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Computational Drug Design

Our drug design program aims to provide complementary computational solutions to the experimental activities that support the development of small-molecule inhibitors to preclinical drug candidates. The computational efforts are designed to guide experimental research, speed-up the overall drug design process, and provide decision support for moving compounds forward. Research topics include virtual screening, lead optimization, pharmacological evaluations, cytochrome P450 metabolism, and potential drug-drug interactions with prescription drugs.

Software

Publications

Liu, R., M. D. M. AbdulHameed, K. Kumar, X. Yu, A. Wallqvist, and J. Reifman. Data-driven prediction of adverse drug reactions induced by drug-drug interactions. BMC Pharmacology and Toxicology. 2017 June 8; 18(1):44. [PDF 2304 KB]

Chaudhury, S., G. D. Gromowski, D. R. Ripoll, I. V. Khavrutskii, V. Desai, and A. Wallqvist. Dengue virus antibody database: systematically linking serotype-specificity with epitope mapping in dengue virus. PLOS Neglected Tropical Diseases. 2017 February 21; 11(2):e0005395. [PDF 1553 KB]

Khavrutskii, I. V., and A. Wallqvist. Beta-aminoalcohols as potential reactivators of aged sarin-/soman-inhibited acetylcholinesterase. ChemistrySelect. 2017 February 13; 2(5):1885-1890. [PDF 3911 KB]

Lee, D. W., I. V. Khavrutskii, A. Wallqvist, S. Bavari, C. L. Cooper, and S. Chaudhury. BRILIA: integrated tool for high-throughput annotation and lineage tree assembly of B-cell repertoires. Frontiers in Immunology. 2017 January 17; 7:681. [PDF 4716 KB]

Liu, R., X. Yu, and A. Wallqvist. Using chemical-induced gene expression in cultured human cells to predict chemical toxicity. Chem Res Toxicol. 2016 November 21; 29(11):1883-1893. [PDF 3918 KB]

Schyman, P., R. Liu, and A. Wallqvist. Using the variable-nearest neighbor method to identify P-glycoprotein substrates and inhibitors. ACS Omega. 2016 November 16; 1(5):923-929. [PDF 1080 KB]

Ripoll, D. R., I. Khavrutskii, A. Wallqvist, and S. Chaudhury. Modeling the role of epitope arrangement on antibody binding stoichiometry in flaviviruses. Biophysical Journal. 2016 October 18; 111(8):1641-1654. [PDF 2770 KB]

AbdulHameed, M. D., D. L. Ippolito, and A. Wallqvist. Predicting rat and human pregnane X receptor activators using Bayesian classification models. Chemical Research in Toxicology. 2016 October 17; 29(10):1729-1740. [PDF 611 KB]

AbdulHameed, M. D., D. L. Ippolito, J. D. Stallings, and A. Wallqvist. Mining kidney toxicogenomics using gene co-expression modules. BMC Genomics. 2016 October 10; 17:790. [PDF 3575 KB]

Te, J. A., M. D. AbdulHameed, and A. Wallqvist. Systems toxicology of chemically induced liver and kidney injuries: histopathology-associated gene co-expression modules. Journal of Applied Toxicology. 2016 September; 36(9):1137-1149. [PDF 526 KB]

Chaudhury, S., C. F. Ockenhouse, J. A. Regules, S. Dutta, A. Wallqvist, E. Jongert, N. C. Waters, F. Lemiale, and E. Bergmann-Leitner. The biological function of antibodies induced by the RTS,S/AS01 malaria vaccine candidate is determined by their fine specificity. Malaria Journal. 2016 May 31; 15:301. [PDF 1538 KB]

Schyman, P., R. Liu, and A. Wallqvist. General purpose 2D and 3D similarity approach to identify hERG blockers. Journal of Chemical Information and Modeling. 2016 January 25; 56(1):213-222. [PDF 2185 KB]

