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SMALL-MOLECULE PROTEIN INTERACTIONS

Small-Molecule Protein Interactions

The aims of these projects are to 1) efficiently deploy computational chemistry tools on DoD high-performance computing assets, 2) model how enzymes process substrate molecules, and 3) develop simulation techniques to accurately calculate changes in drug- or protein-binding free energies. We use these methods to study human serum paraoxonase 1 as a potential bioscavenger for nerve agents, binding of small molecules to Botulinum neurotoxins, and mutations that confer resistance in influenza viruses.

Software

Publications

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]

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]

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]

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]

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]

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]

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]

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]

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

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]

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]

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]

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]

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]

Khavrutskii, I., and A. Wallqvist. Computing relative free energies of solvation using single reference thermodynamic integration augmented with Hamiltonian replica exchange. Journal of Chemical Theory and Computation. 2010 October 21; 6(11):3427-3441. [PDF]

Hu, X., X. Jiang, D. E. Lenz, D. M. Cerasoli, and A. Wallqvist. In silico analyses of substrate interactions with human serum paraoxonase 1. Proteins. 2009 May 1; 75(2):486-498. [PDF]

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]

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]

Jiang, X., K. Kumar, A. Wallqvist, and J. Reifman. DOVIS: a tool for high-throughput virtual screening. Proceedings of the HPCMP Users Group Conference. Pittsburgh, PA. 2007 June 18-22; 421-424. [PDF]