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Department of Medicinal Chemistry
Robert J. Doerksen Publications

Peer-reviewed Papers 2006-2009

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Prior Publications


    Invited Presentations 2006-2009

  • R. J. Doerksen "Computational studies for rational design of GSK-3 and CDK5 inhibitors." 2nd Annual Meeting of the Mississippi Biophysical Consortium (MBC 2009), Mississippi State University, Starkville, MS, May 28-29, 2009.
  • R. J. Doerksen "Computational Medicinal Chemistry Approaches for Understanding Protein-Ligand Interactions." Rust College, Holly Springs, MS, March 4, 2009.
  • R. J. Doerksen "Computational Medicinal Chemistry Approaches for Understanding Protein-Ligand Interactions." Rust College, Holly Springs, MS, October 22, 2008.
  • R. J. Doerksen "Rational computer-aided drug design for glycogen synthase kinase-3 inhibition." American Association of Colleges of Pharmacy, Chicago, IL, July 2008.
  • R. J. Doerksen "Computational Medicinal Chemistry Approaches for Understanding Protein-Ligand Interactions." Department of Chemistry, National Changhua Education University, Changhua, Taiwan, June 2008.
  • R. J. Doerksen "Novel peptidomimetic antimicrobial oligomers: Insights from computational modeling." School of Pharmacy, National Taiwan University, Taipei, Taiwan, Jan. 19, 2006.
  • R. J. Doerksen "Computational studies towards controlling the conformation of oligomers: Innovative functional backbones." Institute of Chemistry, Academia Sinica, Taipei, Taiwan, Jan. 18, 2006.

    Conference Oral Presentations 2006-2009

    2009
  • P. R. Daga and R. J. Doerksen "Homology modeling and molecular dynamics simulation of Hepatitis B Virus DNA polymerase: Validation using molecular docking." Division of Computers in Chemistry: 237th American Chemical Society (ACS) National Meeting, Salt Lake City, UT, Mar. 2009.

    • 2008
  • R. J. Doerksen and P. Sivaprakasam "Topological Polar Surface Area: A useful descriptor in 2D-QSAR." 236th ACS National Meeting & Exposition, Philadelphia, PA, Division of Chemical Information, 2008, August 17-21.
  • P. R. Daga and R. J. Doerksen "Binding of Spiroquinazolinones to Phosphodiesterase-7: Insights from Molecular Electrostatic Potential." 35th Annual MALTO Medicinal Chemistry-Pharmacognosy Meeting, Little Rock, AK, May 2008. PR Daga won the Nobles-Sam Award for best oral presentation by a University of Mississippi Department of Medicinal Chemistry student.
  • A. E. Wahba, J. Peng, P. Sivaprakasam, S. Odde, R. J. Doerksen and M. T. Hamann "Regio-controlled nitration of manzamine A as intermediates for producing manzamine analogues with better docking scores with GSK-3Beta." 235th ACS National Meeting & Exposition, New Orleans, LA, Division of Medicinal Chemistry, 2008, April 6-10.

    • 2007
  • P. Sivaprakasam, S. Odde, A. Xie and R. J. Doerksen "Genetic algorithm-guided QSPR model for drug absorption." PharmForum 2007, American Association of Pharmaceutical Scientists 6th Annual Southern Regional Discussion Group, Memphis, TN, May 2007.
  • P. Sivaprakasam, S. Odde, A. Xie and R. J. Doerksen "First pharmacophore model and novel qsar models for antimalarial farnesyltransferase inhibitors." 34th Annual MALTO Medicinal Chemistry-Pharmacognosy Meeting, Monroe, LA, May 2007. P. Sivaprakasam won the Nobles-Sam Award for best oral presentation by a University of Mississippi Department of Medicinal Chemistry student.
  • R. J. Doerksen, S. Odde, A. Xie, R. Mohamed, R. Stanikunite, Zhi Bie, M. T. Hamann and S. A. Ross "Absolute configuration of bioactive flexible natural products from DFT optical rotations based on Monte Carlo conformational search and ab initio geometries." Division of Physical Chemistry, 233rd American Chemical Society National Meeting, Chicago, IL, March 2007.
  • P. Sivaprakasam, A. Xie and R. J. Doerksen "Pharmacophore model for antimalarial farnesyltransferase inhibition" 2007 Annual Meeting of the Mississippi Academy of Sciences in Starkville, MS, February 21-23, 2007.

