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Dr. Jeffry Madura

Jeffry Madura

Bayer School of Natural and Environmental Sciences Chemistry & Biochemistry
Lambert F. Minucci Endowed Chair in Engineering & Computational Sciences

Mellon Hall 320
Phone: 412.396.4129


Post-doctoral Research Associate, University of Houston, 1990
Ph.D., Physical Chemistry, Purdue University, 1985
B.A., Chemistry, Thiel College, 1980

Dr. Jeffry D. Madura is a professor in the Department of Chemistry and Biochemistry at Duquesne University located in Pittsburgh, Pa. In 2013, Dr. Madura was named the inaugural Lambert F. Minucci Endowed Chair in Engineering & Computational Sciences. He has been a member of Duquense faculty since 1998 and was Department Chair from 2000-2010.

Dr. Madura earned a B.A. in Chemistry from Thiel College in 1980 and a Ph.D. in Physical Chemistry from Purdue University in 1985. The Ph.D. was followed by a postdoctoral fellowship in computational biophysics with Professor J. Andrew McCammon at the University of Houston.

Dr. Madura's research interests are in computational chemistry and biophysics, including simulations of biological processes such as protein folding and dynamics, computer-aided drug design, and modeling of organic reactions. He has published more than 100 papers in physical chemistry and chemical physics.

Dr. Madura has taught chemistry from the undergraduate to graduate level for 24 years and was the recipient of the 1997-1998 Dreyfus Teacher-Scholar Award. He is co-author to a textbook titled General Chemistry: Principles and Modern Applications as well as a co-author to the physical chemistry solutions manual, Principles of Physical Chemistry by Kuhn, Foersterling, and Waldeck. Dr. Madura is also currently the co-editor to the Journal of Molecular Graphics and Modeling.

He was elected as an ACS Fellow in 2011, and in 2008, Dr. Madura was inducted into the Duquesne University Office of Research Hall of Fame. He also received the Bayer School of Natural and Environmental Sciences and the Duquesne University Presidential Award for Excellence in Scholarship in 2007 and the Bayer School of Natural and Environmental Sciences Award for Excellence in Service in 2004.


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.

Selected Peer-reviewed Publications

(In chronological order and out of 100+ publications; Undergraduate authors bolded.)