Ippolito, D. L., M. D. AbdulHameed, G. J. Tawa, C. E. Baer, M. G. Permenter, B. C. McDyre, W. E. Dennis, M. H. Boyle, C. A. Hobbs, M. A. Streicker, B. S. Snowden, J. A. Lewis, A. Wallqvist, and J. D. Stallings. Gene expression patterns associated with histopathology in toxic liver fibrosis. Toxicological Sciences. 2016 January; 149(1):67-88. [PDF 2369 KB]

Loers, G., V. Saini, B. Mishra, S. Gul, S. Chaudhury, A. Wallqvist, G. Kaur, and M. Schachner. Vinorelbine and epirubicin share common features with polysialic acid and modulate neuronal and glial functions. Journal of Neurochemistry. 2016 January; 136(1):48-62. [PDF 1109 KB]

Stallings, J. D., D. L. Ippolito, A. Wallqvist, B. C. McDyre, and J. Reifman. Host response to environmental hazards: using literature, bioinformatics, and computation to derive candidate biomarkers of toxic industrial chemical exposure. Proceedings of the HFM-254 Symposium on Health Surveillance and Informatics in Missions: Multidisciplinary Approaches and Perspectives. Paris, France. 2015 October 12-14; 7:1-14. [PDF 1376 KB]

Te, J. A., K. D. Spradling-Reeves, J. F. Dillman III, and A. Wallqvist. Neuroprotective mechanisms activated in non-seizing rats exposed to sarin. Brain Research. 2015 June 4; 1618:136-148. [PDF 1126 KB]

Liu, R., X. Yu, and A. Wallqvist. Data-driven identification of structural alerts for mitigating the risk of drug-induced human liver injuries. Journal of Cheminformatics. 2015 February 11; 7:4. [PDF 421 KB]

Liu, R., P. Schyman, and A. Wallqvist. Critically assessing the predictive power of QSAR models for human liver microsomal stability. Journal of Chemical Information and Modeling. 2015; 55(8):1566-1575. [PDF 2342 KB]

Khavrutskii, I. V., P. M. Legler, A. M. Friedlander, and A. Wallqvist. A reaction path study of the catalysis and inhibition of the Bacillus anthracis CapD gamma-glutamyl transpeptidase. Biochemistry. 2014 November 11; 53(44):6954-6967. [PDF 8340 KB]

AbdulHameed, M. D., G. J. Tawa, K. Kumar, D. L. Ippolito, J. A. Lewis, J. D. Stallings, and A. Wallqvist. Systems level analysis and identification of pathways and networks associated with liver fibrosis. PLOS ONE. 2014 November 8; 9(11):e112193. [PDF 2476 KB]

Chaudhury, S., J. Reifman, and A. Wallqvist. Simulation of B cell affinity maturation explains enhanced antibody cross-reactivity induced by the polyvalent malaria vaccine AMA1. Journal of Immunology. 2014 September 1; 193(5):2073-2086. [PDF 1832 KB]

Tawa, G. J., M. D. AbdulHameed, X. Yu, K. Kumar, D. L. Ippolito, J. A. Lewis, J. D. Stallings, and A. Wallqvist. Characterization of chemically induced liver injuries using gene co-expression modules. PLOS ONE. 2014 September; 9(9):e107230. [PDF 1775 KB]

Liu, R., N. Singh, G. J. Tawa, A. Wallqvist, and J. Reifman. Exploiting large-scale drug-protein interaction information for computational drug repurposing. BMC Bioinformatics. 2014 June 20; 15:210. [PDF 1845 KB]

Bushman, J., B. Mishra, M. Ezra, S. Gul, C. Schulze, S. Chaudhury, D. Ripoll, A. Wallqvist, J. Kohn, M. Schachner, and G. Loers. Tegaserod mimics the neurostimulatory glycan polysialic acid and promotes nervous system repair. Neuropharmacology. 2014 April; 79:456-466. [PDF 2364 KB]

