Mapping the Active Site of the Bacterial Enzyme LpxC Using Novel Carbohydrate‐Based Hydroxamic Acid Inhibitors*

2005 ◽  
Vol 24 (4-6) ◽  
pp. 583-609 ◽  
Author(s):  
Xuechen Li ◽  
Amanda McClerren ◽  
Christian Raetz ◽  
Ole Hindsgaul
Keyword(s):  
Active Site ◽  
Hydroxamic Acid ◽  
Bacterial Enzyme

The crystal structure of Proteus vulgaris tryptophan indole-lyase complexed with oxindolyl-L-alanine: implications for the reaction mechanism

2018 ◽  
Vol 74 (8) ◽  
pp. 748-759
Author(s):  
Robert S. Phillips ◽  
Adriaan A. Buisman ◽  
Sarah Choi ◽  
Anusha Hussaini ◽  
Zachary A. Wood
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Aromatic Ring ◽  
Active Site ◽  
Enzymatic Reaction ◽  
Proteus Vulgaris ◽  
Bacterial Enzyme ◽  
Small Domain ◽  
Out Of Plane ◽  
Reversible Formation

Tryptophan indole-lyase (TIL) is a bacterial enzyme which catalyzes the reversible formation of indole and ammonium pyruvate from L-tryptophan. Oxindolyl-L-alanine (OIA) is an inhibitor of TIL, with a K i value of about 5 µM. The crystal structure of the complex of Proteus vulgaris TIL with OIA has now been determined at 2.1 Å resolution. The ligand forms a closed quinonoid complex with the pyridoxal 5′-phosphate (PLP) cofactor. The small domain rotates about 10° to close the active site, bringing His458 into position to donate a hydrogen bond to Asp133, which also accepts a hydrogen bond from the heterocyclic NH of the inhibitor. This brings Phe37 and Phe459 into van der Waals contact with the aromatic ring of OIA. Mutation of the homologous Phe464 in Escherichia coli TIL to Ala results in a 500-fold decrease in k cat/K m for L-tryptophan, with less effect on the reaction of other nonphysiological β-elimination substrates. Stopped-flow kinetic experiments of F464A TIL show that the mutation has no effect on the formation of quinonoid intermediates. An aminoacrylate intermediate is observed in the reaction of F464A TIL with S-ethyl-L-cysteine and benzimidazole. A model of the L-tryptophan quinonoid complex with PLP in the active site of P. vulgaris TIL shows that there would be a severe clash of Phe459 (∼1.5 Å apart) and Phe37 (∼2 Å apart) with the benzene ring of the substrate. It is proposed that this creates distortion of the substrate aromatic ring out of plane and moves the substrate upwards on the reaction coordinate towards the transition state, thus reducing the activation energy and accelerating the enzymatic reaction.

Synthesis of a Carbohydrate-Derived Hydroxamic Acid Inhibitor of the Bacterial Enzyme (LpxC) Involved in Lipid A Biosynthesis

2003 ◽  
Vol 5 (4) ◽  
pp. 539-541 ◽  
Author(s):  
Xuechen Li ◽  
Taketo Uchiyama ◽  
Christian R. H. Raetz ◽  
Ole Hindsgaul
Keyword(s):  
Hydroxamic Acid ◽  
Lipid A ◽  
Acid Inhibitor ◽  
Bacterial Enzyme ◽  
Lipid A Biosynthesis

scholarly journals Structure-Based Design of Tetrahydroisoquinoline-Based Hydroxamic Acid Derivatives Inhibiting Human Histone Deacetylase 8

2021 ◽  
Vol 5 (1) ◽  
pp. 504-538
Author(s):  
Eugene Megnassan ◽  
◽  
Issouf Fofana ◽  
Brice Dali ◽  
Frederica Mansilla Koblavi ◽  
...  
Keyword(s):  
Histone Deacetylase ◽  
Active Site ◽  
Hydroxamic Acid ◽  
Combinatorial Library ◽  
Structural Information ◽  
Qsar Model ◽  
Interaction Energies ◽  
Histone Deacetylase 8 ◽  
Hdac8 Inhibitors ◽  
Hydroxamic Acid Derivatives

