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Dynamics of epigenetic modifications such as acetylation and deacetylation of histone proteins have been shown to be crucial for the life cycle development and survival of Plasmodium falciparum, the deadliest malaria parasite. In this study, we present a novel series of peptoid-based histone deacetylase (HDAC) inhibitors incorporating nitrogen-containing bicyclic heteroaryl residues as a new generation of antiplasmodial peptoid-based HDAC inhibitors. We synthesized the HDAC inhibitors by an efficient multicomponent protocol based on the Ugi four-component reaction. The subsequent screening of 16 compounds from our mini-library identified 6i as the most promising candidate, demonstrating potent activity against asexual blood-stage parasites (IC 50 Pf3D7 = 30 nM; IC 50 PfDd2 = 98 nM), low submicromolar activity against liver-stage parasites (IC 50 PbEEF = 0.25 μM), excellent microsomal stability (t 1/2  > 60 min), and low cytotoxicity to HEK293 cells (IC 50  = 136 μM)., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Masson SAS.. All rights reserved.)

In this study, we synthesized and evaluated novel histone deacetylase (HDAC) inhibitors derived from the clinical candidate quisinostat. A library of 16 compounds categorized in three novel chemotypes was rapidly generated using multicomponent reactions (MCRs), enabling efficient structure-activity relationship studies. First, the compounds were evaluated for their activity against the Plasmodium falciparum strains 3D7 and Dd2, the main malaria-causing parasite, identifying compound 18b of the type C series as the most potent. It demonstrated low nanomolar IC 50 values (IC 50 (3D7) = 0.023 μM; IC 50 (Dd2) = 0.047 μM) and high parasite selectivity (SI MRC-5/Pf3D7  > 2174). HDAC inhibition assays confirmed substantial inhibition of the P. falciparum enzyme PfHDAC1 (IC 50  = 0.037 μM) as well as of human HDAC1 (IC 50  = 0.021 μM) and HDAC6 (IC 50  = 0.25 μM). Docking studies suggested distinct binding modes of 18b in P. falciparum and human HDAC1. Additionally, the in vitro anticancer activity was evaluated in Cal27 (head-neck carcinoma), HepG2 (hepatocellular carcinoma), A2780 (ovarian carcinoma), and U87 (glioblastoma) cell lines. Compounds 9b, 9d, and 13f showed potent antiproliferative activity and caspase 3/7 activation, in contrast to 18b. Furthermore, these compounds caused hyperacetylation of histone H3 and α-tubulin, indicating robust cellular target engagement. Overall, in this work we have identified the HDAC inhibitor 18b with selective antiplasmodial and 9b, 9d, and 13f with selective anticancer activities, providing valuable hits for further drug development efforts aimed at creating derivatives with reduced cytotoxicity against non-cancer cells compared to quisinostat., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Masson SAS.. All rights reserved.)

Artemisinin-based combination therapies (ACTs) are the gold standard for the treatment of malaria, but the efficacy is threatened by the development of parasite resistance. Histone deacetylase inhibitors (HDACis) are an emerging new class of potential antiplasmodial drugs. In this work, we present the design, synthesis, and biological evaluation of a mini library of dihydroartemisinin-HDACi hybrid molecules. The screening of the hybrid molecules for their activity against selected human HDAC isoforms, asexual blood stage P. falciparum parasites, and a panel of leukemia cell lines delivered important structure-activity relationships. All synthesized compounds demonstrated potent activity against the 3D7 and Dd2 line of P. falciparum with IC 50 values in the single-digit nanomolar range. Furthermore, the hybrid (α)- 7c displayed improved activity against artemisinin-resistant parasites compared to dihydroartemisinin. The screening of the compounds against five cell lines from different leukemia entities revealed that all hydroxamate-based hybrids ( 7a-e ) and the ortho -aminoanilide 8 exceeded the antiproliferative activity of dihydroartemisinin in four out of five cell lines. Taken together, this series of hybrid molecules represents an excellent starting point toward the development of antimalarial and antileukemia drug leads.

