Exploring structure-activity relationships around the phosphomannose isomerase inhibitor AF14049 via combinatorial synthesis.

Phosphomannose Isomerase (PMI) has been shown by genetic methods to be an essential enzyme in fungal cell wall biosynthesis. The PMI inhibitor AF14049 was discovered as an unanticipated side product from high-throughput library screening against the enzyme from C, albicans. Solid-phase synthetic methods were developed and a series of libraries and discrete analogs synthesized to explore SAR around AF14049.

Generation and screening of an oligonucleotide-encoded synthetic peptide library.

We have prepared a library of approximately 10(6) different peptide sequences on small, spherical (10-microns diameter) beads by the combinatorial chemical coupling of both L- and D-amino acid building blocks. To each bead is covalently attached many copies of a single peptide sequence and, additionally, copies of a unique single-stranded oligonucleotide that codes for that peptide sequence. The oligonucleotide tags are synthesized through a parallel combinatorial procedure that effectively records the process by which the encoded peptide sequence is assembled. The collection of beads was screened for binding to a fluorescently labeled anti-peptide antibody using a fluorescence-activated cell sorting instrument. Those beads to which the antibody bound tightly were isolated by fluorescence-activated sorting, and the oligonucleotide identifiers attached to individual sorted beads were amplified by the PCR. Sequences of the amplified DNAs were determined to reveal the identity of peptide sequences that bound to the antibody with high affinity. By combining the capacity for information storage in an oligonucleotide code with the tremendous level of amplification possible through the PCR, we have devised a means for specifying the identity of each member of a vast library of molecules synthesized from both natural and unnatural chemical building blocks. In addition, we have shown that the use of flow cytometry instrumentation permits facile isolation of individual beads that bear high-affinity ligands for biological receptors.

Determinants of EcoRI endonuclease sequence discrimination.

The arginine at position 200 of EcoRI endonuclease is thought to make two hydrogen bonds to the guanine of the sequence GAATTC and thus be an important determinant of sequence discrimination. Arg-200 was replaced by each of the other 19 naturally occurring amino acids, and the mutant endonucleases were assessed for activities in vivo and in vitro. The mutant endonuclease with lysine at position 200 exhibits the most in vivo activity of all the position 200 mutants, although the in vitro activity is less than 1/100th of wild-type activity. Five other mutants show more drastically reduced levels of in vivo activity (Cys, Pro, Val, Ser, and Trp). The Cys, Val, and Ser mutant enzymes appear to have in vivo activity which is specific for the wild-type canonical site despite the loss of hydrogen bonding potential at position 200. The Pro and Trp mutants retain in vivo activity which is independent of the presence of the EcoRI methylase. In crude cell lysates, only the Cys mutant shows a very low level of in vitro activity. None of the mutant enzymes show a preference for alternative sites in assays in vitro. The implications of these results are discussed.

The evolution of nucleotides.

There has been much speculation about the types of molecules that were present in the first living forms. Recent discoveries show that RNA is a more versatile molecule than was previously believed, but whether it was ever able, for example, to synthesize its own monomers from available precursors is not yet known. If amino acids coexisted with nucleosides on the prebiotic Earth, then it seems likely that these two classes of molecules would have interacted with each other. We have been studying oligonucleotide-directed peptide bond formation, and during this work we discovered that aminoacylation of the internal 2'-hydroxyl groups of RNA occurred stereoselectively. Investigation of the mechanism of this reaction has been aided by the use of 3'-inosine methyl phosphate (as a simplified model for a dinucleoside monophosphate) and proton nmr spectroscopy of t-butoxycarbonyl-alanyl esters of nucleosides as models for the transition state of the aminoacylation reaction itself.

On the stereoselective aminoacylation of RNA.

Aminoacylation of the "internal" 2'hydroxyl groups of poly(A) with the imidazolide of racemic DL-leucine resulted in the formation of an enantiomeric excess of the D-ester, whereas aminoacylation with the imidazolide of racemic N-3,5-dinitrobenzoyl-DL-leucine gave an enantiomeric excess of the L-ester. Comparison of these results with those obtained earlier for alanine shows that the larger side chain tends to favor the formation of the D-ester. High resolution proton magnetic resonance spectroscopy was performed on the D- and L-alanyl "internal" 2'-esters of 3'5'-ApA. The resonance of the side chain methyl group of the D-ester is upfield from that of the L-ester, and the separation of the peaks increases with a decrease in temperature.