ACCOMPLISHMENTS of the laboratory are described
in over 530
research papers. For historical reasons and convenience these papers
are listed both by the dates of publication and by the research topic
(see papers). Through the years, studies have been carried out in
thirty two discernable areas related to biochemical problems. Professor
Bruice invented the term BIOORGANIC CHEMISTRY and defined the field.
Significant advances have been made in this laboratory in the elucidation
of the catalytic processes in acyl and phosphate transfer reactions,
the mechanisms of cofactor reactions (pyridoxal, flavins, lipoic
acid, dihydronicotinimides) and metalloporphyrin chemistry.
AREAS of investigation include the design, synthesis
and study of putative antisense and antigene agents as well as
the use of computational methods in the study of reaction mechanisms
and in particular enzyme catalysis and drug design.
DNA and RNA Binding Agents
CATIONIC ANALOGS OF DNA.
An area of research under study in this lab is the creation
of oligonucleoside analogues. Oligonucleoside
analogues capable of arresting cellular processes at the translational
and transcriptional levels via recognition and binding to complementary
RNA or DNA are known, as antisense and antigene agents, respectively.
Solid-Phase synthesis of cationic analogues of DNA and RNA
have been pioneered in this lab. Oligmers with the phosphate
replaced with guanidine (DNG/RNG) or S-methylthiourea (DNmt)
have been created. The guanidium linkage is resistant to nucleases
and the positive charges of the backbone may give rise to cell
membrane permeability through electrostatic attraction of the
oligonucleoside to the negatively charged phosphate groups
of the cell surface. Both DNG and DNmt are able to discriminate
between their complementary strands and noncomplementary base-pairs.
479. Linkletter, B.
A.; Szabo, I. E.; Bruice, T. C.. Solid-phase synthesis of
deoxynucleic guanidine (DNG)
oligomers and melting point and circular dichroism analysis
of binding fidelity of octameric thymidyl oligomers with DNA
oligomers. J. Am. Chem. Soc. 1999, 121, 3888–3896. PDF
499. Barakar, D. A.; Kwok;
Y.; Bruice, T. W. and Bruice, T. C.. Deoxynucleic Guanidine/Peptide
Acid Chimeras: Synthesis, Binding and Invasion Studies with
DNA. J. Am. Chem Soc. 2000, 122, 5244. PDF
512. Challa, H. & Bruice,
T. C.. Incorporation of positively charged deoxynucleic S-methylthiourea
into oligonucleotides: Synthesis and characterization of DNmt/DNA
chimera. Bioorg. Med. Chem. Lett. 2001, 11, 2423-2427. PDF
517. Kojima, N.; Szabo,
I. E. & Bruice,
T. C.. Synthesis of ribonucleic guanidine: Replacement of the
negative phosphodiester linkages of RNA with positive guanidinium
linkages. Tetrahedron 2002, 58, 867-879. PDF
(MGTs) are a novel class of minor groove binding
ligands that consists of an A+T selective DNA minor groove binding
tripyrrole peptide and polyamine chains attached to the central
pyrrole that extend drug contact into the DNA major groove. Interaction
of the MGTs polyamine moiety with the phosphate backbone leads
to extremely tight binding and results in bending of DNA. MGTs
are extraordinary effective inhibitors of the associtation of
the transcription factors E2 factor 1 to its DNA promotor element.
Our goal is to design a new class of MGTs to further investigate
the structure-activity relationship between DNA binding strengths,
transcription factor inhibition, and phophate backbone interaction.
We have designed a minor groove binding vehicle that can readily
functionalized and is based upon the widely used DNA fluorophore
Hoeshst 33258, which is known to bind A+T rich sequences of dsDNA.
489. Satz, A. L.; Bruice,
T. C.. Synthesis of fluorescent microgonotropen (FMGT–1)
and its interactions with the dodecamer d(CCGGAATTCCGG).
Bioorg. Med. Chem. Lett.
