymes of the diaminopimelate biosyntheticpathway as potential targets. Specifically, dihydrodipicolinate reductase, the essential gene product of dapB, was screened fornovel inhibitors. Inhibitors were identified both by a molecular modeling approach which utilized the available crystalstructure of the enzyme with an inhibitor bound at the active site as well as by more conventional screening strategies. Theresulting compounds contain a number of structural motifs and were all found to be competitive with respect to the DHDPsubstrate. The Ki values for the inhibitors range from 10 to 90 WM. The molecular modeling approach was very effective inidentifying novel inhibitors of the enzyme. These compounds were obtained at a higher frequency based on the number ofcompounds analyzed than those inhibitors discovered via conventional screening. However, conventional screening provedbeneficial in identifying compounds with greater structural diversity. ß 2001 Elsevier Science B.V. All rights reserved.

Keywords: Diaminopimelate; Dihydrodipicolinate; Enzyme inhibitor; Molecular modeling; (Mycobacterium tuberculosis)

1. Introduction

Mycobacterium tuberculosis (TB) is one of theleading causes of infectious disease in the world to-

day. Overall, it was estimated that 90 million newcases resulting in 30 million deaths would occur inthe last decade of the 20th century [1,2]. Contribut-ing to this outlook is the increase in the number ofMycobacterium tuberculosis infections among immu-nocompromised individuals as a consequence of HIVinfection, particularly in developing countries. Coun-tries in eastern Europe and the former Soviet Unionare also experiencing increases in the number of TBcases [3]. In addition, the emergence of multiple drugresistant (MDR) strains of M. tuberculosis poses aserious threat to the control of this disease.

A variety of drug therapies for the treatment oftubercular infections have been developed over the

0167-4838 / 01 / $ ^ see front matter ß 2001 Elsevier Science B.V. All rights reserved.PII: S 0 1 6 7 - 4 8 3 8 ( 0 0 ) 0 0 2 6 2 - 4

Abbreviations: DHDP, 2,4-dihydrodipicolinate; THDP,2,4,5,6-tetrahydrodipicolinate; 2,6-PDC, 2,6-pyridinedicarboxylicacid

* Corresponding author. Fax: +1-732-594-5365;E-mail : [email protected]

1 Present address: Department of Structural Chemistry, GlaxoWellcome, 5 Moore Drive, Research Triangle Park, NC 27709,USA.

BBAPRO 36334 23-1-01 Cyaan Magenta Geel Zwart

Biochimica et Biophysica Acta 1545 (2001) 67^77www.elsevier.com/locate/bba

last 40 years. Current combination therapies include,but are not limited to, rifampicin, £uoroquinolones,isoniazide, ethambutol and streptomycin. Rifampicinis known to inhibit nucleic acid synthesis by inhibit-ing elongation of full length transcripts from RNApolymerase [4]. Fluoroquinolones inhibit DNA gy-rase, a type II topoisomerase, and topoisomeraseIV preventing negative supercoiling of DNA [5]. Iso-niazid, the oldest and most prescribed antituberculartherapy, inhibits mycolic acid biosynthesis [6]. It isknown to be a prodrug and is cleaved by the actionof catalase^peroxidase [7]. While the speci¢c bio-chemical target of ethambutol is unknown, severalstudies have implicated this drug in the inhibitionof cell wall biosynthesis [8]. Streptomycin targetsprotein synthesis by a¡ecting the accuracy and speedof mRNA translation [9]. Resistance has emerged tothese therapies due in part to di¤culty with patientcompliance to therapeutic regimens that may lastover 6 months.

Our search for new enzyme targets to combat M.tuberculosis has focused on the diaminopimelate bio-synthetic pathway. In mycobacteria, as in other bac-teria, the diaminopimelate pathway is used to synthe-size lysine and diaminopimelate from L-aspartate[10,11]. Diaminopimelate is an essential componentof the cell wall peptidoglycan in both Gram-positiveand Gram-negative bacteria and disruption of diami-nopimelate biosynthesis in mycobacteria is known toresult in cell death [12]. The pathway begins withphosphorylation of L-aspartate followed by reductionto L-aspartic-L-semialdehyde which is also an inter-mediate in the biosynthesis of methionine, threonine,and isoleucine. An aldol condensation between pyr-uvic acid and L-aspartic-L-semialdehyde, catalyzedby dihydrodipicolinate synthase, gives rise to 2,3-di-hydrodipicolinate (DHDP) (Fig. 1). This product isthen reduced by dihydrodipicolinate reductase withthe cofactor NADPH to produce 2,3,4,5-tetrahydro-picolinic acid (THDP). At this point there are threevariations of the pathway leading to diaminopime-late [13]. THDP can either be succinylated or acety-lated before undergoing transamination followed bydesuccinylation or deacetylation and then epimeriza-tion to yield D,L-diaminopimelate. Alternatively,THDP can undergo reductive amination to directlyform D,L-diaminopimelate. Di¡erent bacterial speciesare known to use one or more of these pathways.

