Research

The Doerksen research group focuses on applying the methods of computational medicinal chemistry to a wide variety of problems in rational drug design, including studies of the structure, interactions, reactions and function of molecules relevant to many human diseases, such as Alzheimer’s disease and malaria. We have a major emphasis on collaboration, with the goal of a team approach as an optimal approach to solving complex problems.

Here are a few of our research interests, including, in some cases, certain sources of funding (for which we are eternally grateful!), published papers, and relevant conference presentations.

Cannabinoid Research

Through computational modeling of the requirements for modulating the cannabinoid (CB) receptor subtypes, CB1 and CB2, which are class-A G-protein coupled receptors (GPCRs), we intend to discover molecules which act through the CB receptors and that could later be developed into new drugs to treat many important human ailments including neuropathic pain, neuroinflammation, ischemic/reperfusion injury, anxiety, multiple sclerosis, and epilepsy.

Publications:
  • H Liu; RY Patel; RJ Doerksen “Structure of the cannabinoid receptor 1: Homology modeling of the inactive state and enrichment study based on CB1 antagonist docking.” MedChemComm, 5, 1297-1302 (2014). doi: 10.1039/C4MD00121D Inside cover article.
  • S Liu; RY Patel; PR Daga; H Liu; G Fu; RJ Doerksen; Y Chen; D Wilkins “Combined rule extraction and feature elimination in supervised classification,” IEEE Transactions on Nanobioscience, 11, 228-236 (2012). doi: 10.1109/TNB.2012.2213264; PMID: 22987128
  • LK Brents; F Medina-Bolivar; KA Seely; V Nair; SM Bratton; A Gallus-Zawada; L Ñopo; RY Patel; H Liu; RJ Doerksen; PL Prather; A Radominska-Pandya “Natural prenylated resveratrol analogs arachidin-1 and -3 demonstrate improved glucuronidation profiles and have affinity for cannabinoid receptors,” Xenobiotica, 42, 139-156 (2012). doi: 10.3109/00498254.2011.609570
Current Funding:
  • National Institutes of Health. R15. “Computer-aided Design and In vitro Testing of Novel Cannabinoid Receptor Modulators.” 5/1/2016-4/30/2019. Robert J. Doerksen, Principal Investigator.
Past Funding:
  • University of Mississippi’s National Institutes of Health (NIH) National Center for Research Resources (NCRR) Center of Research Excellence in Natural Products Neuroscience (CORE-NPN) Phase II. “CORE-NPN: Rational Design of Novel Natural Product-Derived Cannabinoid Ligands.” P20GM104932. 9/1/2015-8/31/2016. Robert J. Doerksen, Chemistry Core Participant (PI: Dr. Stephen J. Cutler, University of Mississippi.) Funding for 3 months of postdoctoral fellow support.
  • University of Mississippi’s National Institutes of Health (NIH) National Center for Research Resources (NCRR) Center of Research Excellence in Natural Products Neuroscience (CORE-NPN) Phase II. “CORE-NPN: Rational Design of Novel Natural Product-Derived Cannabinoid Ligands.” P20GM104932. Robert J. Doerksen, Junior Investigator. (PI: Dr. Stephen J. Cutler, University of Mississippi.) 7/1/2012-8/31/2015.
  • Extreme Science and Engineering Discovery Environment (XSEDE) grant of supercomputer time, MCB140248 “Computational insights into the characteristic features of the active state 3D structure of the human CB2 receptor, mode of agonist recognition and agonist-induced conformational changes during receptor activation.” Robert J. Doerksen, Co-Investigator. (PI: Dr. Kuldeep K. Roy, postdoctoral fellow) 9/2014-11/2015.
  • University of Mississippi’s National Institutes of Health (NIH) National Center for Research Resources (NCRR) Center of Research Excellence in Natural Products Neuroscience (CORE-NPN) Junior Investigator Program. “CORE-NPN: Rational Design of Novel Natural Product-Derived Cannabinoid Ligands.” Robert J. Doerksen, Principal Investigator. (PI: Dr. Stephen J. Cutler, University of Mississippi.) 7/1/2009-6/30/2011.
  • National Science Foundation. Mississippi EPSCoR Program. Targeted Seed Grant. “Combined Computational Chemistry and Computational Biology Modeling for Understanding Protein-Protein and Protein-Ligand Interactions.” 1/1/2011-12/31/2011. Robert J. Doerksen, Principal Investigator.

