Structure of MurF from <i>Streptococcus pneumoniae</i> co‐crystallized with a small molecule inhibitor exhibits interdomain closure

Longenecker, K.L.; Stamper, G.F.; Hajduk, Philip J.; Fry, Elizabeth H.; Jakob, C.G.; Harlan, John E.; Edalji, Rohinton; Bartley, Diane; Walter, Karl A.; Solomon, Larry R.; Holzman, Thomas F.; Gu, Yu; Lerner, Claude G.; Beutel, Bruce A.; Stoll, V.S.

doi:10.1110/ps.051604805

Cited by 57 publications

(67 citation statements)

References 25 publications

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“…Furthermore, the open and closed X-ray structures of free and complexed MurD [11e13] and MurF [14,15] show that the Cterminal domain undergoes substantial conformational changes upon substrate or inhibitor binding [16].…”

Section: Introductionmentioning

confidence: 99%

Second-generation sulfonamide inhibitors of d-glutamic acid-adding enzyme: Activity optimisation with conformationally rigid analogues of d-glutamic acid

Sosič¹,

Barreteau²,

Simčič³

et al. 2011

European Journal of Medicinal Chemistry

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a b s t r a c t D-Glutamic acid-adding enzyme (MurD) catalyses the essential addition of D-glutamic acid to the cytoplasmic peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanine, and as such it represents an important antibacterial drug-discovery target enzyme. Based on a series of naphthalene-N-sulfonyl-DGlu derivatives synthesised recently, we synthesised two series of new, optimised sulfonamide inhibitors of MurD that incorporate rigidified mimetics of D-Glu. The compounds that contained either constrained D-Glu or related rigid D-Glu mimetics showed significantly better inhibitory activities than the parent compounds, thereby confirming the advantage of molecular rigidisation in the design of MurD inhibitors. The binding modes of the best inhibitors were examined with high-resolution NMR spectroscopy and X-ray crystallography. We have solved a new crystal structure of the complex of MurD with an inhibitor bearing a 4-aminocyclohexane-1,3-dicarboxyl moiety. These data provide an additional step towards the development of sulfonamide inhibitors with potential antibacterial activities.

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Section: Introductionmentioning

confidence: 99%

Second-generation sulfonamide inhibitors of d-glutamic acid-adding enzyme: Activity optimisation with conformationally rigid analogues of d-glutamic acid

Sosič¹,

Barreteau²,

Simčič³

et al. 2011

European Journal of Medicinal Chemistry

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“…The crystal structures of MurF from E. coli (30) and S. pneumoniae (14) indicate that these are monomeric enzymes with multiple domains; it is possible that some of the binding compounds alter domain interactions, stabilizing the protein without inhibiting the enzyme. Since the ThermoFluor assay identified compounds that produced an increase in MurF T m , presumably by binding to and stabilizing the protein, it is unlikely that the compounds that inhibited MurF activity act by causing protein denaturation, since denaturation should decrease the MurF melting temperature.…”

Section: Discussionmentioning

confidence: 99%

“…These include a nonhydrolyzable ATP analog (1) and phosphinate transition state analogs (16). Gu et al have reported on a series of sulfonamides (11), and Longenecker et al have cocrystallized an inhibitor with Streptococcus pneumoniae MurF (14). In addition, we have reported on a series of thiazolylaminopyrimidines that inhibit Escherichia coli MurF (2).…”