Mycobacteria, like Escherichia coli and otherGram-negative organisms, utilize the succinylasepathway [10,11,14,15]. Most of these enzymes havebeen cloned and a number have been crystallized andstudied in detail [15^18]. The available protein crystalstructures allow for molecular modeling approachesto aid in the search for novel inhibitors of theseenzymes. Bacterial diaminopimelate metabolism asa target for antibiotic design has been recently re-viewed [13].

Because DHDP reductase, the product of the dapBgene, occurs early in the diaminopimelate biosyn-thetic pathway and is common to all forms of bac-teria it was chosen for further scrutiny. This enzymehas previously been found to play an essential role incell wall biosynthesis [12]. Inhibitors of DHDP re-ductase discovered to date are relatively simple com-pounds with modest inhibitory properties such as2,6-pyridinedicarboxylic acid (2,6-PDC) [19] whichalso inhibits DHDP synthase [20]. By taking advan-

Fig. 1. Dihydrodipicolinate synthase and reductase reactions ofthe diaminopimelate pathway. The DHDP reductase enzyme ac-tivity assay measures the production of THDP indirectlythrough the oxidation of NADPH to NADP� by monitoringthe decrease in absorbance at 340 nm.


A.M. Paiva et al. / Biochimica et Biophysica Acta 1545 (2001) 67^7768

tage of the available crystal structure for the E. colienzyme with 2,6-PDC bound [21] along with the se-quence of the M. tuberculosis enzyme [10,11], wehoped that more potent inhibitors with antimicrobialactivity could be identi¢ed.

In this paper, we present results obtained from thecombination of molecular modeling approaches andconventional drug development screening strategiesto identify novel inhibitors of DHDP reductase. Ap-proximately a dozen compounds of modest inhibi-tory activity with Ki values ranging from 10 to 90WM were discovered. The molecular modeling ap-proach proved bene¢cial in the identi¢cation of anumber of sulfonamides as inhibitors of DHDP re-ductase. These compounds represent potential leadstructures for the development of new treatment op-tions in mycobacterial infections.

2. Materials and methods

2.1. Reagents

Puri¢ed, recombinant dihydrodipicolinate(DHDP) synthase from E. coli and DHDP reductasefrom E. coli and M. tuberculosis were prepared aspreviously described [19]. The tri£uoroacetate saltof L-aspartate-L-semialdehyde (ASA-TFA) was syn-thesized according to the methods of Robins et al.[22,23]. E. coli strains LS583 and LS584 have beenpreviously described [24]. Potential inhibitors forscreening against DHDP reductase were obtainedfrom the Merck Chemical Repository, Departmentof Chemical Data, Rahway, NJ. All other reagentswere purchased from Sigma, Aldrich, or Fisher Sci-enti¢c.

2.2. Molecular modeling

The X-ray crystal structure of E. coli DHDP re-ductase determined recently with 2,6-PDC bound inthe active site [21] was used with the FLOG systemfor database searching and docking to identify en-zyme inhibitors as previously described [25^27]. Fol-lowing the addition of polar hydrogens and assign-ment of hydrogen bonds and appropriate tautomericstates of imidazoles, the grids used to represent theactive site were calculated with 0.3 Aî spacing and

included the entire residue of any atom within 8 or12 Aî of the 2,6-PDC molecule (two separate sets ofcalculations) but not 2,6-PDC itself. Match centersfor docking ligands were generated at favorable in-teraction sites in the grid. The databases of threedimensional structures or £exibases [27] typicallycontained between 5 and 25 conformations of eachcandidate inhibitor, with heavy atoms represented byseven atom types (hydrogen bond donors, hydrogenbond acceptors, polar (both donor and acceptor),hydrophobic, cationic, anionic and other). The activesite cavity depicted in Fig. 2 was generated with theMOLCAD program in the SYBYL software package(Tripos, St. Louis, MO). The NAD� was included inthe calculation, but the 2,6-PDC and solvent waterswere excluded.