  1. Discovery of novel-scaffold monoamine transporter ligands via in silico screening with the S1 pocket of the serotonin transporter. TL Nolan, LM Geffert, BJ Kolber, JD Madura, CK Surratt. ACS chemical neuroscience (2014). 5(9), 784-792.
  2. B-amyloid and neprilysin computational studies identify critical residues implicated in binding specificity. D Pope, JD Madura, M Cascio. Journal of chemical information and modeling (2014). 54(4),1157-1165.
  3. Exploring the physicochemical properties of oxime-reactivation therapeutics for Cyclosarin, Sarin,Tabun, and VX inactivated Acetylcholinesterase. EX Esposito, TR Stouch, T Wymore, JD Madura. Chemical research in toxicology (2014). 27(1), 99-110.
  4. Sodium versus potassium effects on the glutamic acid side-chains interaction on an heptapeptide.EK Asciutto, T Gaborek, JD Madura. Journal of theoretical and computational chemistry (2014).13(3), doi: 10.1142/S0219633614400045.
  5. A review of monoamine transporter-ligand interactions. K Immadisetty, JD Madura. Current computer-aided drug design (2013). 9(4), 556-568.
  6. New design strategies for antidepressant drugs. K Immadisetty, LM Geffert, CK Surratt, JD Madura. Expert opinion on drug discovery (2013). 8(11), 1399-1414.
  7. Global transitions of proteins explored by a multi scale hybrid methodology: Applications to adenylate kinase. M Gur, JD Madura, I Bahar. Biophyical journal (2013). 105(7), 1643-1652.
  8. Conformational free-energy landscapes for a peptide in saline environments. TJ Gaborek, C Chipot, JD Madura. Biophysical journal (2012). 103(12), 2513-2520.
  9. Monoamine transporter structure, function, dynamics, and drug discovery: a computational perspective. S Manepalli, CK Surratt, JD Madura, TL Nolan. The AAPS Journal (2012). 12(4), 820-831.
  10. Insights from molecular dynamics: The binding site of cocaine in the dopamine transporter and permeations pathways of substrates in the lucine and dopamine transporters. BA Merchant, JD Madura. Journal of molecular graphics and modeling (2012). 38, 1-12.
  11. Solution structural ensembles of substrate-free cytochrome P450(cam). EK Asciutto, MJ Young, JD Madura, SS Pochapsky, TC Pochapsky. Biochemistry (2012). 51(16), 3383-3393.
  12. A review of coarse-grained molecular dynamics techniques to access extended spatial and temporal scales in biomolecular simulations. BA Merchant, JD Madura. Annual reports in computational chemistry (2011). 7, 67-87.
  13. Discovery of novel selective serotonin reuptake inhibitors through development of a protein-based pharmacophore. S Manepalli, LM Geffert, CK Surratt, JD Madura. Journal of chemical information and modeling (2011). 51(9), 247-2426.
  14. Solvation of metal cations in non-aqueous liquids. MJ Ziegler, JD Madura. Journal of solution chemistry (2011). 40(8), 1383-1398.
  15. Identification of a novel selective serotonin reuptake inhibitor by coupling monoamine transporter-based virtual screening and rational molecular hybridization. TL Nolan, DJ Lapinsky, JN Talbot, M Indarte, Y Liu, S Manepalli, LM Geffert, ME Amos, PN Taylor, JD Madura, CK Surratt. ACS chemical neuroscience (2011). 2(9), 544-552.
  16. Experimentally restrained molecular dynamics simulations for characterizing the open states of cytochrome P450(cam). EK Asciutto, M Dang, SS Pochapsky, JD Madura, TC Pochapsky. Biochemistry (2011). 50(10), 1664-1671.
  17. Design, synthesis, and testing of an 6-O-linked series of benzimidazole based inhibitors of CDK5/p25. P Jain, PT Flaherty, S Yi, I Chopra, G Bleasdell, J Lipay, Y Ferandin, L Meijer, JD Madura. Bioorganic & medicinal chemistry (2011). 19(1), 359-373.
  18. Benchmarking docking and scoring protocol for the identification of potential acetylcholinesterase inhibitors. SA Halim, R Uddin, JD Madura. Journal of molecular graphics and modeling (2010). 28(8), 870-882.
  19. Molecular Dynamics of Leucine and Dopamine Transporter Proteins in a Model Cell Membrane Lipid Bilayer. PG Gedeon, M Indarte, CK Surratt, JD Madura. Proteins: Structure, Function and Bioinformatics (2010). 78(4), 797-811.
  20. Sodium perchlorate effects on the helical stability of a mainly alanine peptide. EK Asciutto, IJ General, K Xiong, SA Asher, JD Madura. Biophysical journal (2010). 98(2), 186-196.
  21. Receptor-based discovery of a plasmalemmal monoamine transporter inhibitor via high-throughput docking and pharmacophore modeling. M Indarte, Y Liu, JD Madura, CK Surratt. Chemical neuroscience (2010). 1(3), 223-233.
  22. Free energy perturbation Monte Carlo simulations of salt influences on aqueous freezing point depression. TJ Dick, A Wierzbicki, JD Madura. Practical aspects of computational chemistry (2010). 359-370.
  23. CO2(aq) parameterization through free energy perturbation/ Monte Carlo simulations for use in CO2 sequestration. TJ Dick, A Wierzbicki, JD Madura, SA Asher. Biochemistry (2010). 337-357.

Fall 2014: CHEM 321: Physical Chemistry I

This course provides an understanding of atomic and molecular structure and energy. The material covered involves the Schrodinger equation, particle in a box, postulates of quantum mechanics, the harmonic oscillator and rigid roto, and the hydrogen atom. The class objective is to establish a solid foundation in quantum chemistry to be applied and understood in more advanced topics of chemical bonding and molecular spectroscopy.

Dr. Madura has taught both regular and honors General Chemistry, Physical Chemistry, Physical Chemistry for Life Sciences, Statistical Thermodynamics and Molecular Modeling courses. He has also created and currently runs a Pennsylvania Junior Academy of Sciences Workshop for one-half day on Designer Drugs. He has developed and taught six-hours of lecture and nine-hours of lab for the NSF/NIH
Bioengineering and Bioinformatics Summer Institute and the NSF-sponsored TECBio program at the University of Pittsburgh.


Pittsburgh Award, 2014

Lambert F. Minucci Endowed Chair in Engineering & Computational Sciences, 2013

ACS Fellow, 2011

Duquesne University Offce of Research Hall of Fame, 2008 Inductee

Duquesne University President's Award for Excellence in Scholarship, 2007

Bayer School of Natural & Environmental Sciences Award for Excellence in Scholarship, 2007

Bayer School of Natural & Environmental Sciences Award for Excellence in Service, 2002

Duquesne University Department of Chemistry and Biochemistry Chair, 2000-2010

Computational Chemistry Gordon Research Conference Chair, 1998

Henry Dreyfus Teacher-Scholar, 1997

Computational Chemistry Gordon Research Conference vice-chair, 1996