Biomedical subjects
Publications and source records attributed to Dale G Drueckhammer.
A pair of water-soluble molecular tweezers designed using the computer program CAVEAT were prepared and their binding to an N-ethylquinolinium cation was demonstrated by 1H NMR spectroscopy.
A macrocycle containing a pair of bipyridine moieties with a linker designed using the computer program CAVEAT exhibits unique selectivity in the binding of zinc ion relative to other metals.
[reaction: see text] A catalyst for enolate formation was designed that incorporates an amine base along with a thiourea to bind to the oxygen atom of the substrate and enolate through hydrogen bonding. A computational model of the transition state was developed in which the thiourea (modeled initially as a urea) and amine were separate molecules. This model and models incorporating one or two methanol molecules in place of the urea showed an out-of-plane hydrogen bond, apparently to the carbonyl pi-bond, in addition to an in-plane hydrogen bond to an unshared electron pair. In contrast, optimized complexes of the ketone and the fully formed enolate showed only in-plane hydrogen bonding. The transition state model with the urea and amine was used to define a database search with the computer program CAVEAT to identify structures suitable for linking the amine and urea/thiourea moieties in the transition state. On the basis of a group of structures identified from this search, a flexible but conformationally biased linker was designed to connect the two catalytic moieties. The molecule having the amine and thiourea moieties connected by this linker was synthesized and was shown to catalyze proton exchange between methanol and deuterated acetone. The catalyst was about 5-fold more efficient than the amine and thiourea as separate molecules and relative to a similar but less conformationally biased catalyst.
Analogues of coenzyme A (CoA) and of CoA thioesters have been prepared in which the amide bond nearest the thiol group has been modified. An analogue of acetyl-CoA in which this amide bond is replaced with an ester linkage was a good substrate for the enzymes carnitine acetyltransferase, chloramphenicol acetyltransferase, and citrate synthase, with K(m) values 2- to 8-fold higher than those of acetyl-CoA and V(max) values from 14 to >80% those of the natural substrate. An analogue in which an extra methylene group was inserted between the amide bond and the thiol group showed less than 4-fold diminished binding to the three enzymes but exhibited less than 1% activity relative to acetyl-CoA with carnitine acetyltransferase and no measurable activity with the other two enzymes. Analogues of several CoA thioesters in which the amide bond was replaced with a hemithioacetal linkage exhibited no measurable activity with the appropriate enzymes. The results indicate that some aspects of the amide bond and proper distance between this amide and the thiol/thioester moiety are critical for activity of CoA ester-utilizing enzymes.
Tetrahydrodipicolinate N-succinyltransferase (DapD) catalyzes the succinyl-CoA-dependent acylation of L-2-amino-6-oxopimelate to 2-N-succinyl-6-oxopimelate as part of the succinylase branch of the meso-diaminopimelate/lysine biosynthetic pathway of bacteria, blue-green algae, and plants. This pathway provides meso-diaminopimelate as a building block for cell wall peptidoglycan in most bacteria, and is regarded as a target pathway for antibacterial agents. We have solved the X-ray crystal structures of DapD in ternary complexes with pimelate/succinyl-CoA and L-2-aminopimelate with the nonreactive cofactor analog, succinamide-CoA. These structures define the binding conformation of the cofactor succinyl group and its interactions with the enzyme and place its thioester carbonyl carbon in close proximity to the nucleophilic 2-amino group of the acceptor, in support of a direct attack ternary complex mechanism. The acyl group specificity differences between homologous tetrahydrodipicolinate N-acetyl- and N-succinyltransferases can be rationalized with reference to at least three amino acids that interact with or give accessible active site volume to the cofactor succinyl group. These residues account at least in part for the substrate specificity that commits metabolic intermediates to either the succinylase or acetylase branches of the meso-diaminopimelate/lysine biosynthetic pathway.
Three new virtual databases have been developed for use with the bond-orientation-based database searching program CAVEAT. These consist of a database of trisubstituted monocyclic hydrocarbons having ethyl, vinyl, and phenyl substituents; a database of unsubstituted bicyclic hydrocarbons; and a database of core structures from established combinatorial synthetic methods having hydrogen, ethyl, vinyl, and phenyl substituents at the readily varied positions. Each collection of molecules was subjected to a batch conformational search, minimization, and conversion to a vector database for use with CAVEAT.