Protein Kinases

We study several aspects of protein kinases, the important proteins which phosphorylate a wide variety of protein substrates and play key roles in signalling.

  • Systematic study of the nature of protein kinase-ligand interactions, based on structural information from the protein databank (PDB) and on static and molecular dynamics (MD) calculations of such structures.
  • Protein modeling, which is useful when there are no experimental structures available for a protein or when studying the dynamics and interactions of proteins.
  • Protein-protein interactions.
  • Detailed study of protein kinase-ligand interactions for particular classes of protein and ligand commencing from PDB or homology model structures, proceeding through docking of ligands, molecular force field static and dynamics calculations and binding free energy estimations.
Publications:
  • A Chatterjee; SJ Cutler; RJ Doerksen; IA Khan; JS Williamson “Discovery of novel thienoquinolone derivatives as selective and ATP non-competitive CDK5/p25 inhibitors by structure-based virtual screening,” Bioorganic & Medicinal Chemistry, 22, 6409-6421 (2014). doi: 10.1016/j.bmc.2014.09.043
  • G Fu; P. Sivaprakasam; OR Dale; SP Manly; SJ Cutler; RJ Doerksen “Pharmacophore modeling, Ensemble docking, virtual screening, and biological evaluation on glycogen synthase kinase-3β.” Molecular Informatics, 33, 610–626 (2014). doi: 10.1002/minf.201400044
  • G Fu; S Liu; X Nan; OR Dale; Z Zhao; Y Chen; DE Wilkins; SP Manly; SJ Cutler; RJ Doerksen “Quantitative structure-activity relationship analysis and a combined ligand-based/structure-based virtual screening study for glycogen synthase kinase-3.” Molecular Informatics, 33, 627–640 (2014). doi: 10.1002/minf.201400045
  • RY Patel; RJ Doerksen “Protein kinases-inhibitor database: analysis of structure variability and protein-inhibitor interactions within the P-loop,” Journal of Proteome Research, 9, 4433-4442 (2010). doi: 10.1021/pr100662s; PMID: 20681595 Cited >24 times.
  • J Peng; S Kudrimoti; S Prasanna; S Odde; RJ Doerksen; HK Pennaka; Y-M Choo; KV Rao; BL Tekwani; V Madgula; SI Khan; B Wang; AMS Mayer; MR Jacob; LC Tu; J Gertsch; MT Hamann “Structure activity relationship and mechanism of action studies of manzamine analogues for the control of neuroinflammation and cerebral infections,” Journal of Medicinal Chemistry, 53, 61-76 (2010). doi: 10.1021/jm900672t; PMID: 20017491 Cited >35 times.
  • S Prasanna; PR Daga; A Xie; RJ Doerksen “Glycogen synthase kinase-3 inhibition by 3-anilino-4-phenylmaleimides: Insights from 3D-QSAR and docking,” Journal of Computer-Aided Molecular Design, 23, 113-127 (2009). doi: 10.1007/s10822-008-9244-1 PMID: 18839067 Cited >17 times.
Past funding:
  • National Science Foundation. Mississippi EPSCoR Program “Modeling and Simulation of Complex Systems.” NSF EPS 0903787 and NSF EPS 1006883. 8/2009-8/2016. Robert J. Doerksen, Co-Investigator. (PI: Dr. Sandra Harpole, Mississippi State University.)
  • National Science Foundation. Mississippi EPSCoR Program. Targeted Seed Grant. “Combined Computational Chemistry and Computational Biology Modeling for Understanding Protein-Protein and Protein-Ligand Interactions.” 1/1/2011-12/31/2011. Robert J. Doerksen, Principal Investigator.
  • National Science Foundation. Mississippi EPSCoR Program. Bridge Funding (between programs). “Innovations through Computational Sciences.” EPS-0556308. Robert J. Doerksen, Investigator. (Dr. Sandra Harpole, PI, Mississippi State University.) 8/2009-10/31/2009.
  • American Association of Colleges of Pharmacy 2007-2008 New Investigators Program for Pharmacy Faculty. “Rational computer-aided drug design for glycogen synthase kinase-3 inhibition.” Robert J. Doerksen (Principal Investigator). 12/15/2007-6/31/2008.
  • University of Mississippi’s National Institutes of Health (NIH) National Center for Research Resources (NCRR) Center of Research Excellence in Natural Products Neuroscience (CORE-NPN) Small Grants Program. “Computational studies on manzamine inhibition of GSK-3beta and CDK5 for treatment of neuroinflammation.” Robert J. Doerksen (PI). 7/1/2007-6/30/2009.
  • National Science Foundation. Mississippi EPSCoR Program. “Innovations through Computational Sciences.” EPS-0556308. Robert J. Doerksen, Investigator. (Dr. Sandra Harpole, PI, Mississippi State University). 5/1/2006-4/30/2009.
  • National Science Foundation. Mississippi EPSCoR Program. “Innovations through Computational Sciences.” EPS-0556308. Robert J. Doerksen, Investigator. (Dr. Sandra Harpole, PI, Mississippi State University). Education & Outreach funding from 5/2008-8/2009 (administered at U. Mississippi by Dr. Peter Sukanek from Dept. of Chemical Engineering) provided support for several key personnel in the Doerksen research group. 5/1/2006-4/30/2009.