In all areas related to protein adsorption, from medicine to biotechnology to heterogeneous nucleation, the question about its dominant forces and control arises. In this study, we used ellipsometry and quartz-crystal microbalance with dissipation (QCM-D), as well as density-functional theory (DFT) to obtain insight into the mechanism behind a wetting transition of a protein solution. We established that using multivalent ions in a net negatively charged globular protein solution (BSA) can either cause simple adsorption on a negatively charged interface, or a (diverging) wetting layer when approaching liquid-liquid phase separation (LLPS) by changing protein concentration (c p ) or temperature (T). We observed that the water to protein ratio in the wetting layer is substantially larger compared to simple adsorption. In the corresponding theoretical model, we treated the proteins as limited-valence (patchy) particles and identified a wetting transition for this complex system. This wetting is driven by a bulk instability introduced by metastable LLPS exposed to an ion-activated attractive substrate.

For a standard model of patchy colloidal fluids with patch number M = 2, where chain formation (polymerization) occurs, we show that Wertheim theory predicts critical behavior at vanishing density and temperature. The analysis is based on determining lines in the phase diagram of maximal correlation length and compressibility. Simulation studies identify the latter line and confirm our prediction of Fisher-Widom crossover, i.e., the asymptotic decay of the pair correlation function changes from monotonic to damped oscillatory as the density is increased. For M > 2, it is known that phase separation occurs with a true critical point. Our results support the notion that a "disappearing" critical point occurs in the limit M = 2 and we uncover its remnants.

We revisit the competition between attractive and repulsive interparticle forces in simple fluids and how this governs and connects the macroscopic phase behavior and structural properties, as manifested in pair correlation functions. We focus on the asymptotic decay of the total correlation function h(r) which is, in turn, controlled by the form of the pair direct correlation function c(r). The decay of rh(r) to zero can be exponential (monotonic) if attraction dominates repulsion and exponentially damped oscillatory otherwise. The Fisher-Widom (FW) line separates the phase diagram into two regions characterized by the two different types of asymptotic decays. We show that there is a new and physically intuitive thermodynamic criterion which approximates well the actual FW line. This new criterion defines a line where the isothermal compressibility takes its ideal gas value χ T =χ T id . We test our hypothesis by considering four commonly used models for simple fluids. In all cases, the new criterion yields a line in the phase diagram that is close to the actual FW line for the thermodynamic state points that are most relevant. We also investigate (Widom) lines of maximal correlation length, emphasizing the importance of distinguishing between the true and Ornstein-Zernike correlation lengths.

We investigate bulk structural properties of tetravalent associating particles within the framework of classical density functional theory, building upon Wertheim's thermodynamic perturbation theory. To this end, we calculate density profiles within an effective test-particle geometry and compare to radial distribution functions obtained from computer simulations. We demonstrate that a modified version of the functional proposed by Yu and Wu [J. Chem. Phys. 116 , 7094 (2002)] based on fundamental measure theory for hard spheres produces accurate results, although the functional does not satisfy the exactly known low-density limit. In addition, at low temperatures where particles start to form an amorphous tetrahedral network, quantitative differences between simulations and theory emerge due to the absence of geometrical information regarding the patch arrangement in the latter. Indeed, here we find that the theory fits better to simulations of the floating-bond model [E. Zaccarelli et al. , J. Chem. Phys. 127 , 174501 (2007)], which exhibits a weaker tetrahedral order due to more flexible bonds between particles. We also demonstrate that another common density functional approach by Segura et al. [Mol. Phys. 90 , 759 (1997)] fails to capture fundamental structural properties.

By means of classical density functional theory and its dynamical extension, we consider a colloidal fluid with spherically symmetric competing interactions, which are well known to exhibit a rich bulk phase behavior. This includes complex three-dimensional periodically ordered cluster phases such as lamellae, two-dimensional hexagonally packed cylinders, gyroid structures, or spherical micelles. While the bulk phase behavior has been studied extensively in earlier work, in this paper we focus on such structures confined between planar repulsive walls under shear flow. For sufficiently high shear rates, we observe that microphase separation can become fully suppressed. For lower shear rates, however, we find that, e.g., the gyroid structure undergoes a kinetic phase transition to a hexagonally packed cylindrical phase, which is found experimentally and theoretically in amphiphilic block copolymer systems. As such, besides the known similarities between the latter and colloidal systems regarding the equilibrium phase behavior, our work reveals further intriguing nonequilibrium relations between copolymer melts and colloidal fluids with competing interactions.

