Effects of Macromolecular Crowding on the Inhibition of Virus Assembly and Virus-Cell Receptor Recognition

Abstract

Biological fluids contain a very high total concentration of macromolecules that leads to volume exclusion by one molecule to another. Theory and experiment have shown that this condition, termed macromolecular crowding, can have significant effects on molecular recognition. However, the influence of molecular crowding on recognition events involving virus particles, and their inhibition by antiviral compounds, is virtually unexplored. Among these processes, capsid self-assembly during viral morphogenesis and capsid-cell receptor recognition during virus entry into cells are receiving increasing attention as targets for the development of new antiviral drugs. In this study, we have analyzed the effect of macromolecular crowding on the inhibition of these two processes by peptides. Macromolecular crowding led to a significant reduction in the inhibitory activity of: 1), a capsid-binding peptide and a small capsid protein domain that interfere with assembly of the human immunodeficiency virus capsid, and 2), a RGD-containing peptide able to block the interaction between foot-and-mouth disease virus and receptor molecules on the host cell membrane (in this case, the effect was dependent on the conditions used). The results, discussed in the light of macromolecular crowding theory, are relevant for a quantitative understanding of molecular recognition processes during virus infection and its inhibition.

What Macromolecular Crowding Can Do to a Protein

“…The assembly-promoting potential of crowding agents is expected to depend on the size of crowding agents and the relative dimensions of interacting proteins [ 28 ]. In agreement with this model, macromolecular crowding differently affected the polymerization of the HIV-1 capsid protein CA and inhibition of this process by short peptides, or inhibition of interaction between the foot-and-mouth disease virus (FMDV) and receptor molecules on the host cell membrane by short peptides [ 224 ]. In fact, although the assembly of the FMDV) and receptor molecules on the host cell HIV-1 capsid protein CA to capsid-like particles was accelerated in the presence of high concentrations of Ficoll 70 and dextran 10 [ 193 ], inhibition of this process by a small C -terminal domain (CTD) of protein CA (which is responsible for CA dimerization and, in its isolated form, is able to efficiently inhibit the in vitro assembly of the HIV-1 capsid) or by a short CTD-binding dodecapeptide CAI was efficiently inhibited by a variety of the macromolecular crowding agents, such as Ficoll 70, dextran 40, or BSA [ 224 ].…”

Rationally Designed Interfacial Peptides Are Efficient In Vitro Inhibitors of HIV-1 Capsid Assembly with Antiviral Activity

“…CAI was also very efficient at inhibiting in vitro capsid assembly under macromolecular crowding conditions (Fig. 5A), although its inhibitory activity was reduced in these conditions [53]. As the binding sites in CA of CAI/NYAD-1, CAC1/CAC1C/CAC1M, and H8 are different, we considered the use of cocktails of some of these interfacial peptides to inhibit HIV-1 capsid assembly at least as efficiently as with single peptides, but using lower doses of each peptide.…”

Influence of crowded cellular environments on protein folding, binding, and oligomerization: Biological consequences and potentials of atomistic modeling

“…3). This expectation is borne out by a recent study on the inhibition of the assembly of the HIV-1 capsid protein by a capsid protein fragment or a short peptide [78]. In dilution solution, both inhibitors were found to be effective in slowing down the assembly and reducing the total assembled mass.…”