Antimalarial Drugs

There is an urgent need for new antimalarial drugs, in part because the protozoa that cause the disease rapidly evolve resistance to drugs. We are also involved in study of the mechanism of action for the antimalarial effect and for side effects of the existing antimalarials, especially of the 8-aminoquinoline drugs which are the mainstay for liver-stage malaria.

Publications:
  • Y Ding; H Liu; BL Tekwani; NPD Nanayakkara; IA Khan; LA Walker; RJ Doerksen “Methemoglobinemia hemotoxicity of some antimalarial 8-aminoquinoline analogues and their hydroxylated derivatives: Density functional theory computation of ionization potentials,” Chemical Research in Toxicology, 29, 1132-1141 (2016). (Published online, 5/25/2016) doi: 10.1021/acs.chemrestox.6b00063
  • H Liu; Y Ding; LA Walker; RJ Doerksen “Computational study on the effect of exocyclic substituents on the ionization potential of primaquine: Insights into the design of primaquine-based antimalarial drugs with less methemoglobin generation,” Chemical Research in Toxicology, 28, 169-174 (2015). doi: 10.1021/tx500230t PMID: 25222923
  • Y Ding; H Liu; NPD Nanayakkara; IA Khan; BL Tekwani; LA Walker; RJ Doerksen “Hydroxylated derivatives of NPC1161: Theoretical insights into their potential toxicity and the feasibility and regioselectivity of their formation,” Journal of Physical Chemistry A, 118, 5501–5507 (2014). doi: 10.1021/jp502612t
  • H Liu; BL Tekwani; NPD Nanayakkara; LA Walker; RJ Doerksen “Methemoglobin generation by 8-aminoquinolines: Effect of substitution at 5-position of primaquine,” Chemical Research in Toxicology, 26, 1801-1809 (2013). doi: 10.1021/tx400067a
  • H Liu; Y Ding; LA Walker; RJ Doerksen “Effect of antimalarial drug primaquine and its derivatives on the ionization potential of hemoglobin: A QM/MM study,” MedChemComm, 4, 1145-1147 (2013). doi: 10.1039/C3MD00045A Cover article, August 2013.
  • A Shayanfar; S Ghasemi; S Soltani; K Asadpour-Zeynali; RJ Doerksen; A Jouyban “Quantitative structure-activity relationships of imidazole-containing farnesyltransferase inhibitors using different chemometric methods,” Medicinal Chemistry, 9, 434-448 (2013). doi: 10.2174/1573406411309030014
  • H Liu; LA Walker; RJ Doerksen “DFT study on the radical anions formed by primaquine and its derivatives,” Chemical Research in Toxicology, 24, 1476-1485 (2011). doi: 10.1021/tx200094v; PMID: 21699254
  • H Liu; LA Walker; NPD Nanayakkara; RJ Doerksen “Methemoglobinemia caused by 8-aminoquinoline drugs: DFT calculations suggest an analogy to H4B’s role in nitric oxide synthase,” Journal of the American Chemical Society, 133, 1172-1175 (2011). doi: 10.1021/ja107472c; PMID: 21244096
