Specific, noncovalent binding is central to many biological functions, such as signaling and immunity; and most drugs are small molecules that bind a specific protein and modulate its function. This project aims fr a deeper and more quantitative understanding of noncovalent binding, coupled with increasingly predictive and insightful modeling technologies that will speed the discover of new medications. One goal is to develop best practices for computing not only bindin free energies, but also numerically precise binding enthalpies, using molecular dynamics simulations with an explicit treatment of water. We will then apply these practices to seek mechanistic explanations of often puzzling experimental calorimetric data, such as observations that ligand preorganization may strengthen binding not entropically, as expected, but enthalpically; and the common, but still poorly understood, phenomenon of entropy-enthalpy compensation. We will also work on a new method to test the force fields used in molecular simulations. Today, force fields are tested primarily by computing small molecule hydration free energies and the physical properties of pure liquids, and comparing these results with experiment. Thus, although simulations are widely used to model binding, experimental binding data plays little role in the testig and optimization of simulation force fields. Here, we aim to establish host-guest bindng data as a new benchmark for testing force fields, by assembling a panel of experimentally characterized, computationally tractable, host-guest systems, along with computational scripts which automate the calculation of their binding free energies and enthalpies and the comparison of these results with experiment. This "validation engine" will be used to test widely used force fields, and will also be shared freely with ther groups. Finally, we will integrate free energy simulation methods into two collaborative drug??discovery projects. One project centers on a human enzyme called soluble epoxide hydrolase, whose three-dimensional structure is known and which is therapeutically relevant to cardiovascular and inflammatory disease. In our preliminary studies, conventional docking approaches have provided little or no useful guidance; we now aim to apply more sophisticated fre energy simulation methods to this challenging case. The second project, which is at a earlier stage, concerns a bacterial virulence factor called Cif. This, too, is an epoide hydrolase, and its inhibition is expected to be helpful to patients with Pseudomonas pneumonia. We plan to use docking and free energy methods to help discover potent Cif inhibitors for use as chemical probes and, potentially, as first steps toward a ne medication.

Public Health Relevance

Our goal is to help pharmaceutical scientists develop new medications more quickly and at lower cost. We aim, in particular, to use computer simulations to study how drug molecules work;to improve the accuracy of computer simulations of drugs and their interactions with other molecules;and to use state of the art simulations to help two drug-discovery projects, one related to cardiovascular and inflammatory disease, the other related to lung infections and cystic fibrosis.

Agency
National Institute of Health (NIH)
Type
Research Project (R01)
Project #
2R01GM061300-14
Application #
8760244
Study Section
Macromolecular Structure and Function D Study Section (MSFD)
Program Officer
Preusch, Peter
Project Start
Project End
Budget Start
Budget End
Support Year
14
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of California San Diego
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Muddana, Hari S; Yin, Jian; Sapra, Neil V et al. (2014) Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method. J Comput Aided Mol Des 28:463-74
Muddana, Hari S; Sapra, Neil V; Fenley, Andrew T et al. (2014) The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations. J Comput Aided Mol Des 28:277-87
Fenley, Andrew T; Killian, Benjamin J; Hnizdo, Vladimir et al. (2014) Correlation as a determinant of configurational entropy in supramolecular and protein systems. J Phys Chem B 118:6447-55
Muddana, Hari S; Fenley, Andrew T; Mobley, David L et al. (2014) The SAMPL4 host-guest blind prediction challenge: an overview. J Comput Aided Mol Des 28:305-17
Velez-Vega, Camilo; Gilson, Michael K (2013) Overcoming dissipation in the calculation of standard binding free energies by ligand extraction. J Comput Chem 34:2360-71
Muddana, Hari S; Sapra, Neil V; Fenley, Andrew T et al. (2013) The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling. J Chem Phys 138:224504
Muddana, Hari S; Varnado, C Daniel; Bielawski, Christopher W et al. (2012) Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. J Comput Aided Mol Des 26:475-87
Pereira, Alban R; Kale, Andrew J; Fenley, Andrew T et al. (2012) The carmaphycins: new proteasome inhibitors exhibiting an ?,?-epoxyketone warhead from a marine cyanobacterium. Chembiochem 13:810-7
Gilson, Michael K; Radford, Sheena E (2011) Protein folding and binding: from biology to physics and back again. Curr Opin Struct Biol 21:1-3
Moghaddam, Sarvin; Yang, Cheng; Rekharsky, Mikhail et al. (2011) New ultrahigh affinity host-guest complexes of cucurbit[7]uril with bicyclo[2.2.2]octane and adamantane guests: thermodynamic analysis and evaluation of M2 affinity calculations. J Am Chem Soc 133:3570-81

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