Donald B. Boyd
Research
The objective of our research is to learn about
and apply relationships between structure and properties of molecules.
We are interested in all sorts of molecules, but have a special
interest in pharmaceutically relevant molecules.
Most medicines exert their therapeutic effect by interaction with
a protein or nucleic acid. The part of the macromolecule where
a particular drug binds is the receptor. A small molecule, such
as a drug, that binds to a receptor is called a ligand. The interaction
of ligand and receptor involves electrostatic attraction and repulsion,
hydrogen bonding, and van der Waals contacts. These forces are
the result of electronic distribution, steric shape, and conformational
properties. Modern computer-based methods, such as molecular modeling,
are well suited for predicting these molecular properties. The
strength of the interactions between ligand and receptor will determine
recognition and affinity. The greater the strength and the more
specific the interactions, the greater the potency of the biologically
active molecule and the less likely it will cause side effects.
The economics of drug discovery has led to a prominent role for
computer-aided drug design (CADD) methodologies in pharmaceutical
companies. The cost of bringing a new pharmaceutical from the laboratory
to the patient has risen rapidly. The high cost is related to the
low odds of successfully finding safe and effective new medicines:
tens of thousands of compounds may be made and tested to find one
with the attributes to be a significant therapeutic product. CADD
helps determine which structures are more promising as drug candidates.
Besides cost, there is another factor driving the increased use
of CADD. The causes of disease are being unraveled at the molecular
level by genomics. These experiments reveal which biomacromolecules
play a role in a disease state. Computational chemistry is uniquely
positioned to maximize the usefulness of this molecular-level information.
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Recent Publications
D. B. Boyd "Molecular Modeling", Chapter 3, in: Ullmann's Modeling and Simulation,
Wiley-VCH, Weinheim, 2007, pp. 307-322.
Donald B. Boyd "How Computational Chemistry Became Important in the
Pharmaceutical Industry" in: Reviews in Computational Chemistry, K. B.
Lipkowitz and T. Cundari, Eds., Wiley-VCH, New York,
2007, Vol. 23,
pp. 401-451.
T. Ercanli and Donald B. Boyd "Exploration of the Conformational Space
of a Polymeric Material that Inhibits Human Immunodeficiency Virus" J.
Chem. Inf. Mod. 2006, 46, 1321-1333.
Donald B. Boyd and M. M. Marsh "History of Computers in Pharmaceutical
Research and Development: A Narrative" in: Computer Applications in
Pharmaceutical Research and Development, S. Ekins, Ed., Wiley, New
York, 2006, pp. 1-50.
Donald B. Boyd "Molecular Modeling - Industrial Relevance and
Applications" in: Ullmann's Encyclopedia of Industrial Chemistry, 7th
edition, Wiley-VCH, Weinheim, 2006, online.
Donald B. Boyd "The Power of Computational Chemistry to Leverage
Stress Testing of Pharmaceuticals" in: Understanding Drug Degradation,
S. W. Baertschi, Ed., Taylor and Francis, London, U.K.,
2005, Ch. 12, pp. 355-418.
P. Franchetti, L. Cappellacci, M. Pasqualini, R. Petrelli, V.
Jayaprakasan, H. N. Jayaram, D. B. Boyd, M. D. Jain, and M. Grifantini
"Synthesis, Conformational Analysis, and Biological Activity of New
Analogues of Thiazole-4-carboxamide Adenine Dinucleotide (TAD) as IMP
Dehydrogenase Inhibitors" Bioorg. Med. Chem. 2005, 13,
2045-2053.
T. Ercanli and Donald B. Boyd "Evaluation of Computational Chemistry
Methods: Crystallographic and Cheminformatics Analysis of
Aminothiazole Methoximes"
J. Chem. Inf. Mod. 2005, 45, 591-601.
Z. Wang, G. L. Durst, R. C. Eberhart, D. B. Boyd, and Z. Ben Miled
"Particle Swarm Optimization and Neural Network Application for QSAR"
HiCOMP 2004 (Online Proceedings of Third IEEE
International Workshop on High Performance
Computational Biology, Santa Fe, New Mexico, April 26, 2004).
Donald B. Boyd, Book Review of: "Computational Medicinal Chemistry for
Drug Discovery" [Patrick Bultinck, Hans De Winter, Wilfried
Langenaeker, and Jan P. Tollenaere, Eds., Marcel Dekker, New York,
2004] J. Med. Chem. 2004, 47, 6433.
Professor Boyd's resume and a more complete list of publications,
click on Boyd Lab Homepage.
Publications prior to 2004
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