  • J Peng; S Kudrimoti; S Prasanna; S Odde; RJ Doerksen; HK Pennaka; Y-M Choo; KV Rao; BL Tekwani; V Madgula; SI Khan; B Wang; AMS Mayer; MR Jacob; LC Tu; J Gertsch; MT Hamann “Structure activity relationship and mechanism of action studies of manzamine analogues for the control of neuroinflammation and cerebral infections,” Journal of Medicinal Chemistry, 53, 61-76 (2010). doi: 10.1021/jm900672t; PMID: 20017491 Cited >35 times.
  • P Sivaprakasam; PN Tosso; RJ Doerksen “Structure-activity relationship and comparative docking studies for cycloguanil analogs as PfDHFR-TS inhibitors,” Journal of Chemical Information & Modeling, 49, 1787-1796 (2009). doi: 10.1021/ci9000663; PMID: 19588935
  • A Xie; S Odde; P Sivaprakasam; RJ Doerksen “Imidazole-containing farnesyltransferase inhibitors: 3D quantitative structure-activity relationship and molecular docking studies,” Journal of Computer-Aided Molecular Design, 23, 431-448 (2009). doi: 10.1007/s10822-009-9278-z; PMID: 19479325
  • A Xie; SR Clark; S Prasanna; RJ Doerksen “3D quantitative structure-farnesyltransferase inhibition analysis for some diaminobenzophenones,” Journal of Enzyme Inhibition & Medicinal Chemistry, 24, 1220-1228 (2009). doi: 10.3109/14756360902781389; PMID: 19912055
  • MA Ibrahim; AG Shilabin; S Prasanna; M Jacob; SI Khan; RJ Doerksen; MT Hamann “2-N-Methyl modifications and SAR studies of manzamine A,” Bioorganic & Medicinal Chemistry, 16, 6702-6706 (2008). PMID: 18595720
  • A Xie; P Sivaprakasam; RJ Doerksen “3D-QSAR analysis of antimalarial farnesyltransferase inhibitors based on a 2, 5-diaminobenzophenone scaffold,” Bioorganic & Medicinal Chemistry 14, 7311-7323 (2006). doi: 10.1016/j.bmc.2006.06.041; PMID: 16837204 Cited >30 times.
Past funding:
  • USAID (American Council on Education/US Agency for International Development). “Africa-U.S. Network of Centers of Excellence in Water & Environmental Science & Technology.” AEG-A-00-05-00007. Robert J. Doerksen, Co-Investigator. (PI: Dr. Nosa Egiebor, University of Mississippi.) 8/1/2014-6/30/2015.
  • Department of Defense USAMRMC. “Development of Safer Antimalarial and Antileishmanial Drugs for US Troops and Travelers.” Robert J. Doerksen, Investigator. (PI: Dr. Larry Walker, University of Mississippi.) 9/2009-12/2012.
  • Centers for Disease Control and Prevention (CDC) National Center for Zoonotic, Vector-Borne, and Enteric Diseases (NCZVED). “Development and Testing of New Antimalarial Drugs.” Robert J. Doerksen, Investigator. (Dr. Mitchell Avery, PI, University of Mississippi.) 8/1/2004-7/31/2009.