    • 2006
  • R. J. Doerksen "Computational approaches to antimalarial drug targets." Antimalarial Consortium Meeting, Oxford, MS, Oct. 2006.
  • S. R. Clark, A. Xie and R. J. Doerksen "3D-QSAR analysis of inhibitors of farnesyltransferase." 2006 Summer Research Institute for Undergraduates Research Symposium, University of Mississippi, University, MS, Jul. 2006.
  • P. N. Tosso, P. Sivaprakasam and R. J. Doerksen "2D and 3D-QSAR analysis of Plasmodium falciparum dihydrofolate reductase inhibitors." 2006 Summer Research Institute for Undergraduates Research Symposium, University of Mississippi, University, MS, Jul. 2006.

    • Conference Poster Presentations 2006-2009

    2009
  • P. R. Daga and R. J. Doerksen "Homology Modeling, Docking and Molecular Dynamics Simulation of Hepatitis B Virus DNA Polymerase." 36th Annual MALTO Medicinal Chemistry-Pharmacognosy Meeting, Memphis, TN, May 2009.
  • P. R. Daga and R. J. Doerksen "Homology Modeling, Docking and Molecular Dynamics Simulation of Hepatitis B Virus DNA Polymerase." 36th Annual MALTO Medicinal Chemistry-Pharmacognosy Meeting, Memphis, TN, May 2009.
  • P. R. Daga and R. J. Doerksen "Homology Modeling, Docking and Molecular Dynamics Simulation of Hepatitis B Virus DNA Polymerase." 36th Annual MALTO Medicinal Chemistry-Pharmacognosy Meeting, Memphis, TN, May 2009.