2.3. Dihydrodipicolinate reductase assay

Activity of DHDP reductase in the presence orabsence of test compound was determined by mon-itoring NADPH conversion to NADP� with the con-comitant reduction of 2,4-dihydrodipicolinic acid totetrahydrodipicolinate (Fig. 1). The substrate DHDPwas prepared enzymatically by the DHDP synthasecatalyzed aldol condensation of ASA-TFA and so-dium pyruvate. The enzymes DHDP synthase andDHDP reductase were diluted just prior to usewith 1% bovine serum albumin in 25 mM Hepes,pH 7.5. Dihydrodipicolinate synthase concentrationwas adjusted to ensure greater than 95% conversionof ASA-TFA to DHDP in 5 min at 25³C (speci¢cactivity approximately 30 Wmol/mg per min). DHDPreductase was diluted to approximately 4 Wg/Wl. Stan-dard assay conditions included 100 mM Hepes (pH7.5), 45 WM ASA-TFA, 500 WM sodium pyruvate,100 WM NADPH, and 40 Wg of the reductase in atotal volume of 200 Wl. NADPH was added duringDHDP preparation to improve assay throughput. Itsinclusion did not a¡ect the ASA-TFA and pyruvatecondensation reaction. The initial rate of oxidationof NADPH to NADP� was monitored as a decreasein absorbance at 340 nm with a Dynatech microtiterplate reader equipped with BioLinx2 kinetics soft-ware. The concentration of DHDP reductase wasadjusted to yield greater than 95% conversion toTHDP in 30 min with an initial rate of approxi-mately 10^20 mOD340/min. Rate measurements


A.M. Paiva et al. / Biochimica et Biophysica Acta 1545 (2001) 67^77 69

were made on the linear portion of the reaction prog-ress curve, typically the initial 7 min of the reaction.Data collection continued for 30 min in order tomonitor the complete consumption of DHDP whichhad been generated by DHDP synthase. Assays thatindicated a starting concentration 9 35 WM forDHDP generation were repeated. The E. coliDHDP reductase was most commonly used in rou-tine screening assays.

2.4. Compound screening and inhibition

Test compounds at 10^100 WM in dimethylsulfox-ide (DMSO), were added after DHDP generationand prior to the addition of DHDP reductase. Per-cent relative activity was determined based on initialvelocity (Vi) calculating R.I. = (100%3[Vi with inhib-itor/Vi without inhibitor]U100%). Compounds withgreater than 40% R.I. were selected for IC50 testing.

Fig. 2. Active site of dihydrodipicolinate reductase. The competitive inhibitor 2,6-PDC bound in the active site of DHPR, stackedwith nicotinamide ring of the cofactor NAD� (coordinates from Scapin et al. [21], Protein Data Bank accession code 1arz). Forclarity only the amino acid side chains of the protein are shown with the exception of Gly169 and Thr170. The carbon atoms of theprotein, 2,6-PDC and NAD� are colored white, orange and cyan, respectively. The transparent surface represents the active site cavity(excluding 2,6-PDC, but including NAD�) as calculated by MOLCAD. Hydrogen bonds with 2,6-PDC are shown between the pyri-dine nitrogen and Lys163, the carboxylic acid at C2 and Lys163, and between the acid at C6 and Thr170, and the backbone amidesof Gly169 and Thr170. An additional hydrophobic pocket not occupied by 2,6-PDC is outlined by a green dashed line (see text fordetails). A channel leading out of the active site cavity to solvent is indicated with a white arrow at the bottom left of the ¢gure.



The IC50, de¢ned as the inhibitor concentrationyielding 50% relative inhibition, was determined bytitrating the inhibitor in DMSO from 0.1 to 100 WM.IC50 values were calculated with either SigmaPlot oran equivalent program, MRLCalc.

2.5. Fluorometric DHDP reductase inhibitor screeningand IC50 assays

Some compounds could not be screened with thespectrophotometric assay, due to intrinsic absor-bance at or near 340 nm. For these compounds, aversion of the assay which monitored changes inNADPH £uorescence was used to determine percentinhibition at 100 WM and IC50 values. Reaction con-ditions were the same as in the spectrophotometricassay. The £uorescence decrease associated withNADPH to NADP� oxidation was measured intop reading mode with a PerSeptive Biosystems Cy-to£uor 96-well microtiter plate reader equipped with360 nm (40 nm bandpass) excitation and 460 nm (40nm bandpass) emission dichroic ¢lters. The £uores-cence data were sequentially collected over all wellsof a 96-well microtiter plate at a rate of one mea-surement every 45 s for 30 min. All calculations wereperformed as previously described.