Bioactive Natural Products Discovery

Nature is an excellent source of diverse molecules with intriguing properties. Such molecules are being discovered, characterized and tested as potential drug leads for a wide range of human health targets. In collaborative projects with natural product chemists and biologists, my research group performs calculations of the electronic structure of molecules to study their conformational flexibility and to help assign their conformation and absolute configuration. We also study the interactions of the molecules with protein targets to help elucidate their mechanism of bioactivity.

Publications:
  • J Oh; H Liu; HB Park; D Ferreira; G-S Jeong; MT Hamann; RJ Doerksen; MK Na “In silico investigation of lavandulyl flavonoids for the 2 development of potent FAS-inhibitory prototypes,” BBA (Biochimica et Biophysica Acta) General Subjects (accepted 8/8/2016; available online 8/13/2016). doi: 10.1016/j.bbagen.2016.08.001
  • AD Priyanto; RJ Doerksen; C-I Chang; Y-C Lin; T-C Wang; SB Widjanarko; J Kusnadi; J-L Hsu “Screening, discovery, and characterization of angiotensin-I converting enzyme inhibitory peptides derived from proteolytic hydrolysate of bitter melon seed proteins,” Journal of Proteomics, 128, 424-435 (2015). doi: 10.1016/j.jprot.2015.08.018
  • AD Priyanto; RJ Doerksen; C-I Chang; Y-C Lin; T-C Wang; SB Widjanarko; J Kusnadi; J-L Hsu “Data in support of optimized production of angiotensin-I converting enzyme inhibitory peptides derived from proteolytic hydrolysate of bitter melon seed proteins,” Data in Brief, 5, 403-407 (2015). doi: 10.1016/j.dib.2015.09.038
  • P-S Su; RJ Doerksen; S-H Chen; W-C Sung; RDS Rawendra; C-R Chen; J-W Li; Aisha; T-C Huang; C-I Chang; M-H Liao; J-L Hsu “Screening and profiling stilbene-type natural products with angiotensin-converting enzyme inhibitory activity from Ampelopsis brevipedunculata var. hancei (Planch.) Rehder,” Journal of Pharmaceutical and Biomedical Analysis, 108, 70-77 (2015). doi: 10.1016/j.jpba.2015.01.053
  • MM Ghoneim; KM Elokely; AA El-Hela; AEI Mohammad; M Jacob; M Radwan; RJ Doeksen; SJ Cutler; SA Ross “Asphodosides A-E, anti-MRSA metabolites from Asphodelus microcarpus,” Phytochemistry, 105, 79-84 (2014). doi: 10.1016/j.phytochem.2014.06.011
  • MM Ghoneim, KM Elokely; AA El-Hela; AEI Mohammad; M Jacob; SJ Cutler; RJ Doerksen; SA Ross “Isolation and characterization of new secondary metabolites from Asphodelus microcarpus,” Medicinal Chemistry Research, 23, 3510-3515 (2014). doi: 10.1007/s00044-014-0928-x
  • MAM Ibrahim; M Na; J Oh; RF Schinazi; TR McBrayer; T Whitaker; RJ Doerksen; DJ Newman; LG Zachos; MT Hamann “The significance of endangered and threatened plant natural products in the control of human disease,” Proceedings of the National Academy of Sciences of the United States of America, 110, 16832-16837 (2013). doi: 10.1073/pnas.1311528110 Featured article in University of Washington’s Conservation Magazine and “Featured article recommended for teaching” in “F1000Prime”.
  • IH Hwang; J Oh; A Kochanowska-Karamyan; RJ Doerksen; M Na; MT Hamann “A novel natural phenyl alkene with cytotoxic activity,” Tetrahedron Letters, 54, 3872-3876 (2013). doi: 10.1016/j.tetlet.2013.05.032