    • 2008
  • P. R. Daga and R. J. Doerksen "Homology Modeling, Docking and Molecular Dynamics Simulation of Hepatitis B Virus DNA Polymerase." 35th Annual MALTO Medicinal Chemistry-Pharmacognosy Meeting, Little Rock, AK, May 2008.
  • P. Sivaprakasam, M. T. Hamann and R. J. Doerksen "Computational binding site analysis of GSK-3Beta for manzamine A: Docking, molecular dynamics, MM/PBSA binding free energy and alanine scanning studies." Mississippi NSF EPSCoR Annual State Meeting, Starkville, MS, April 18, 2008.
  • P. R. Daga and R. J. Doerksen "Homology modeling and molecular dynamics simulation of Hepatitis B Virus DNA polymerase: Validation using molecular docking." Mississippi NSF EPSCoR Annual State Meeting, Starkville, MS, April 18, 2008.
  • P. Sivaprakasam, M. T. Hamann and R. J. Doerksen "Blind Docking of Manzamines into Glycogen Synthase Kinase-3Beta." 7th Annual Oxford International Conference on the Science of Botanicals & American Society of Pharmacognosy 4th Interim Meeting, University, MS, April 12-16, 2008. Prasanna won the ASP Student Poster Presentation Award.
  • A. E. Wahba, J. Peng, P. Sivaprakasam, S. Odde, R. J. Doerksen and M. T. Hamann "Regio-controlled Nitration of Manzamine A as Intermediates for Producing Manzamine Analogues with Better Docking Scores with GSK-3." 7th Annual Oxford International Conference on the Science of Botanicals & American Society of Pharmacognosy 4th Interim Meeting, University, MS, April 12-16, 2008.
  • J. J. Bowling, P. R. Daga, S. Odde, S. A. Ahmed, M. K. Mesbah, D. T. Youssef, S. Kudrimoti, S. I. Khalifa, R. J. Doerksen and M. T. Hamann "Actin-binding Comparisons of the Marine Natural Product Latrunculin B with Natural and Semi-synthetic Latrunculin B Analogs." 7th Annual Oxford International Conference on the Science of Botanicals & American Society of Pharmacognosy 4th Interim Meeting, University, MS, April 12-16, 2008.
  • P. R. Daga, J. R. Rimoldi and R. J. Doerksen "Homology Modeling of CYP2B6 and Insights into Mechanism-Based Inactivation of Phenyl Diaziridines." Sigma Xi Undergraduate/Graduate Student Poster Symposium, University of Mississippi, University, MS, April 16, 2008.
  • P. Sivaprakasam, M. T. Hamann and R. J. Doerksen "Computational binding site analysis of GSK-3Beta for manzamine A: Docking, molecular dynamics, MM/PBSA binding free energy and alanine scanning studies." Sigma Xi Undergraduate/Graduate Student Poster Symposium, University of Mississippi, University, MS, April 16, 2008.
  • P. R. Daga and R. J. Doerksen "Homology modeling and molecular dynamics simulation of Hepatitis B Virus DNA polymerase: Validation using molecular docking." Division of Medicinal Chemistry: Poster Session, 235th American Chemical Society (ACS) National Meeting, New Orleans, LA, Apr. 2008.
  • J. J. Bowling, S. A. Ahmed, P. R. Daga, S. Odde, M. K. Mesbah, D. T. Youssef, S. Kudrimoti, S. I. Khalifa, R. J. Doerksen and M. T. Hamann "Actin-binding studies of new natural product oxalatrunculin B, latrunculin B, and two semi-synthetic analogs of the latrunculin class." Division of Biological Chemistry: Poster Session, 235th American Chemical Society (ACS) National Meeting, New Orleans, LA, Apr. 2008.
  • S. Prasanna, P. R. Daga, S. Clark, P. N. Tosso, A. Xie, S. Odde, J. R. Duan and R. J. Doerksen "Computational Investigations of Protein-Ligand Interactions." Mississippi NSF EPSCoR First Annual Legislative Day, Jackson, MS, March 23, 2008.
  • P. Sivaprakasam, M. T. Hamann and R. J. Doerksen "Computational binding site analysis of GSK-3Beta for manzamine A: Docking, molecular dynamics, MM/PBSA binding free energy and alanine scanning studies." NIH CoBRE CORE-NPN, External Advisory Board meeting, University of Mississippi, MS, March 11, 2008.
  • J. Peng, A. Place, W. Yoshida, C. Anklin, P. R. Daga, R. J. Doerksen and M. T. Hamann "A structure for a 50 year old toxin from Karlodinium sp. A product of improvements in cryodual NMR techniques." Marine Natural Products Gordon Conference, Ventura, CA, February, 2008.