2.6. Determination of Ki and mode of inhibition

Activity measurements for the purposes of Ki de-terminations were conducted by procedures similarto those utilized for the activity assay. The concen-tration of DHDP (via the conversion of ASA-TFA)was varied from 4.5 to 800 WM (Km = 45 WM), withNADPH held constant at 250 WM (Km = 50 WM).The inhibitor concentration was varied from approx-imately 0.1-times to 10-times the IC50 value. Initialrate measurements, expressed as mOD/min, were an-alyzed and plotted according to Michaelis^Mentenkinetics to determine both the Ki and mode of inhi-bition. Reported values for Ki were calculated by¢tting the data to three di¡erent binding modes ac-cording to the following inhibition models and iden-tifying the best ¢t.

1.1 competitive

y � �Vmax��S�=��S� � Km�1� �I�=K i��

1.2 noncompetitive

y � �Vmax��S�=��S��1� �I�=K i�� Km�1� �I�=K i��

1.3 uncompetitive

y � �Vmax��S�=�Km � �S��1� �I�=K i��

2.7. Biological activity of dihydrodipicolinatereductase inhibitors

Inhibitors of DHDP reductase obtained weretested for potential antimicrobial e¡ects by a wholecell agar di¡usion assay against a permeabilized E.coli strain. LB agar plates were prepared by seedingovernight cultures of either wild-type E. coli strainLS584 or the envA1 mutant LS583 [24]. Test samples(typically 50 Wg) were applied to wells formed in theagar for both strains. The plates were incubatedovernight at 37³C and zones of inhibition measured.

3. Results and discussion

Assessment of DHDP reductase activity utilized acoupled assay system where the substrate, DHDP,was synthesized from ASA-TFA and pyruvate byDHDP synthase. The substrate was generated insitu just prior to assay initiation since it can readilyundergo oxidation to produce dipicolinic acid. Sinceit was not possible to measure THDP productiondirectly, the velocity of the DHDP reductase cata-lyzed hydride transfer was monitored instead by fol-lowing the oxidation of NADPH to NADP�. TheKm for DHDP with the reductase was determinedto be 45 WM in good agreement with the previousreport of 50 WM [19]. This was the concentration ofsubstrate chosen for use in the screening assay. TheNADPH concentration was 100 WM in the screeningassay which is approximately twice its Km value forthe enzyme. The conditions of the assay were there-fore somewhat biased towards compounds bindingto the DHDP site of the reductase.

Screening of compounds from the Merck chemicalcollection was accomplished by two complementaryapproaches; molecular modeling and more conven-tional compound screening. The modeling consistedof a virtual screening approach whereby the rapid



docking of inhibitors into the active site of DHDPreductase was performed to identify those com-pounds most likely to be complementary to, andform key interactions within the active site of theenzyme. However, this search strategy includedonly a subpopulation of the available chemical col-lection and a broader search strategy encompassingthe diversity of the collection was also employed.

The determination of the X-ray crystal structure ofthe enzyme complex with 2,6-PDC bound in the ac-tive site [21] provided a relevant structural view ofthe active site that could be exploited by molecularmodeling to select a relatively small subset of thechemical database for inhibitor screening. Fig. 2shows 2,6-PDC bound in the active site of one mol-ecule of the DHDP reductase tetramer, where thetransparent solvent accessible surface illustrates the

active site cavity. Hydrogen bond interactions be-tween 2,6-PDC and the enzyme are illustrated asdashed white lines.

The FLOG (£exible ligands oriented on a grid)[25^27] approach can scan a database of potentialligands by docking a three dimensional structureinto a grid representation of the active site and cal-culating an `energy' or score for each docking. Grid-based energy evaluation is designed to circumventthe need to calculate all the pairwise interactionsbetween the ligand and protein by representing theactive site as an `interaction energy ¢eld', sampled atuniformly spaced points in a three-dimensional grid[27]. At each point the potential energy within theactive site is calculated and stored for each atom typeused in the ligands. The score of a docked ligand iscalculated as the sum of interaction energies for each

Table 1Modeling-based sulfonamide inhibitors of dihydrodipicolinate reductase

A number of sulfonamide compounds were found to be among the most potent inhibitors discovered through the FLOG-based molec-ular modeling search. All compounds are competitive with respect to DHDP.



ligand atom, based on the stored energies of thenearest grid points. In this study, the grids were cal-culated using residues within 8^12 Aî of the 2,6-PDCmolecule found in the active site of the enzyme. Ineach case V1.6U106 conformers were docked, andthe best V500 scoring compounds from each calcu-lation were chosen for determination of enzyme in-hibition.