  • J Oh; JJ Bowling; Y Zou; AG Chittiboyina; RJ Doerksen; D Ferreira; TD Leininger; MT Hamann “Configurational assignments of conformationally restricted bis-monoterpene hydroquinones: Utility in exploration of endangered plants,” Biochemica et Biophysica Acta (BBA) – General Subjects, 1830, 4229-4234 (2013). doi: 10.1016/j.bbagen.2013.04.029; PMID: 23628705
  • MA Albadry; KM Elokely; B Wang; JJ Bowling; MF Abdelwahab; MH Hossein; RJ Doerksen; MT Hamann “Computationally assisted assignment of Kahalalide Y configuration using an NMR-constrained conformational search,” Journal of Natural Products, 76, 178-185 (2013). doi: 10.1021/np3006088; PMID: 23363083
  • H Liu; A Dasmahapatra; RJ Doerksen “Computational study on the conformations of gambogic acid,” Chemical Physics Letters, 511, 405-412 (2011). doi: 10.1016/j.cplett.2011.06.035; PMID: 22991483
  • R Mohammed; J Peng; M Kelly; M Yousaf; E Winn; S Odde; Z Bie; A Xie; RJ Doerksen; MT Hamann “Polyketide-peroxides from a species of Jamaican plakortis (Porifera: Demospongiae),” Australian Journal of Chemistry, 63, 1-9 (2010). Special Issue. doi: 10.1071/CH09665
  • H Liu; CR McCurdy; RJ Doerksen “Computational study on the conformations of mitragynine and mitragynaline,” Journal of Molecular Structure: Theochem, 945, 57-63 (2010). doi: 10.1016/j.theochem.2010.01.011; PMID: 21293786
  • J Peng; S Kudrimoti; S Prasanna; S Odde; RJ Doerksen; HK Pennaka; Y-M Choo; KV Rao; BL Tekwani; V Madgula; SI Khan; B Wang; AMS Mayer; MR Jacob; LC Tu; J Gertsch; MT Hamann “Structure activity relationship and mechanism of action studies of manzamine analogues for the control of neuroinflammation and cerebral infections,” Journal of Medicinal Chemistry, 53, 61-76 (2010). doi: 10.1021/jm900672t; PMID: 20017491 Cited >35 times.
  • S Kudrimoti; SA Ahmed; PR Daga; AE Wahba; SI Khalifa; RJ Doerksen; MT Hamann “Semisynthetic latrunculin B analogs: Studies of actin docking support a proposed mechanism for latrunculin bioactivity,” Bioorganic & Medicinal Chemistry, 17, 7517-7522 (2009). doi: 10.1016/j.bmc.2009.09.012; PMID: 19800245
  • MA Ibrahim; AG Shilabin; S Prasanna; M Jacob; SI Khan; RJ Doerksen; MT Hamann “2-N-Methyl modifications and SAR studies of manzamine A,” Bioorganic & Medicinal Chemistry, 16, 6702-6706 (2008). PMID: 18595720
  • SA Ahmed; S Odde; PR Daga; JJ Bowling; MK Mesbah; DT Youssef; SI Khalifa; RJ Doerksen; MT Hamann “Latrunculin with a highly oxidized thiazolidinone ring:  Structure assignment and actin docking,” Organic Letters 9, 4773-4776 (2007). doi: 10.1021/ol7020675 Cited >21 times.

Alzheimer’s Disease Drug Discovery

As the number of Alzheimer’s disease (AD) patients rises around the world (with the aging of human population), it is a vital goal to find drugs that can prevent, slow or halt AD. We have been involved in a number of drug discovery efforts, including consideration of various human protein kinases as potential anti-AD targets as well as consideration of the role of cannabinoid receptor ligands to prevent the neurodegeneration that is found in AD.