1999, 9, 3261–3266. PDF
502. Satz, A. L. & Bruice,
T. C.. Synthesis of Fluorescent Microgonotropens (FMGTs)
and Their Interactions
with dsDNA. Bioorg. Med. Chem. 2000, 8, 1871-1880. PDF
507. Satz, A.. L. & Bruice,
T. C.. Recognition of nine base pairs in the minor groove
of dsDNA by a Tripyrrole
Peptide-Hoechst Conjugate. J. Am. Chem. Soc. 2001, 123, 2469-2477.
518. Satz, L. S. & Bruice,
T. C.. Recognition in the Minor Groove of double-stranded
DNA by microgonotropens.
Acc. Chem. Res. 2002, 35, 86-95. PDF
Enzyme Mechanisms. Transition state stabilization is commonly
invoked to explain the amazing ability of enzymes to lower the
activation barrier of reactions. Recent investigations in this
lab and elsewhere, however, have brought into focus the contributions
of thermal motions and ground state conformers associated with
the Michaelis complex to the rate of enzymatic reactions. Computational
studies in this lab utilizing quantum mechanical, molecular dynamics,
and hybrid quantum mechanics/molecular mechanics calculations
on Catechol O-Methyltransferase, Formate Dehydrogenase, Haloalkane
Dehalogenase, and Alcohol Dehydrogenase have shown the importance
of positioning the reactants into Near Attack Conformers (NACs).
NACs are ground state conformers which are geometrically similar
to the transition state. Calculations on model compounds show
a significant decrease in the activation barrier when the reaction
proceeds from a NAC to the transition state. A direct correlation
between the mole fraction of NACs accessible to strain free dicarboxylic
acid monoesters and the relative rate enhancement in the intramolecular
reaction of these molecules to form cyclic anhydrides has been
478. T. C. Bruice & F.
C. Lightstone. Ground State and Transition State Contributions
and Enzymatic Reactions. Acc. Chem Res. 1999, 32, 127. PDF
497. Bruice, T. C.;
Benkovic, S. J.. Chemical basis for enzyme catalysis. Biochemistry
2000, 39, 6267–74. PDF
519. Hur, S.; Bruice, T, C..
The mechanism of catalysis of the chorismate to prephenate
reaction by the
Escherichia coli mutase enzyme. Proc. Natl. Acad. Sci. (USA)
2002, 99, 1176-1181. PDF
520. Bruice, T. C.. A view
at the millennium: the efficiency of enzymatic catalysis. Acc.
Chem. Res. 2002,
35, 139-146. PDF
523. Hur, S.; Bruice, T. C..
The mechanism of cis-trans isomerization of prolyl peptides
J. Am. Chem. Soc. 2002, 124, 7303-7313. PDF
Design. The immunosuppressive drugs FK506
and Rapamycin form complexes with the immunophilin FKBP12.
complex subsequently binds to the protein calcinerin. The binding
of calcinerin to the FKBP12-drug complexes is responsible for
the immunosuppressive activities of the drugs. Modifications
to FK506 or Rapamycin that preclude binding of calcineurin
lead to loss of immunosuppressive activity. Both drugs have
to promote neurite outgrowth. The immunosuppressive and neurite
outgrowth activities of these drugs can be separated into the
effector and binding domains, respectively. Virtual point mutations
to the ketide units in the effector domains of these drugs
have been made to create combinatorial libraries of compounds
may able to promate neurite outgrowth but are non-immunosuppressive.
500. Kahn, K.; Bruice, T.
C.. alpha-Ketoamides and alpha-ketocarbonyls: Conformational
analysis and development of all-atom OPLS force field. Bioorg.
Med. Chem. 2000, 8, 1881-1891. PDF
492. Adalsteinsson, H.;
Bruice, T. C.. Generation of putative neuroregenerative drugs.
1. Virtual point mutations to the polyketide rapamycin. Bioorg.
Med. Chem. 2000, 8, 617–624. PDF
493. Adalsteinsson, H.;
Bruice, T. C.. Generation of putative neuroregenerative drugs.
2. Screening virtual libraries of novel polyketides which
possess the binding domain of rapamycin. Bioorg. Med. Chem.
2000, 8, 625–635. PDF
522. Kahn, K.; Bruice, T.
C.. Parameterization of OPLS–AA force field for the
conformational analysis of macrocyclic polyketides. J. Comput.
Chem. 2002, 23, 977-996. PDF