A number of sulfonamide compounds identi¢ed bythe FLOG modeling search were found to be inhib-itory towards the DHDP reductase. These com-pounds were among the most potent inhibitors ana-lyzed with Ki values from 7 to 48 WM (Table 1). Thesulfonamides are competitive against the DHDP sub-strate as expected from the modeling applicationwhich docked the compounds to this site. Due tolimited availability, these compounds were not wellrepresented in the general screening collection andcould have been easily missed without the directedmodeling approach. The general binding mode dock-ing predictions placed the two sulfonamides in thepositions occupied by the carboxylic acids of 2,6-PDC, making the same hydrogen bond interactionsillustrated in Fig. 2. The most potent compound of

this class (L-613,517) di¡ers from the other fourcompounds in the group in that a sulfone has re-placed one of the sulfonamide groups. This com-pound was equipotent against the E. coli (IC50 = 9.0WM) and M. tuberculosis enzymes (IC50 = 7.2 WM).Comparison of the sulfone containing compoundL-613,517 to the corresponding sulfonamide com-pound L-586,078 reveals a nearly sixfold increase inpotency. Interestingly, structurally related com-pounds which contained dialkyl substitutions on ei-ther one or both of the sulfonamide nitrogens werefound to be noninhibitory (data not shown). In Fig.2 there is an unoccupied region visible on the left-hand side of the active site pocket, adjacent to thecarboxylate oxygen of the 2,6-PDC which is hydro-gen bonded to His160. Fig. 3 represents the potentialorientation of L-613,517 within the active site in aview rotated 90³ relative to Fig. 2. An alkyl substitu-ent positioned in this region, like the isopropyl groupof L-613,517, might interact favorably with Val217,Phe243 and possibly the methylene carbons of theArg240 side chain. On the other hand, dialkyl sub-stitutions, especially at both of the sulfonamide ni-trogens, would be too bulky for the pocket around

Fig. 3. Model of sulfonamide docking in the active site of dihydrodipicolinate reductase. A view of L-613,517 docked in the activesite of DHDP reductase. The surface of the active site cavity is shown in white, NAD� is colored as in Fig. 2, and the carbons of L-613,517 are magenta. The view is looking from the top down with the surface cut away to allow a view of the inhibitor. The alkylsulfone can be seen to just ¢t within the cavity on the left side of the ¢gure, whereas on the right there is only room for the unsubsti-tuted sulfonamide. A dialkyl sulfonamide would encounter poor steric interactions on the side of the cavity shown on the right.



the carboxylic acids. The limitations that the alkylsubstituent of L-613,517 imposes on its binding ori-entation also provides a likely model for the positionof the R1 substituents of this class of compounds,and suggests their involvement in a novel hydropho-bic interaction. An additional hydrophobic pocketlies in region bounded by Phe243, Val143, His235,Ala237 and Val217, and is illustrated in Fig. 2 as thearea encircled by the green dashed line. This pocketis not occupied by any part of the inhibitor 2,6-PDC,and therefore probably not the substrate either. Ifthe structures in Table 1 were bound as just de-scribed for L-613,517, their aliphatic or benzylic R1

substituents would be positioned within this hydro-phobic pocket.

These sulfonamide compounds are reminiscent ofsulfanilamide which was one of the ¢rst known anti-biotics. However, sulfanilamide contains only onesulfonamide group, unlike the disulfonamides identi-¢ed here, and is known to function via disruption offolate biosynthesis [28]. Furthermore, the sulfon-amide compounds described in this paper lackedgood antimicrobial activity.