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confidence: 99%

A MurF Inhibitor That Disrupts Cell Wall Biosynthesis in Escherichia coli

Baum

Crespo-Carbone

Klinger

et al. 2007

Antimicrob Agents Chemother

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MurF is an essential enzyme of bacterial cell wall biosynthesis. Few MurF inhibitors have been reported, and none have displayed measurable antibacterial activity. Through the use of a MurF binding assay, a series of 8-hydroxyquinolines that bound to the Escherichia coli enzyme and inhibited its activity was identified. To derive additional chemotypes lacking 8-hydroxyquinoline, a known chelating moiety, a pharmacophore model was constructed from the series and used to select compounds for testing in the MurF binding and enzymatic inhibition assays. Whereas the original diverse library yielded 0.01% positive compounds in the binding assay, of which 6% inhibited MurF enzymatic activity, the pharmacophore-selected set yielded 14% positive compounds, of which 37% inhibited the enzyme, suggesting that the model enriched for compounds with affinity to MurF. A 4-phenylpiperidine (4-PP) derivative identified by this process displayed antibacterial activity (MIC of 8 g/ml against permeable E. coli) including cell lysis and a 5-log 10 -unit decrease in CFU. Importantly, treatment of E. coli with 4-PP resulted in a 15-fold increase in the amount of the MurF UDP-MurNActripeptide substrate, and a 50% reduction in the amount of the MurF UDP-MurNAc-pentapeptide product, consistent with inhibition of the MurF enzyme within bacterial cells. Thus, 4-PP is the first reported inhibitor of the MurF enzyme that may contribute to antibacterial activity by interfering with cell wall biosynthesis.

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“…Eleven unique compounds were identified by this method as potential inhibitors. Fortunately, MurF was very amenable to NMR techniques, providing readily interpretable 1 H/ 13 C-HSQC spectra [34]. Thus, solution-phase NMR was used to triage the list of AS/MS hits and corroborated the binding of two (Fig.…”

Section: Triage Of Initial Leadsmentioning

confidence: 99%

Synergistic Use of Protein Crystallography and Solution‐phase NMR Spectroscopy in Structure‐based Drug Design: Strategies and Tactics

Abad‐Zapatero

Stamper

Stoll

2006

Fragment‐based Approaches in Drug Discovery

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Structural biology is an integral part of the drug discovery process in the pharmaceutical industry. Two complementary methods dominate among the experimental techniques capable of providing detailed three-dimensional (3D) structural information of therapeutically relevant targets, most often with bound ligands: protein crystallography and solution-phase NMR spectroscopy. The structural information these techniques provide continues to grow in depth and breadth, impacting every step of drug discovery from lead identification to preclinical testing ( Fig. 12.1). Used together, protein crystallography and solution-phase NMR can significantly increase both the pace of discovery and the quality of the resulting compounds that are moved forward into development.The benefits to drug discovery of rapidly available, high-resolution 3D structural information provided by protein crystallography are well established [1,2]. While the technique's success depends on diffraction-quality protein crystals, significant advances in protein biochemistry and protein crystallization technologies have dramatically increased the number of targets amenable to structure determination by X-ray diffraction. Driven in large part by a number of worldwide structural genomics efforts underway in both academia and industry [3], these advances include robotic systems for cloning, expression, protein purification and crystallization [4]. In addition, continued hardware and software developments, both at synchrotron and in-house X-ray sources, have decreased the time of de novo structure solution from months to days, while co-crystal structures are routinely obtained within hours. Thus, once diffraction-quality crystals are obtained, structure determination is not a bottleneck in the discovery process. In fact, a number of drugs on the market were discovered in large part by routine use of structural information provided by protein crystallography [2, 5], a clear indication that this technique has become a driver of the design process and not a retrospective analysis tool.In academia, solution-phase NMR spectroscopy continues to develop as a technique for obtaining 3D structural information of macromolecules including target-ligand complexes. Recent advances have made NMR structural work possible 249 Fragment-based Approaches in Drug Discovery. Edited

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Structure of MurF from Streptococcus pneumoniae co‐crystallized with a small molecule inhibitor exhibits interdomain closure

Cited by 57 publications

References 25 publications

Second-generation sulfonamide inhibitors of d-glutamic acid-adding enzyme: Activity optimisation with conformationally rigid analogues of d-glutamic acid

Second-generation sulfonamide inhibitors of d-glutamic acid-adding enzyme: Activity optimisation with conformationally rigid analogues of d-glutamic acid

A MurF Inhibitor That Disrupts Cell Wall Biosynthesis in Escherichia coli

Synergistic Use of Protein Crystallography and Solution‐phase NMR Spectroscopy in Structure‐based Drug Design: Strategies and Tactics

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