How Do Small Molecule Aggregates Inhibit Enzyme Activity? A Molecular Dynamics Study

Abstract

Small molecule compounds which form colloidal aggregates in solution are problematic in early drug discovery; adsorption of the target protein by these aggregates can lead to false positives in inhibition assays. In this work, we probe the molecular basis of this inhibitory mechanism using molecular dynamics simulations. Specifically, we examine in aqueous solution the adsorption of the enzymes β-lactamase and PTP1B onto aggregates of the drug miconazole. In accordance with experiment, molecular dynamics simulations observe formation of miconazole aggregates as well as subsequent association of these aggregates with β-lactamase and PTP1B. When complexed with aggregate, the proteins do not exhibit significant alteration in protein tertiary structure or dynamics on the microsecond time scale of the simulations, but they do indicate persistent occlusion of the protein active site by miconazole molecules. MD simulations further suggest this occlusion can occur via surficial interactions of protein with miconazole but also potentially by envelopment of the protein by miconazole. The heterogeneous polarity of the miconazole aggregate surface seems to underpin its activity as an invasive and nonspecific inhibitory agent. A deeper understanding of these protein/aggregate systems has implications not only for drug design but also for their exploitation as tools in drug delivery and analytical biochemistry.

Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches

“…The tendency of small organic molecules to spontaneously form colloidal self-aggregates can lead to undesired artifacts in the screening of drug-like compounds, resulting in the identification of false positives [ 203 , 204 ]. The colloidal aggregates formed by these types of compounds exhibit common trends, such as the lack of robust structure-activity relationships, as well as the identification of time-dependent noncompetitive-like inhibition [ 200 , 205 ], likely reflecting the nonspecific inhibitory mechanisms related to adsorption of the target protein onto the aggregates or the induction of conformational alterations that affect the protein’s activity [ 206 ]. In these cases, a critical parameter to be considered is the critical aggregation concentration of the compound, which turns out to be in the micromolar range for a significant number of aggregating drug-like compounds [ 202 , 207 ].…”

Sapogenin based self-assembly structures activating a non-apoptotic cell death via multiple pathways

“…Considering the fact that aggregation behavior of small molecules is also highly dependent on the concentration, the number of molecules as well as the size of the simulation box should be carefully selected in order to mimic experimentally obtained critical assembly concentrations. However it is not always possible to test desired concentration ranges with MD simulation, as lower concentrations require large box sizes with fewer molecules, which in turn require longer simulation times (and hence higher computational capacity) to allow copies of molecules to clash into each other so that aggregation behavior is tested [16]. The systems we could afford to construct for AG as well AG-08 thus included significantly higher concentrations than their observed critical assembly concentration ranges (Table 2).…”

Thermostability mechanisms of β-agarase by analyzing its structure through molecular dynamics simulation

“…Molecular dynamics (MD) simulation can use microscopic computational information to provide insights into thermal enhancing and reducing factors (Karplus and McCammon, 2002 ). This strategy has been a well-known method to understand the structure and properties of numerous enzymes (Sárosi and Lybrand, 2018 ; Chen et al, 2021 ; Ghattas et al, 2020 ; Vahed et al, 2020 ; Kumar et al, 2021 ). However, MD has rarely been employed in β-agarase engineering to provide detailed descriptions of β-agarase folding and unfolding thermal motion at different temperatures.…”