We have designed new human histone deacetylase 8 (HDAC8) inhibitors using structure-based molecular design. 3D models of HDAC8–inhibitor complexes were prepared by in situ modification of the crystal structure of HDAC8 co-crystallized with the hydroxamic acid suberoylanilide (SAHA) and a training set (TS) of tetrahydroisoquinoline-based hydroxamic acid derivatives (DAHTs) with known inhibitory potencies. A QSAR model was elaborated for the TS yielding a linear correlation between the computed Gibbs free energies (GFE) of HDAC8–DAHTs complexation (∆∆Gcom) and observed half-maximal enzyme inhibitory concentrations (IC50exp). From this QSAR model a 3D-QSAR pharmacophore (PH4) was generated. Structural information derived from the 3D model and breakdown of computed HDAC8–DAHTs interaction energies up to individual active site residue contributions helped us to design new more potent HDAC8 inhibitors. We obtained a reasonable agreement ∆∆Gcom and values: (pIC50exp = – 0.0376 × ∆∆Gcom + 7.4605, R2 = 0.89). Similar agreement was established for the PH4 model (pIC50exp = 0.8769 × + 0.7854, R2 = 0.87). A comparative analysis of the contributions of active site residues guided the choice of fragments used in designing a virtual combinatorial library (VCL) of DAHT analogs. The VCL of more than 17 thousand DAHTs was screened by the PH4 and furnished 229 new DAHTs. The best-designed analog displayed predicted inhibitory potency up to 110 times higher than that of DAHT1 (IC50exp = 0.047 µM). Predicted pharmacokinetic profiles of the new analogs were compared to current per oral anticancer compounds. This computational approach, which combines molecular modelling, pharmacophore generation, analysis of HDAC8–DAHTs interaction energies and virtual screening of a combinatorial library of DAHTs resulted in a set of proposed new HDAC8 inhibitors. It can thus direct medicinal chemists in their search for new anticancer agents.

Synthesis and 4D-QSAR Studies of Alanine Hydroxamic Acid Derivatives as Aminopeptidase N Inhibitors

2019 ◽  
Vol 16 ◽  
Author(s):  
Min Gao ◽  
Qiao Li Lv ◽  
Hou Pan Zhang ◽  
Guo Gang Tu
Keyword(s):  
Biological Activity ◽  
Active Site ◽  
Hydroxamic Acid ◽  
Binding Mode ◽  
Qsar Model ◽  
Aminopeptidase N ◽  
Design Synthesis ◽  
Qsar Studies ◽  
Hydroxamic Acid Derivatives

Background: As a target for anticancer treatment, aminopeptidase N (APN) shows its overexpression on diverse malignant tumor cells and associates with cancer invasion, angiogenesis and metastasis. Objective: Design, synthesis and biological activity evaluation of alanine hydroxamic acid derivatives as APN inhibitors, and investigation the binding mode of inhibitors in the APN active site. Methods: Alanine hydroxamic acid derivatives were synthesized and evaluated for their in vitro anti-cancer activity using CCK-8 assay. Molecular docking and 4D-QSAR studies were carried out to suggest the mechanism of biological activity. Results: Compared with Bestatin, compound 9b showed the best APN inhibition activity. The putative binding mode of 9b in the APN active site was also discussed. Moreover, the robust and reliable 4D-QSAR model exhibited the following statistics: R2 = 0.9352, q2LOO = 0.8484, q2LNO =0.7920, R2Pred = 0.8739. Conclusion: Newly synthesized compounds exerted acceptable anticancer activity and further investigation on current scaffold would be beneficial.

scholarly journals Crystal Structure ofStreptococcus pneumoniae N-Acetylglucosamine-1-phosphate Uridyltransferase Bound to Acetyl-coenzyme A Reveals a Novel Active Site Architecture

2000 ◽  
Vol 276 (15) ◽  
pp. 11844-11851 ◽  
Author(s):  
Gerlind Sulzenbacher ◽  
Laurent Gal ◽  
Caroline Peneff ◽  
Florence Fassy ◽  
Yves Bourne
Keyword(s):  
Active Site ◽  
Coenzyme A ◽  
Resistance Mechanisms ◽  
Terminal Region ◽  
Glycopeptide Antibiotics ◽  
Acetyl Coenzyme A ◽  
Acetyl Coenzyme ◽  
Left Handed ◽  
Bacterial Enzyme ◽  
Parallel Fashion

The bifunctional bacterial enzymeN-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU) catalyzes the two-step formation of UDP-GlcNAc, a fundamental precursor in bacterial cell wall biosynthesis. With the emergence of new resistance mechanisms against β-lactam and glycopeptide antibiotics, the biosynthetic pathway of UDP-GlcNAc represents an attractive target for drug design of new antibacterial agents. The crystal structures ofStreptococcus pneumoniaeGlmU in unbound form, in complex with acetyl-coenzyme A (AcCoA) and in complex with both AcCoA and the end product UDP-GlcNAc, have been determined and refined to 2.3, 2.5, and 1.75 Å, respectively. TheS. pneumoniaeGlmU molecule is organized in two separate domains connectedviaa long α-helical linker and associates as a trimer, with the 50-Å-long left-handed β-helix (LβH) C-terminal domains packed against each other in a parallel fashion and the C-terminal region extended far away from the LβH core and exchanged with the β-helix from a neighboring subunit in the trimer. AcCoA binding induces the formation of a long and narrow tunnel, enclosed between two adjacent LβH domains and the interchanged C-terminal region of the third subunit, giving rise to an original active site architecture at the junction of three subunits.

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