Conference Presentations:
  • MA Nael; RJ Doerksen “Identification of natural products as inhibitors of the protein kinase RNA-like endoplasmic reticulum kinase to manage Alzheimer’s disease.” American Society of Pharmacognosy 2014 Annual Meeting, Oxford, MS, Aug 2014.

GABA (γ-aminobutyric acid) Receptor Modulators

Our purpose is to discover novel active hit compounds as GABAB receptor modulators, which can later be developed into lead drug candidates. We seek orthosteric modulators with potential to be used for important neurological diseases and disorders such as spasticity, anxiety, mood disorders, Parkinson’s disease, epilepsy, schizophrenia, and pain; and allosteric modulators for treatment of depression and other cognitive dysfunctions. There is great need for drugs to treat these various conditions.

Publications:
  • KM Brown; KK Roy; GH Hockerman; RJ Doerksen; DA Colby “Activation of the γ-aminobutyric acid type B (GABAB) receptor by agonists and positive allosteric modulators.“ Journal of Medicinal Chemistry, 58, 6336-6347 (2015). (Miniperspective) doi: 10.1021/jm5018913

Optimal Drug Delivery

We work with collaborators in UM’s Department of Pharmaceutics and Drug Delivery to find novel designs and practical methods for delivery of drugs, such as to kill cancer cells with minimized side effects on healthy cells. We perform an assortment of computations, such as on docking of nanoparticles to proteins and binding modes and energetics for interactions of drug molecules and cyclodextrins.

Conference Presentations:
  • C Popescu; VK Shankar; P Pandey; ZG Cuny; A Vo; RJ Doerksen; SN Murthy “Indomethacin: β-Cyclodextrin complexation and characterization.” American Association of Pharmaceutical Scientists, Denver, CO, Nov 2016. Abstract No. 35W1000.
  • C Popescu; VK Shankar; P Pandey; ZG Cuny; A Vo; RJ Doerksen; SN Murthy “Piroxicam solubility enhancement by native and modified β-cyclodextrins.” American Association of Pharmaceutical Scientists, Denver, CO, Nov 2016. Abstract No. 01T0400.
  • VK Shankar; P Pandey; ZG Cuny; RJ Doerksen; SN Murthy “Preparation and characterization of Captisol® enabled silymarin constituents: A phase solubility and molecular modeling approach.” American Association of Pharmaceutical Scientists, Denver, CO, Nov 2016. Abstract No. 20R1130.
  • C Popescu; VK Shankar; P Pandey; ZG Cuny; A Vo; RJ Doerksen; SN Murthy “Inclusion complex of valsartan with cyclodextrin derivatives.” American Association of Pharmaceutical Scientists, Denver, CO, Nov 2016. Abstract No. 02R1130.
 Publications:
  • NN Mohammed; P Pandey; KM Elokely; HL Liu; RJ Doerksen; MA Repka “Clotrimazole-cyclodextrin based approach for the management and treatment of Candidiasis. A formulation and chemistry based evaluation,” Pharmaceutical Development and Technology, 21, 619-629 (2016). doi: 10.3109/10837450.2015.1041041
  • J Bae; MA Nael; L Jiang; PT Hwang; F Mahdi; H-W Jun; WM Elshamy; Y-D Zhou; SN Murthy; RJ Doerksen; S Jo “Quinone propionic acid-based redox-triggered polymer nanoparticles for drug delivery: Computational analysis and in vitro evaluation,” Journal of Applied Polymer Science, 131 (2014). doi: 10.1002/app.40461
Past funding:
  • National Science Foundation. Mississippi EPSCoR Program. Year 4 Seed Grant. “Computational modeling-aided design, synthesis and optimization of redox-sensitive polymer nanoparticles with optimal colloid-forming and DT-diaphorase-substrate properties.” Robert J. Doerksen, Co-Investigator. (PI: Dr. Seongbong Jo, University of Mississippi.) 9/1/2012-8/31/2013.
  • National Science Foundation. Mississippi EPSCoR Program. Year 3 Seed Grant. “Computational modeling-aided design, synthesis and evaluation of redox-sensitive polymer nanoparticles for cancer targeted drug delivery.” Robert J. Doerksen, Co-Investigator. (PI: Dr. Seongbong Jo, University of Mississippi.) 9/1/2011-8/31/2012.

