Drug design

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Department of Chemistry and Biochemistry, Duquesne University
Ph.D., Physical Chemistry, Purdue University, 1985
Summary:

Research in the laboratory consists of the development and application of computational methods in collaboration with experimental research laboratories. Our research interests fall into the areas of computational biophysics and computational material sciences.

Some our current research projects involve, studying the transport mechanism of neurotransmitter sodium symporter proteins, where we are simulating in vivo conditions using molecular dynamics simulations to observe changes in conformation of proteins upon substrate transport. We are researching computer-aided drug design by applying free energy calculations to elucidate intermolecular interactions of various substrates and inhibitors with monoamine transporters. We are investigating conformational properties of polyglutamine peptide systems by applying molecular dynamics, using the metadynmics sampling algorithm, to explore the conformational free energy landscape of polyglutamine peptides in solvent. We are involved in the electronic structure calculations of extended solids, where we are applying computational methods to investigate and predict physicochemical properties of materials. We are also studying smart materials such as hydrogels of PNIPAM.

In the past, we have studied antifreeze proteins at ice/water interfaces and interaction of N-acetylglucosamine with chitnase. The folding of small peptides in salt solution, and structure, function, and dynamics of monoamine transporters have been studied as well.

Dr. Madura is also one of the primary authors to the Brownian dynamics program UHBD, which is used to calculate the diffusion-controlled rate-constants for biomolecular encounters.

Most Cited Publications
  1. "Comparison of simple potential functions for simulating liquid water," William L. Jorgensen, Jayaraman Chandrasekhar, and Jeffry D. Madura, Roger W. Impey and Michael L. Klein, J. Chem. Phys. 79, 926 (1983)
  2. "Optimized intermolecular potential functions for liquid hydrocarbons," William L. Jorgensen, Jeffry D. Madura, Carol J. Swenson, J. Am. Chem. Soc. 106, 6638 (1984)
  3. "Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew," Hans W. Horn, William C. Swope, and Jed W. Pitera, Jeffry D. Madura and Thomas, J. Dick Greg, L. Hura, Teresa Head-Gordon, J. Chem. Phys.120, 9665 (2004)
  4. "Temperature and size dependence for Monte Carlo simulations of TIP4P water," William L. Jorgensen & Jeffry D. MaduraMolecular Physics 56, 1381 (1985)
  5. "Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program," Jeffry D. Madura, James M. Briggs, Rebecca C. Wade, Malcolm E. Davis, Brock A. Luty, Andrew Ilin, Jan Antosiewicz, Michael K. Gilson, Babak Bagheri, L.Ridgway Scott, J.Andrew McCammon, Computer Physics Communications 91, 57 (1995)
Recent Publications
  1. "Polyglutamine Fibrils: New Insights into Antiparallel β-sheet Conformational Preference and Side Chain Structure," David Punihaole, Riley J Workman, Zhenmin Hong, Jeffry D Madura, Sanford A Asher, J. Phys. Chem. B 120, 3012 (2016)
  2. "2-Substituted 3β-Aryltropane Cocaine Analogs Produce Atypical DAT Inhibitor Effects Without Inducing Inward-Facing DAT Conformations," Weimin C. Hong, Theresa A. Kopajtic, Lifen Xu, Stacey A. Lomenzo, Bernandie Jean, Jeffry D. Madura, Christopher K. Surratt, Mark L. Trudell and Jonathan L. Katz, J Pharmacol Exp Ther 356, 624 (2016)
  3. "Human alpha1 Glycine Receptor Allostery as Identified by State-Dependent Crosslinking Studies," Michael Cascio, Rathna J Veeramachaneni, Jeffry MaduraBiophysical Journal 110, 201a (2016)
  4. "Crosslinking/MS Studies of Cholesterol Interactions with Human alpha1 Glycine Receptor," Nicholas Ferraro, Emily Benner, Jeffry Madura, Michael Cascio, Biophysical Journal 110, 355a (2016)
  5. "Computational Investigation of the Transport Mechanism of Neurotransmitter Sodium Symporters using a Physiological Ion Gradient," Emily M Benner, Jeffry D MaduraBiophysical Journal 3, 626a (2016)

Theoretical Chemistry Research Looks to Reduce Side Effects of Medications for Depression, Addiction, Disease

  • By Aude Marjolin
  • 14 February 2013

A research team including PQI faculty Dr. Jeffry D. Madura is attempting to unravel the regulation of dopamine, which leads to happiness. By mapping how these critical neurotransmitters are controlled, Madura and colleagues are trying to better understand the function and structure of the proteins that modulate the receptor/transporter processes of dopamine and serotonin as well as amphetamines and cocaine. The group already has identified a compound as a potential new class of serotonin inhibitors, which would work with the proteins that transport the hormone.

Their initial findings were reported in the Biophysical Journal, with their detailed analysis expected to be published soon.