    • 2007
  • S. Prasanna, P. R. Daga, S. Clark, P. N. Tosso, A. Xie, S. Odde, J. R. Duan and R. J. Doerksen "Computational Investigations of Protein-Ligand Interactions." 2007 National EPSCoR Meeting, Hawaii, November 2007.
  • P. R. Daga, S. Prasanna, A. Xie, G. Fu, S. Odde and R. J. Doerksen "Computational Medicinal Chemistry using MCSR." SC07 (Supercomputer Conference), (Poster presented by Mr. Jason Hale of Mississippi Center for Supercomputing Research.) Reno, NV, November 2007.
  • P. Sivaprakasam, M. T. Hamann and R. J. Doerksen "Manzamine A Interaction with CDK5: Docking, Molecular Dynamics Simulations and Binding Free Energy Calculations." 16th Conference on Current Trends in Computational Chemistry, Jackson, MS, 2007, November 2-3.
  • P. R. Daga, J. R. Rimoldi and R. J. Doerksen "Homology Modeling of CYP2B6 and Insights into Mechanism-Based Inactivation of Phenyl Diaziridines." 16th Conference on Current Trends in Computational Chemistry, Jackson, MS, 2007, November 2-3.
  • P. Sivaprakasam and R. J. Doerksen "Active site analysis of wild type PfDHFR-TS using docking and molecular dynamics." Mississippi Center for Supercomputing Research (MCSR) Research Symposium, University, MS, September 6-7, 2007.
  • P. Sivaprakasam, P. N. Tosso and R. J. Doerksen "Computational insights into PfDHFR-TS: Application of 2D, 3D-QSAR and docking studies to cycloguanil derivatives." 34th Annual MALTO Medicinal Chemistry-Pharmacognosy Meeting, Monroe, LA, May 2007. P. Sivaprakasam won the Lemke Award for best poster presentation.
  • P. Sivaprakasam, P. R. Daga, A. Xie and R. J. Doerksen "Targeting glycogen synthase kinase-3: A promising Alzheimer's disease target, NIH CoBRE CORE-NPN, External Advisory Board meeting, University of Mississippi, MS, April 3-4, 2007.
  • P. R. Daga and R. J. Doerksen "Is the acidity of the N1 proton in spiroquinazolinones important for PDE7 inhibitory activity?" 2007 Sigma Xi Student Research Symposium Poster Competition, University of Mississippi, University, MS, Mar. 2007.
  • P. Sivaprakasam, P. R. Daga, A. Xie and R. J. Doerksen "3D-QSAR and docking studies on 3-anilino-4-phenylmaleimides for glycogen synthase kinase-3 inhibition." Division of Medicinal Chemistry, 233rd American Chemical Society National Meeting, Chicago, IL, March 2007.
  • S. Odde, P. Sivaprakasam and R. J. Doerksen "Docking and 3D-QSAR analysis of HCV NS5B RNA-dependent RNA polymerase inhibitors based on a common benzothiadiazine scaffold." Division of Medicinal Chemistry, 233rd American Chemical Society National Meeting, Chicago, IL, March 2007.
  • A. Xie, S. Odde, P. Sivaprakasam and R. J. Doerksen "Imidazole-containing farnesyltransferase inhibitors: 3D quantitative structure-activity relationship and molecular docking studies." Division of Medicinal Chemistry, 233rd American Chemical Society National Meeting, Chicago, IL, March 2007.
  • P. Sivaprakasam, A. Xie, P. N. Tosso and R. J. Doerksen "Genetic Function Approximation insights into Plasmodium falciparum Dihydrofolate Reductase and Farnesyltransferase inhibition." Division of Computers in Chemistry, 233rd American Chemical Society National Meeting, Chicago, IL, March 2007.
  • S. R. Clark, A. Xie and R. J. Doerksen "3D-QSAR analysis of farnesyltransferase inhibition for antimalarial diaminobenzophenones" 2007 Annual Meeting of the Mississippi Academy of Sciences in Starkville, MS, February 21-23, 2007.

    • 2006
  • S. R. Clark, A. Xie and R. J. Doerksen "3D-QSAR analysis of farnesyltransferase inhibition for antimalarial diaminobenzophenones" Annual Biomedical Research Conference for Minority Students, Anaheim, CA, Nov. 8-11, 2006.
  • A. Xie, S. R. Clark and R. J. Doerksen "3D quantitative structure-farnesyltransferase inhibition analysis for some diaminobenzophenones." 15th Conference on Current Trends in Computational Chemistry, Jackson, MS, Nov. 3-4, 2006.
  • P. Sivaprakasam, A. Xie and R. J. Doerksen "DFT studies on structurally diverse farnesyltransferase inhibitors: Multivariate analysis of correlation between physicochemical properties and antimalarial activity." 15th Conference on Current Trends in Computational Chemistry, Jackson, MS, Nov. 3-4, 2006.
  • A. Xie, P. Sivaprakasam, S. R. Clark, S. Odde and R. J. Doerksen "Computational approaches to antimalarial drug targets: Non-thiol farnesyltransferase inhibitors." Antimalarial Consortium Meeting, Oxford, MS, Oct. 2006.
  • P. Sivaprakasam, A. Xie, P. R. Daga, P. N. Tosso and R. J. Doerksen "Computational approaches to antimalarial drug targets: Glycogen synthase kinase-3 and dihydrofolate reductase." Antimalarial Consortium Meeting, Oxford, MS, Oct. 2006.
  • P. Sivaprakasam, P. R. Daga, A. Xie and R. J. Doerksen "Physico-chemical and structural requirements among 3-anilino-4-arylmaleimides for GSK-3 inhibitory activity enhancement through 2D and 3D quantitative structure activity relationships (QSARs)." 2006 Sigma Xi Student Research Symposium Poster Competition, University of Mississippi, University, MS, Apr. 2006.

    • Prior Publications
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