Inhibition of Clostridium difficile TcdA and TcdB toxins with transition state analogues

AbstractClostridium difficile causes life-threatening diarrhea and is the leading cause of healthcare-associated bacterial infections in the United States. TcdA and TcdB bacterial toxins are primary determinants of disease pathogenesis and are attractive therapeutic targets. TcdA and TcdB contain domains that use UDP-glucose to glucosylate and inactivate host Rho GTPases, resulting in cytoskeletal changes causing cell rounding and loss of intestinal integrity. Transition state analysis revealed glucocationic character for the TcdA and TcdB transition states. We identified transition state analogue inhibitors and characterized them by kinetic, thermodynamic and structural analysis. Iminosugars, isofagomine and noeuromycin mimic the transition state and inhibit both TcdA and TcdB by forming ternary complexes with Tcd and UDP, a product of the TcdA- and TcdB-catalyzed reactions. Both iminosugars prevent TcdA- and TcdB-induced cytotoxicity in cultured mammalian cells by preventing glucosylation of Rho GTPases. Iminosugar transition state analogues of the Tcd toxins show potential as therapeutics for C. difficile pathology.

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Observation of a tetrahedral reaction intermediate in the HIV-1 protease–substrate complex

Biochemical Journal ◽

10.1042/bj20041804 ◽

2005 ◽

Vol 389 (2) ◽

pp. 365-371 ◽

Cited By ~ 21

Author(s):

Mukesh Kumar ◽

Vishal Prashar ◽

Smita Mahale ◽

Madhusoodan V. Hosur

Keyword(s):

Transition State ◽

Three Dimensional ◽

Substrate Complex ◽

Reaction Intermediate ◽

Hydrogen Bonding Interactions ◽

Transition State Analogue ◽

Transition State Analogues ◽

Protease Substrate ◽

Transition State Analogue Inhibitors ◽

Hiv 1

HIV-1 protease is an effective target for the design of drugs against AIDS. To help this process of drug design, three-dimensional structures have been determined of complexes between HIV-1 protease and a variety of transition-state analogue inhibitors. The true transition state, however, has not been structurally characterized. The crystal structure of the C95M/C1095A HIV-1 protease tethered dimer shows a distinctive feature in which the two flaps of the enzyme are in a ‘closed conformation’ even in the unliganded state. This unique feature has been utilized here to study the structure of HIV-1 protease complexed to an oligopeptide substrate of amino acid sequence His-Lys-Ala-Arg-Val-Leu*NPhe-Glu-Ala-Nle-Ser (where* denotes the cleavage site, and NPhe and Nle denote p-nitrophenylalanine and norleucine residues respectively). The X-ray structure of the complex refined against 2.03 Å (0.203 nm) resolution synchrotron data shows that the substrate is trapped as a tetrahedral reaction intermediate in the crystal. The hydrogen-bonding interactions between the reaction intermediate and the catalytic aspartates are different from those observed previously using transition-state analogues. The reaction intermediate did not dissociate to release the products, possibly due to the inflexibility introduced in the flaps when the enzyme is packed inside crystals.

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Faculty Opinions recommendation of L-Enantiomers of transition state analogue inhibitors bound to human purine nucleoside phosphorylase.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1097544.553622 ◽

2008 ◽

Author(s):

Wayne Guida

Keyword(s):

Transition State ◽

Purine Nucleoside Phosphorylase ◽

Purine Nucleoside ◽

Nucleoside Phosphorylase ◽

Transition State Analogue ◽

Transition State Analogue Inhibitors

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A new class of C-nucleoside analogues. 1-(S)-aryl-1,4-dideoxy-1,4-imino-D-ribitols, transition state analogue inhibitors of nucleoside hydrolase

Tetrahedron Letters ◽

10.1016/s0040-4039(00)79290-2 ◽

1993 ◽

Vol 34 (45) ◽

pp. 7213-7216 ◽

Cited By ~ 51

Author(s):

Benjamin A. Horenstein ◽

Roger F. Zabinski ◽

Vern L. Schramm

Keyword(s):

Transition State ◽

Nucleoside Analogues ◽

New Class ◽

Nucleoside Hydrolase ◽

Transition State Analogue ◽

Transition State Analogue Inhibitors

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Transition State Analogue Inhibitors of 5′-Deoxyadenosine/5′-Methylthioadenosine Nucleosidase from Mycobacterium tuberculosis

Biochemistry ◽

10.1021/acs.biochem.7b00576 ◽

2017 ◽

Vol 56 (38) ◽

pp. 5090-5098 ◽

Cited By ~ 9

Author(s):

Hilda A. Namanja-Magliano ◽

Gary B. Evans ◽

Rajesh K. Harijan ◽

Peter C. Tyler ◽

Vern L. Schramm

Keyword(s):

Mycobacterium Tuberculosis ◽

Transition State ◽

Transition State Analogue ◽

Transition State Analogue Inhibitors

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DFT and Docking Study of Potential Transition State Analogue Inhibitors of Glycosyltransferases

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc20080591 ◽

2008 ◽

Vol 73 (5) ◽

pp. 591-607 ◽

Cited By ~ 4

Author(s):

Lucie Sihelniková ◽

Stanislav Kozmon ◽

Igor Tvaroška

Keyword(s):

Transition State ◽

Density Functional ◽

Density Functional Theory Method ◽

Docking Study ◽

Binding Mode ◽

Functional Theory ◽

Sulfate Anion ◽

Transition State Analogue ◽

Transition State Analogue Inhibitors ◽

Energy Maps

Conformational behavior of the [(2S,3R,4R,5S)-3,4,5-trihydroxy-2-(phenylsulfanyl)tetrahydrofuran-2-yl]methyl sulfate anion (2), which is the potential transition state (TS) analogue of the inverting glycosyltransferases, was studied by means of two-dimensional potential-energy maps, using a density functional theory method at the B3LYP/6-31+G* level. The maps revealed the presence of eight low-energy domains which were refined at the B3LYP/6-311++G** level and led to six conformers in vacuum. In aqueous solution, two conformers dominate at equilibrium. The preferred conformers superimpose well with the transition state structure, as determined previously for glycosyltransferase GnT-I. The conformations of 2 in the active site of glycosyltransferase GnT-I were obtained by docking methods. It was found that one of the two best docking poses mimics the binding mode of TS. These results suggest that the proposed TS mimics 2 have the potential to be used as a scaffold for the design of TS analogue inhibitors.

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