Design and synthesis of peptides as stabilizers of histone deacetylase 4.

Histone deacetylase 4 (HDAC4) contributes to gene repression by complex formation with HDAC3 and the corepressor silencing mediator for retinoid or thyroid hormone receptors (SMRT). We hypothesized that peptides derived from the class IIa specific binding site of SMRT would stabilize a specific conformation of its target protein and modulate its activity. Based on the SMRT-motif 1 (SM1) involved in the interaction of SMRT with HDAC4, we systematically developed cyclic peptides that exhibit Ki values that are 9 to 56 times lower than that of the linear SMRT peptide. The peptide macrocycles stabilize the wildtype of the catalytic domain of HDAC4 (cHDAC4) considerably better than its thermally more stable 'gain-of-function' (GOF) variant, cHDAC4-H976Y. Molecular docking and mutagenesis studies indicated that the cyclic peptides bind in a similar but not identical manner as the linear SMRT peptide to a discontinuous binding site. Ion mobility mass spectrometry showed no major changes in the protein fold upon peptide binding. Consistent with these results, preliminary hydrogen-deuterium exchange mass spectrometry measurements indicated only minor conformational changes. Taken together, the cyclic SMRT peptides most likely stabilize the apo form of cHDAC4.

Mechanistic Insights into Binding of Ligands with Thiazolidinedione Warhead to Human Histone Deacetylase 4.

Recently, we have reported that non-hydroxamate thiazolidinedione (TZD) analogs are capable of inhibiting human deacetylase 4 (HDAC4). This study aims at the dissection of the molecular determinants and kinetics of the molecular recognition of TZD ligands by HDAC4. For this purpose, a structure activity relationship analysis of 225 analogs was combined with a comprehensive study of the enzyme and binding kinetics of a variety of HDAC4 mutant variants. The experimental data were rationalized by docking to the two major conformations of HDAC4. TZD ligands are competitive inhibitors and bind via a two-step mechanism involving principal molecular recognition and induced fit. The residence time of 24 g is (34 ± 3) min and thus much larger than that of the canonical pan-HDAC inhibitor SAHA ((5 ± 2) min). Importantly, the binding kinetics can be tuned by varying the structure of the CAP group.

Oligolayer-coated nanoparticles: impact of surface topography at the nanobio interface.

Layer-by-layer coating of nanoparticles with a layer number in the single-digit range has gained increasing attention in the field of nanomedicinal research. However, the impact of using various polyelectrolytes on oligolayer formation and, more importantly, their influence on the interaction with the biological system has not often been considered in the past. Hence, we investigated the polyelectrolyte deposition profiles and resulting surface topographies of up to three polyelectrolyte layers on a flat gold sensor surface using three different polycations, namely, poly(ethylene imine) (PEI), poly(allylamine hydrochloride) (PAH), and poly(diallylammonium chloride) (PD), each in combination with poly(styrenesulfonate) (PSS). Surface plasmon resonance spectroscopy and atomic force microscopy revealed that the PEI/PSS pair in particular showed a so-called overshoot phenomenon, which is associated with partial polyelectrolyte desorption from the surface. This is also reflected by a significant increase in the surface roughness. Then, after having transferred the oligolayer assembly onto nanoparticles of ∼32 nm, we realized that quite similar surface topographies must have emerged on a curved gold surface. A major finding was that the extent of surface roughness contributes significantly to the fashion by which the oligolayer-coated nanoparticles interact with serum proteins and associate with cells. For example, for the PEI/PSS system, both the surface roughness and protein adsorption increased by a factor of ∼12 from the second to third coating layer and, at the same time, the cell association massively decreased to only one-third. Our study shows that surface roughness, along with other particle properties such as size, shape, zeta potential, and hydrophobicity, is another decisive factor for nanoparticles in a biological context, which has indeed been discussed previously but has not to date been investigated for oligolayers.

Layer-by-layer assembled gold nanoparticles for the delivery of nucleic acids.

The delivery of nucleic acids to mammalian cells requires a potent particulate carrier system. The physicochemical properties of the used particles, such as size and surface charge, strongly influence the cellular uptake and thereby the extent of the subsequent biological effect. However the knowledge of this process is still fragmentary because heterogeneous particle collectives are applied. Therefore we present a strategy to synthesize carriers with a highly specific appearance on the basis of gold nanoparticles (AuNPs) and the Layer-by-Layer (LbL) technique. The LbL method is based on the alternate deposition of oppositely charged (bio-)polymers, in our case poly(ethylenimine) and nucleic acids. The size and surface charge of those particles can be easily modified and accordingly systematic studies on cellular uptake are accessible.

Layer-by-layer coated gold nanoparticles: size-dependent delivery of DNA into cells.

Because nanoparticles are finding uses in myriad biomedical applications, including the delivery of nucleic acids, a detailed knowledge of their interaction with the biological system is of utmost importance. Here the size-dependent uptake of gold nanoparticles (AuNPs) (20, 30, 50 and 80 nm), coated with a layer-by-layer approach with nucleic acid and poly(ethylene imine) (PEI), into a variety of mammalian cell lines is studied. In contrast to other studies, the optimal particle diameter for cellular uptake is determined but also the number of therapeutic cargo molecules per cell. It is found that 20 nm AuNPs, with diameters of about 32 nm after the coating process and about 88 nm including the protein corona after incubation in cell culture medium, yield the highest number of nanoparticles and therapeutic DNA molecules per cell. Interestingly, PEI, which is known for its toxicity, can be applied at significantly higher concentrations than its IC(50) value, most likely because it is tightly bound to the AuNP surface and/or covered by a protein corona. These results are important for the future design of nanomaterials for the delivery of nucleic acids in two ways. They demonstrate that changes in the nanoparticle size can lead to significant differences in the number of therapeutic molecules delivered per cell, and they reveal that the toxicity of polyelectrolytes can be modulated by an appropriate binding to the nanoparticle surface.