This renewal proposal seeks to continue the development and application of continuous constant pH molecular dynamics (CpHMD) tools to advance molecular understanding of proteases, kinases and sodium/proton an- tiporters which are involved in Alzheimer's disease, cancer and hypertension, respectively. The objectives of this proposal are to 1) further develop, accelerate and disseminate CpHMD; 2) discover electrostatic modulators of aspartyl proteases and kinases towards selective inhibition; and 3) elucidate the mechanisms of sodium/proton antiporters. Development of a pH stat to properly control solution pH has been a long-standing goal in the MD community. Our recent development of PME-based all-atom CpHMD brought us closer to the goal.
In Aim 1, we will add a polarizable force ?eld to take the accuracy of CpHMD to the next level. We will implement CpHMD in other packages to enable alternative implicit-solvent models and force ?elds. We will implement the code on the GPU platform to allow routine microsecond-scale simulations. The new developments will push the boundary of current MD simulations, transforming pKa calculations and studies of proton-mediated processes. Protonation states and pH effects are a neglected aspect in structure-based drug design due to the lack of tools and understanding. We recently discovered a pH-regulated dynamics-activity relationship for -secretase (a major Alzheimer's drug target) and demonstrated signi?cant pH dependence in small-molecule binding.
In Aim 2, we will continue the study of -secretase related aspartyl proteases, and we will tackle challenging questions regarding kinase activation and selective inhibition. Conventional ?xed-protonation-state MD with static-structure-based electrostatic calculations cannot reliably iden- tify proton-binding residues and elucidate proton-coupled conformational dynamics. We recently developed the membrane hybrid-solvent CpHMD, which allowed the ?rst constant pH simulations of a proton channel (M2), a sodium/proton antiporter (NhaA) and an ef?ux pump (AcrB).
In Aim 3, we plan to apply this and the new tools developed in Aim 1 to gain further insights into the sodium-proton exchange process in NhaA and to elucidate the distinctive mechanism of another sodium-proton antiporter. These studies will further validate CpHMD and establish it as a powerful tool for studies of proton-coupled transmembrane proteins. In summary, the proposed project will push the boundary of the current predictive power of molecular simulations, transform studies of proton-mediated processes, and generate new insights to accelerate drug discovery targeting Alzheimer's disease, cancer and hypertension.

Public Health Relevance

This project seeks to advance the molecular-level knowledge of proteases, kinases and ion-proton antiporters, which are the proteins involved in Alzheimer's disease, cancer and hypertension. The results will push the boundary of the current predictive power of molecular simulations to elucidate the proton-mediated processes controlling the structure-function relationships of these proteins and generate new insights to accelerate drug discovery efforts.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function D Study Section (MSFD)
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Lyster, Peter
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University of Maryland Baltimore
Schools of Pharmacy
United States
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Shen, Jana (2018) Zooming in on a small multidrug transporter reveals details of asymmetric protonation. Proc Natl Acad Sci U S A 115:8060-8062
Yue, Zhi; Shen, Jana (2018) pH-Dependent cooperativity and existence of a dry molten globule in the folding of a miniprotein BBL. Phys Chem Chem Phys 20:3523-3530
Yue, Zhi; Chen, Wei; Zgurskaya, Helen I et al. (2017) Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump. J Chem Theory Comput 13:6405-6414
Harris, Robert C; Tsai, Cheng-Chieh; Ellis, Christopher R et al. (2017) Proton-Coupled Conformational Allostery Modulates the Inhibitor Selectivity for ?-Secretase. J Phys Chem Lett 8:4832-4837
Ellis, Christopher R; Tsai, Cheng-Chieh; Lin, Fang-Yu et al. (2017) Conformational dynamics of cathepsin D and binding to a small-molecule BACE1 inhibitor. J Comput Chem 38:1260-1269
Ellis, Christopher R; Tsai, Cheng-Chieh; Hou, Xinjun et al. (2016) Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors. J Phys Chem Lett 7:944-9
Chen, Wei; Huang, Yandong; Shen, Jana (2016) Conformational Activation of a Transmembrane Proton Channel from Constant pH Molecular Dynamics. J Phys Chem Lett 7:3961-3966
Huang, Yandong; Chen, Wei; Wallace, Jason A et al. (2016) All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water. J Chem Theory Comput 12:5411-5421
Huang, Yandong; Chen, Wei; Dotson, David L et al. (2016) Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA. Nat Commun 7:12940
Morrow, Brian H; Payne, Gregory F; Shen, Jana (2015) pH-Responsive Self-Assembly of Polysaccharide through a Rugged Energy Landscape. J Am Chem Soc 137:13024-30

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