Crystal structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA and inhibitors reveal the functional roles of the N-terminal region.

Protein N-myristoylation catalyzed by myristoyl-CoA:protein N-myristoyltransferase (NMT) plays an important role in a variety of critical cellular processes and thus is an attractive target for development of antifungal drugs. We report here three crystal structures of Saccharomyces cerevisiae NMT: in binary complex with myristoyl-CoA (MYA) alone and in two ternary complexes involving MYA and two different non-peptidic inhibitors. In all three structures, the majority of the N-terminal region, absent in all previously reported structures, forms a well defined motif that is located in the vicinity of the peptide substrate-binding site and is involved in the binding of MYA. The Ab loop, which might be involved in substrate recognition, adopts an open conformation, whereas a loop of the N-terminal region (residues 22-24) that covers the top of the substrate-binding site is in the position occupied by the Ab loop when in the closed conformation. Structural comparisons with other NMTs, together with mutagenesis data, suggest that the N-terminal region of NMT plays an important role in the binding of both MYA and peptide substrate, but not in subsequent steps of the catalytic mechanism. The two inhibitors occupy the peptide substrate-binding site and interact with the protein through primarily hydrophobic contacts. Analyses of the inhibitorenzyme interactions provide valuable information for further improvement of antifungal inhibitors targeting NMT.

Computational Characterization of Metal Binding Groups for Metalloenzyme Inhibitors.

The mode of action of many pest or disease control agents involves inhibition of some metalloenzyme that is essential for the survival of the target organism. These inhibitors typically consist of a functional group that is capable of a primary binding interaction with the metal and a scaffold that is capable of secondary interactions with the remainder of the enzyme. To characterize the binding ability of various metal binding groups (BGs), we have performed electronic structure calculations on ligand displacement reactions in a model system related to the metalloenzyme, peptide deformylase: E-M-R + BG → E-M-BG + R. Here E represents a model coordination environment for the metal M, and R is a reference ligand (e.g., water) that may be displaced by a metal binding group. Since the oxidation state of many of the metals considered allows for multiple spin states, we also studied the influence of spin state on the coordination environment. Qualitative considerations of electronic structure inspired by the calculations provide an understanding of binding energy trends across a variety of ligands for a given metal and across a variety of metals for a given ligand.

A novel class of inhibitors of peptide deformylase discovered through high-throughput screening and virtual ligand screening.

Peptide deformylase (PDF) has been identified as a promising antibacterial and herbicide target. A structurally novel class of inhibitors containing a 2-thioxo-thiazolidin-4-one heterocycle substituted by an arylidene group at the 5-position and a hexanoic acid side chain at the 3-position was discovered independently via high-throughput screening and virtual ligand screening. Data mining and analogue synthesis established a structure--activity relationship for the side chain region that is consistent with the docked structure.

The use of a pharmacophore model for identification of novel ligands for the benzodiazepine binding site of the GABAA receptor.

A Catalyst pharmacophore model has been developed for the benzodiazepine site within the GABA(A) receptor complex. The model is based on a pharmacophore model originally proposed by Cook and co-workers (Drug Des. Discovery 1995, 12, 193-248) and further developed by Kahnberg et al. (J. Med. Chem. 2002, 45, 4188-4201). The Catalyst pharmacophore model has been validated by using a series of flavonoids with varying affinities for the benzodiazepine receptor and has then been used as a search query in database searching with the aim of finding novel structures which have the possibility to be modified into novel lead compounds. Five of the hits from the database searching were purchased and their affinities for the benzodiazepine site of the GABA(A) receptor were determined. Two of the compounds displayed K(i) values below 10 microM. The substance showing highest potency in-vitro displayed an affinity of 121 nM making it an interesting compound for optimization. The false positive compounds (K(i) values >10 microM affinities) have been analysed in terms of conformational energy penalties and possibilities for hydrogen bond interactions. The analysis clearly demonstrates the need for post processing of Catalyst hits.

