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Researcher Information

Alexander D. MacKerell, Ph.D.
Associate Professor

Department:
Department of Pharmaceutical Sciences
School of Pharmacy

UMGCC Research Program:
Experimental Therapeutics Program

Education/Training:
College Degree: A.S., Biology, Gloucester County College, Sewell, NJ
B.S., Chemistry, University of Hawaii, Honolulu, HI
Ph.D., Biochemistry, Rutgers University, New Brunswick, NJ
Post Doctoral Degree: Karolinska Institutet, Department of Medical Biophysics, Stockholm, Sweden
Harvard University, Department of Chemistry, Cambridge, MA

Contact Information:

Mailing Address: Department of Pharmaceutical Sciences
School of Pharmacy
University of Maryland, Baltimore
20 Penn Street
Baltimore, MD 21201
USA
Email: amackere@rx.umaryland.edu
Phone: 410-706-7442
Fax: 410-706-0346

Research Interests:
Research involves computational and theoretical studies of biological and chemical systems, focusing on the interpretation of experimental data using theoretical methods. Specific areas of interest include structure-function relationships of proteins and nucleic acids; computer-aided drug design targeting cancer, AIDS, immunosuppression and other disease states and empirical force field parametrization of biological and pharmaceutical compounds.

These studies are performed in close collaboration with experimental work allowing for a more detailed interpretation of experimental results and the identification of lead compounds that may be developed into novel therapeutic agents while simultaneously leading to the refinement and development of novel theoretical approaches.

Methods used include molecular modeling based on ab initio, semi-empirical, and empirical force field calculations, Monte Carlo and molecular dynamics simulations, free energy perturbation calculations, macroscopic continuum dielectric calculations, database searching via Docking approaches, and quantitative structure-activity relationships (QSAR).

Publications:
Priyakumar, U.D. and MacKerell, Jr., A.D. “Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER and BMS,” Journal of Chemical Theory and Computing, 2006, 2:187-200.

Markowitz, J., MacKerell, A. D., Jr., Carrier, F., Charpentier, T.H., Weber, D. J. Design of Inhibitors of S100B,” Current Topics in Medicinal Chemistry, 2005, 5: 1093-1108.

Bernard, D.; Coop, A.; MacKerell, A. D., Jr., “Conformationally Sampled Pharmacophore for Peptidic ä Opioid Ligands,: Journal of Medicinal Chemistry, 2005, 48: 7773-7780.

Macias, A.T., Mia, M.Y., Xia, G., Hayashi, J. and MacKerell, Jr., A.D., “Lead Validation and SAR Development via Chemical Similarity Searching; Application to Compounds Targeting the pY+3 Site of the SH2 Domain of p56lck,” Journal of Chemical Information and Modeling, 2005, 45: 1759-1766.

Buck, M., Bonnet, S., Pastor, R.W. and MacKerell, Jr., A.D. “Importance(of the CMAP correction to the CHARMM22 Protein Force Field: dynamics of hen lysozyme" Biophysical Journal, 2006, 90: L36-38L On line: Dec. 16, 2005, doi:10.1529/biophysj.105.078154.

Lamoureux, G., Harder, E., Vorobyov, I.V., Roux, B. and MacKerell, Jr , A.D. “A polarizable model of water for molecular dynamics simulations of biomolecules,” Chemical Physics Letters, 2006, 418: 245-249.

Priyakumar , U.D. and and MacKerell, Jr., A.D. “NMR Imino Proton Exchange Experiments on Duplex DNA Primarily Monitor the Opening of Purine Bases” Journal of the American Chemical Society (Communication), 2006, 128:678-679.

Hancock, C.N., Macias, A., MacKerell, Jr. A.D., and Shapiro, P., “Mitogen Activated Protein (MAP) Kinases: Development of ATP and Non-ATP Dependent Inhibitors,” Medicinal Chemistry, 2006, 2, 213-222.

Priyakumar, U.D. and MacKerell, Jr., A.D. “Computational Approaches for Investigating Base Flipping in Oligonucleotides,” Chemical Reviews, 2006, 106: 489-505.