New Methods for Chemoinformatics

We are interested to develop and test new methods for handling the enormous volumes of chemical information in order to find patterns and to build predictive models. For some of our work, we collaborate with research groups in UM’s Department of Computer & Information Science.

 Publications:
  • G Fu; S Liu; X Nan; OR Dale; Z Zhao; Y Chen; DE Wilkins; SP Manly; SJ Cutler; RJ Doerksen “Quantitative structure-activity relationship analysis and a combined ligand-based/structure-based virtual screening study for glycogen synthase kinase-3.” Molecular Informatics, 33, 627–640 (2014). doi: 10.1002/minf.201400045
  • Z Zhao; G Fu; S Liu; KM Elokely; RJ Doerksen; Y Chen; DE Wilkins “Drug activity prediction using multiple-instance learning via joint instance and feature selection,” BMC Bioinformatics, 14 (Suppl 14), S16 (12 pp) (2013). (2013 MCBIOS Proceedings). doi: 10.1186/1471-2105-14-S14-S16
  • A Shayanfar; S Ghasemi; S Soltani; K Asadpour-Zeynali; RJ Doerksen; A Jouyban “Quantitative structure-activity relationships of imidazole-containing farnesyltransferase inhibitors using different chemometric methods,” Medicinal Chemistry, 9, 434-448 (2013). doi: 10.2174/1573406411309030014
  • G Fu; X Nan; H Liu; RY Patel; PR Daga; Y Chen; DE Wilkins; RJ Doerksen “Implementation of multiple-instance learning in drug activity prediction,” BMC Bioinformatics, 13, (Suppl 15) S3 (2012). doi: 10.1186/1471-2105-13-S15-S3; PMID: 23046442 (2012 MCBIOS Proceedings).
  • S Liu; RY Patel; PR Daga; H Liu; G Fu; RJ Doerksen; Y Chen; D Wilkins “Combined rule extraction and feature elimination in supervised classification,” IEEE Transactions on Nanobioscience, 11, 228-236 (2012). doi: 10.1109/TNB.2012.2213264; PMID: 22987128
  • X Nan; G Fu; Z Zhao; S Liu; RY Patel; H Liu; PR Daga; RJ Doerksen; X Dang; Y Chen; D Wilkins “Leveraging domain information to restructure biological prediction.” BMC Bioinformatics, 12, S22 (15 pp.) (2011) (2011 MCBIOS Proceedings). doi: 10.1186/1471-2105-12-S10-S22; PMID: 22166097
  • S Prasanna; RJ Doerksen “Topological polar surface area: A useful descriptor in 2D-QSAR,” Current Medicinal Chemistry, 16, 21-41 (2009). doi: 10.2174/092986709787002817 PMID: 19149561 Cited >25 times.
Past funding:
  • National Science Foundation. Mississippi EPSCoR Program. Targeted Seed Grant. NSF EPS 0903787. “Combined Computational Chemistry and Computational Biology Modeling for Understanding Protein-Protein and Protein-Ligand Interactions.” 8/16/2015-8/15/2016. Robert J. Doerksen, Principal Investigator
  • National Science Foundation. Mississippi EPSCoR Program “Modeling and Simulation of Complex Systems.” NSF EPS 0903787 and NSF EPS 1006883. 8/2009-8/2016. Robert J. Doerksen, Co-Investigator. (PI: Dr. Sandra Harpole, Mississippi State University.)
  • National Science Foundation. Mississippi EPSCoR Program. Targeted Seed Grant. “Combined Computational Chemistry and Computational Biology Modeling for Understanding Protein-Protein and Protein-Ligand Interactions.” 1/1/2011-12/31/2011.