Liu, R., and A. Wallqvist. Merging applicability domains for in silico assessment of chemical mutagenicity. Journal of Chemical Information and Modeling. 2014 March 24; 54(3):793-800. [PDF 751 KB]

Munagala, S., G. Sirasani, P. Kokkonda, M. Phadke, N. Krynetskaia, P. Lu, F. J. Sharom, S. Chaudhury, M. D. AbdulHameed, G. Tawa, A. Wallqvist, R. Martinez, W. Childers, M. Abou-Gharbia, E. Krynetskiy, and R. B. Andrade. Synthesis and evaluation of Strychnos alkaloids as MDR reversal agents for cancer cell eradication. Bioorganic & Medicinal Chemistry. 2014 February 1; 22(3):1148-1155. [PDF 1086 KB]

Loers, G., V. Saini, B. Mishra, F. Papastefanaki, D. Lutz, S. Chaudhury, D. R. Ripoll, A. Wallqvist, S. Gul, M. Schachner, and G. Kaur. Nonyloxytryptamine mimics polysialic acid and modulates neuronal and glial functions in cell culture. Journal of Neurochemistry. 2014 January; 128(1):88-100. [PDF 1000 KB]

Liu, J., G. J. Tawa, and A. Wallqvist. Identifying cytochrome P450 functional networks and their allosteric regulatory elements. PLOS ONE. 2013 December 3; 8(12):e81980. [PDF 1515 KB]

Khavrutskii, I. V., J. B. Smith, and A. Wallqvist. Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization. Journal of Chemical Physics. 2013 October 25; 139(16):165104. [PDF 749 KB]

Koehler, J. W., J. M. Smith, D. R. Ripoll, K. W. Spik, S. L. Taylor, C. V. Badger, R. J. Grant, M. M. Ogg, A. Wallqvist, M. C. Guttieri, R. F. Garry, and C. S. Schmaljohn. A fusion-inhibiting peptide against Rift Valley fever virus inhibits multiple, diverse viruses. PLOS Neglected Tropical Diseases. 2013 September 12; 7(9):e2430. [PDF 2822 KB]

Bergmann-Leitner, E. S., S. Chaudhury, N. J. Steers, M. Sabato, V. Delvecchio, A. S. Wallqvist, C. F. Ockenhouse, and E. Angov. Computational and experimental validation of B and T-cell epitopes of the in vivo immune response to a novel malarial antigen. PLOS ONE. 2013 August 16; 8(8):e71610. [PDF 1460 KB]

Hu, X., J. R. Compton, M. D. AbdulHameed, C. L. Marchand, K. L. Robertson, D. H. Leary, A. Jadhav, J. R. Hershfield, A. Wallqvist, A. M. Friedlander, and P. M. Legler. 3-substituted indole inhibitors against Francisella tularensis FabI identified by structure-based virtual screening. Journal of Medicinal Chemistry. 2013 July 1; 56(13):5275-5287. [PDF 4884 KB]

Chaudhury, S., M. D. AbdulHameed, N. Singh, G. Tawa, P. M. D'haeseleer, A. T. Zemla, A. Navid, C. E. Zhou, M. C. Franklin, J. Cheung, M. J. Rudolph, J. Love, J. F. Graf, D. A. Rozack, J. L. Dankmeyer, K. Amemiya, S. Daefler, and A. Wallqvist. Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. PLOS ONE. 2013 May 21; 8(5):e63369. [PDF 609 KB]

Singh, N., S. Chaudhury, R. Liu, M. D. AbdulHameed, G. Tawa, and A. Wallqvist. QSAR classification model for antibacterial compounds and its use in virtual screening. Journal of Chemical Information and Modeling. 2012 October 22; 52(10):2559-2569. [PDF 1917 KB]

Liu, R., G. Tawa, and A. Wallqvist. Locally weighted learning methods for predicting dose-dependent toxicity with application to the human maximum recommended daily dose. Chemical Research in Toxicology. 2012 October 15; 25(10):2216-2226. [PDF 449 KB]