Stereochemical definition and chirospecific synthesis of the peptide deformylase inhibitor Sch 382583.

The recently reported natural product Sch 382583 (1), an inhibitor of peptide deformylase, has been synthesized in 16 steps from commercially available starting materials. The three chiral centers were set by a combination of chiral auxiliary and chiral pool approaches. The succinate 5 and piperazic acid 9 moieties were obtained by Evans oxazolidinone imide enolate alkylation and hydrazination/cyclization, respectively, and the aminohexanone side chain 13 was prepared via Grignard substitution of the Weinreb amide derived from l-valine. Spectroscopic data for the resulting synthetic material, compared with the data reported for the natural product, established that the previously unassigned valine ketone stereocenter (C-4) has the S-configuration.

Reaction of 2,2-bis(trifluoromethyl)-1,1-dicyanoethylene with 6,6-dimethylfulvene: cycloadditions and a rearrangement.

Reaction of 2,2-bis(trifluoromethyl)-1,1-dicyanoethylene (BTF; 1) with 6,6-dimethylfulvene (2) affords the expected Diels-Alder cycloadduct, 7-(1-methylethylidene)-3,3-bis(trifluoromethyl)bicyclo[2.2.1]hept-5-ene-2,2-dicarbonitrile (3), in good yield. The cycloadduct 3 is unstable and exists in equilibrium with the starting materials in less polar solvents. In more polar environment, the [4 + 2] adduct 3 either reverts to starting materials, or, in a competing process, is converted to the formal [2 + 2] adduct, 2-(1-methylethylidene)-7,7-bis(trifluoromethyl)bicyclo[3.2.0]hept-3-ene-6,6-dicarbonitrile (6). In the presence of acid, 3 is converted to a third isomeric form, 1,3a,5,6-tetrahydro-7-methyl-5,5-bis(trifluoromethyl)-4H-indene-4,4-dicarbonitrile (8). Both 6 and 8 are formed with complete regiospecificity. Quantum mechanical calculations and X-ray crystallographic studies of this ensemble of reactions by BTF, and the analogous set of reactions by its progenitor, tetracyanoethylene (TCNE), reveal several interesting facets. The conversion of 3 to 6 occurs in certain polar solvents, in the presence of silica gel and alumina, as well as in the solid state. Single crystals of 3 were observed by X-ray crystallography to undergo crystal-to-crystal rearrangement to 6. The conversion of 3 to 8 proceeds by the initial retro-Diels-Alder reaction followed by isomerization of the fulvene to 1-isopropenyl-1,3-cyclopentadiene that then reacts with BTF to give the alternative Diels-Alder product as a single regioisomer. A hybrid density functional theory (DFT) method at the B3LYP/6-31G(d) level of theory gave calculated relative energies of 0.0, -9.0, and -18.8 kcal/mol for 3, 6, and 8, respectively. The same method was also used to correctly predict the regiochemical outcome of the cycloaddition of BTF with 1-isopropenyl-1,3-cyclopentadiene. Finally, an explanation is offered for the preference of the persubstituted cyanoolefins BTF and TCNE to add to the exocyclic diene portion of 1-isopropenyl-1,3-cyclopentadiene and the contrasting preference of 2-acetyloxy-2-propenenitrile to add to the endocyclic diene.

Target molecules - design, optimization and production. The Knud Lind Larsen Symposium. 25-26 January 2002, Copenhagen, Denmark.

The Knud Lind Larsen Symposium, sponsored by the Danish Academy of Technical Sciences, was held on 25-26 January in Copenhagen, Denmark. A diverse line-up of lecturers presented research on target molecules, those molecules intended for particular applications such as binding to biological or synthetic receptors or as materials or catalysts. The symposium was well attended and highly interactive. Of interest to those involved in drug discovery were lectures on histone deacetylase inhibitors, which are being investigated as anticancer agents, second generation non-nucleoside reverse transcriptase inhibitors based on Sustiva (efavirenz), and a phage display approach to new insulin mimetics.