Other compounds identi¢ed from the FLOGsearch were of a variety of structural motifs. Theywere all competitive with respect to the DHDP sub-strate and were generally less potent than the sulfon-amides. They are similar in potency, however, tothe inhibitor 2,6-PDC bound in the crystal structureof the enzyme used in the FLOG search. The overallhit rate (de¢ned as IC50 values 6 100 WM) for theFLOG identi¢ed compounds, including the sulfon-amides, was approximately 6%. This is a much high-er rate than typically observed with general screeningmethods and is consistent with preselection of com-pounds based on predicted interactions within theenzyme active site. A recurring motif in three ofthe best compounds shown in Table 2 is one ormore nitro groups attached to a benzene ring. Oneof these compounds, L-271,336, was found to haveantimicrobial properties against a permeabilizedstrain of E. coli (envA1 mutant LS583) [24] givinga 9-mm zone of inhibition even though it is a rela-tively poor enzyme inhibitor. However, the com-pound did not show signi¢cant killing of the corre-sponding wild-type strain.

Table 2Modeling based nonsulfonamide inhibitors of dihydrodipicolinate reductase

A range of heterocyclic and aromatic inhibitors of DHDP reductase were identi¢ed from the molecular modeling search in additionto the sulfonamide compounds. Compounds containing chiral centers are racemic.



The remaining inhibitors identi¢ed through com-prehensive screening of thousands of compoundswere also found to be competitive with respect toDHDP (Table 3) as anticipated from the subsaturat-ing concentration of DHDP used in the assay. Theoverall range of Ki or IC50 values was greater likelydue to the diversity of structures found within thisgroup. The overall hit rate in identifying compoundswith similar potency to those found via the FLOGsearch was much lower, 90.2%, as expected. Withinthis group of compounds, the known inhibitor 2,6-pyridinedicarboxylic acid was picked up although itwas somewhat less potent in our hands (120 WM Ki

compared to the previously reported value of 26 WM[19]). None of the inhibitors identi¢ed from the mo-

lecular modeling were detected in the general screen-ing and further analysis con¢rmed their absence inthe available screening library.

Overall, many of the structures identi¢ed from thegeneral screening e¡ort have a more extended chainof hydrophobic benzyl and heterocyclic rings. As arepresentative of this set of compounds, L-298,878was tested against both DHDP reductases and foundto have very similar IC50 values: E. coli = 54 WM andM. tuberculosis = 35 WM. An interesting pair of com-pounds from this set are the relatively simple struc-tures, L-674,305 and L-273,552 (Table 3). Compari-son of these two compounds reveals that the IC50

decreases more than threefold going from approxi-mately 300 WM for the dimethoxy ether arm to less

Table 3General screening-based inhibitors of dihydrodipicolinate reductase

Heterocyclic and aromatic inhibitors of DHDP reductase identi¢ed from general screening. Samples with limited availability were ana-lyzed for IC50 only. All compounds are competitive with respect to DHDP. Compounds containing chiral centers are racemic.



than 100 WM for the methoxy substituted compound.A model of these compounds in the active site of theenzyme suggested that they bind in approximatelythe same position as 2,6-PDC, with the cyano moietynear either His160 or Arg240. This would place themethoxy or dimethoxy substituents in the more re-stricted cavity near Gly169 and Thr170, where thebulkier dimethoxy group of L-674,305 would clearlybe disfavored. Modeling of the remaining com-pounds from Table 3 in the crystal structure activesite led to somewhat ambiguous results. While inter-actions with the hydrophobic pocket appeared pos-sible for all three compounds, alternative bindingmodes which formed interactions within a channelleading to solvent could not be ruled out.

The dual screening approach employed in thisstudy highlights the bene¢ts that can be achievedby each method. The molecular modeling approachbased on the enzyme crystal structure o¡ered an ad-vantage over conventional screening in that a muchhigher percentage of compounds actually screenedagainst the enzyme were found to be inhibitors.This shortened the time required to identify newleads and also focused attention on compoundswhich were not well represented in the general col-lection. Compounds discovered via conventional gen-eral screening also contributed insights into addition-al interactions within the protein structure whichcould be used to enhance binding. The compoundsidenti¢ed through our e¡orts to discover novel inhib-itors of dihydrodipicolinate reductase represent aninteresting set of structures which could be used asleads to make further modi¢cations necessary to in-crease potency and gain antibacterial characteristics.

Acknowledgements

We wish to thank Laura Gegnas for preparing thetri£uoroacetate salt of L-aspartate semialdehyde andJanet Sti¡ey-Wilusz for performing the whole cellagar di¡usion assay. We also wish to thank SreelathaReddy for helpful discussions and Marge Proctor forassistance with MRLCalc.

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