Peach, M. L., A. V. Zakharov, R. Liu, A. Pugliese, G. Tawa, A. Wallqvist, and M. C. Nicklaus. Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software. Future Medicinal Chemistry. 2012 October; 4(15):1907-1932. [PDF 1467 KB]

Ripoll, D. R., I. V. Khavrutskii, S. Chaudhury, J. Liu, R. A. Kuschner, A. Wallqvist, and J. Reifman. Quantitative predictions of binding free energy changes in drug-resistant influenza neuraminidase. PLOS Computational Biology. 2012 August; 8(8):e1002665. [PDF 2032 KB]

Liu, R., J. Liu, G. Tawa, and A. Wallqvist. 2D SMARTCyp reactivity-based site of metabolism prediction for major drug-metabolizing cytochrome P450 enzymes. Journal of Chemical Information and Modeling. 2012 June 25; 52(6):1698-1712. [PDF 873 KB]

Cardellina, J. H., V. Roxas-Duncan, V. Montgomery, V. Eccard, Y. Campbell, X. Hu, I. Khavrutskii, G. Tawa, A. Wallqvist, J. Gloer, N. Phatak, U. Hoeller, A. Soman, B. Joshi, S. Hein, D. Wicklow, and L. A. Smith. Fungal bis-naphthopyrones as inhibitors of botulinum neurotoxin serotype A. ACS Medicinal Chemistry Letters. 2012 April 2; 3(5):387-391. [PDF 3092 KB]

Sun, H., G. Tawa, and A. Wallqvist. Classification of scaffold-hopping approaches. Drug Discovery Today. 2012 April; 17(7-8):310-324. [PDF 1623 KB]

AbdulHameed, M. D., S. Chaudhury, N. Singh, H. Sun, A. Wallqvist, and G. J. Tawa. Exploring polypharmacology using a ROCS-based target fishing approach. Journal of Chemical Information Model. 2012 February 27; 52(2):492-505. [PDF 806 KB]

Singh, N., H. Sun, S. Chaudhury, M. D. AbdulHameed, A. Wallqvist, and G. Tawa. A physicochemical descriptor-based scoring scheme for effective and rapid filtering of kinase-like chemical space. Journal of Cheminformatics. 2012 February 8; 4:4. [PDF 1933 KB]

Hu, X., P. M. Legler, I. Khavrutskii, A. Scorpio, J. R. Compton, K. L. Robertson, A. M. Friedlander, and A. Wallqvist. Probing the donor and acceptor substrate specificity of the y-glutamyl transpeptidase. Biochemistry. 2012 January 17; 51(6):1199-1212. [PDF 4752 KB]

Khavrutskii, I., and A. Wallqvist. Improved binding free energy predictions from single-reference thermodynamic integration augmented with Hamiltonian replica exchange. Journal of Chemical Theory and Computation. 2011 August 15; 7(9):3001-3011. [PDF 2559 KB]

Cardellina, J. H., R. Vieira, V. Eccard, J. Skerry, V. Montgomery, Y. Campbell, V. Roxas-Duncan, W. Leister, C. A. LeClair, D. J. Maloney, D. Padula, G. Pescitelli, I. Khavrutskii, X. Hu, A. Wallqvist, and L. A. Smith. Separation of Betti reaction product enantiomers: absolute configuration and inhibition of botulinum neurotoxin A. ACS Medicinal Chemistry Letters. 2011 March; 2(5):396-401. [PDF 2554 KB]

Jiang, X., K. Kumar, X. Hu, A. Wallqvist, and J. Reifman. DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0. Chemistry Central Journal. 2008 September 8; 2(1):18. [PDF 289 KB]

Zhang, S., K. Kumar, X. Jiang, A. Wallqvist, and J. Reifman. DOVIS: an implementation for high-throughput virtual screening using AutoDock. BMC Bioinformatics. 2008 February 29; 9:126. [PDF 190 KB]