From Proteases to Antiporters: Advancing Drug Design Efforts with Continuous-Constant pH Molecular Dynamics Simulations

Abstract

Proton-mediated processes play essential roles in biology and human diseases. These processes are challenging to study experimentally and model with traditional simulation techniques because they rely on fixed protonation states. Continuous-constant pH molecular dynamics (CpHMD) is a computer simulation that provides atomic-level details of proton-coupled mechanisms. In this dissertation, several proteases (Beta-secretases 1/2, plasmepsin II, main proteases, and papain-like proteases) and a sodium-proton antiporter (NhaA) are investigated, elucidating protonation states of critical residues and proton-coupled dynamics to aid drug design efforts.

In Chapter 2, CpHMD is used to investigate several aspartyl proteases. Human Beta-secretase 1 (BACE1) was considered a lead drug target based on the Beta-amyloid hypothesis for Alzheimer's disease. First, simulations reveal how water plays a vital role in improving the selectivity of an inhibitor for BACE1 over the closely related off-target BACE2. Next, simulations of plasmepsin II, a drug target against malaria, reveal the acid-base role of its catalytic aspartates and how binding of the substrate analog inhibitor pepstatin induces pH-dependent dynamics of its active site.

In Chapter 3, simulations of two types of coronavirus cysteine proteases, the papain-like proteases (PLpros) and main proteases (MPros), are performed to aid the broad-spectrum inhibitor design against coronaviruses (CoVs). Here, the protonation states of PLpro from SARS-CoV, SARS-CoV-2, and MERS-CoV reveal the function of the catalytic residues. Moreover, the protonation state of cysteine on the second blocking loop is found to modulate the dynamics of a druggable subpocket. Investigation of the Mpros of SARS-CoV and SARS-CoV-2 uncovers a reactive cysteine residue that covalent inhibitors could target and protonation of a conserved histidine leads to the partial collapse of the S1 pocket.

In Chapter 4, simulations are applied to the E. coli sodium-proton antiporter NhaA which facilitates the exchange of two protons for one sodium ion across the lipid bilayer. One proton binding site is generally accepted, while the other is controversial due to a series of mutations study showing retained activity. The simulations show that in the presence of various mutations, an alternative proton binding site can accept the second proton, and long-distance proton coupling occurs in some cases.