Using dynamical density functional theory (DDFT), we theoretically study Brownian self-diffusion and structural relaxation of hard disks and compare to experimental results on quasi two-dimensional colloidal hard spheres. To this end, we calculate the self-van Hove correlation function and distinct van Hove correlation function by extending a recently proposed DDFT-approach for three-dimensional systems to two dimensions. We find that the theoretical results for both self-part and distinct part of the van Hove function are in very good quantitative agreement with the experiments up to relatively high fluid packing fractions of roughly 0.60. However, at even higher densities, deviations between the experiment and the theoretical approach become clearly visible. Upon increasing packing fraction, in experiments, the short-time self-diffusive behavior is strongly affected by hydrodynamic effects and leads to a significant decrease in the respective mean-squared displacement. By contrast, and in accordance with previous simulation studies, the present DDFT, which neglects hydrodynamic effects, shows no dependence on the particle density for this quantity.

Protein adsorption at the solid-liquid interface is an important phenomenon that often can be observed as a first step in biological processes. Despite its inherent importance, still relatively little is known about the underlying microscopic mechanisms. Here, using multivalent ions, we demonstrate the control of the interactions and the corresponding adsorption of net-negatively charged proteins (bovine serum albumin) at a solid-liquid interface. This is demonstrated by ellipsometry and corroborated by neutron reflectivity and quartz-crystal microbalance experiments. We show that the reentrant condensation observed within the rich bulk phase behavior of the system featuring a nonmonotonic dependence of the second virial coefficient on salt concentration c_{s} is reflected in an intriguing way in the protein adsorption d(c_{s}) at the interface. Our findings are successfully described and understood by a model of ion-activated patchy interactions within the framework of the classical density functional theory. In addition to the general challenge of connecting bulk and interface behavior, our work has implications for, inter alia, nucleation at interfaces.

Using classical density functional theory, we investigate systems exhibiting interactions where a short-range anisotropic attractive force competes with a long-range spherically symmetric repulsive force. The former is modelled within Wertheim's first-order perturbation theory for patchy particles, and the repulsive part is assumed to be a Yukawa potential which is taken into account via a mean-field approximation. From previous studies of systems with spherically symmetric competing interactions, it is well known that such systems can exhibit stable bulk cluster phases (microphase separation) provided that the repulsion is sufficiently weak compared to the attraction. For the present model system, we find rich phase diagrams including both reentrant clustering and liquid-gas binodals. In particular, the model predicts inhomogeneous bulk phases at extremely low packing fractions, which cannot be observed in systems with isotropic competing interactions.

In this paper, we discuss the ability to numerically minimize the grand potential of hard disks in two-dimensional and of hard spheres in three-dimensional space within the framework of classical density functional and fundamental measure theory on modern graphics cards. Our main finding is that a massively parallel minimization leads to an enormous performance gain in comparison to standard sequential minimization schemes. Furthermore, the results indicate that in complex multi-dimensional situations, a heavy parallel minimization of the grand potential seems to be mandatory in order to reach a reasonable balance between accuracy and computational cost.

Within the Asakura-Oosawa model, we study structural relaxation in mixtures of colloids and polymers subject to Brownian motion in the overdamped limit. We obtain the time evolution of the self and distinct parts of the van Hove distribution function G(r,t) by means of dynamical density functional theory (DDFT) using an accurate free-energy functional based on Rosenfeld's fundamental measure theory. In order to remove unphysical interactions within the self part, we extend the recently proposed quenched functional framework (Stopper et al 2015 J. Chem. Phys. 143 181105) toward mixtures. In addition, we obtain results for the long-time self diffusion coefficients of colloids and polymers from dynamic Monte Carlo simulations, which we incorporate into the DDFT. From the resulting DDFT equations we calculate G(r, t), which we find to agree very well with our simulations. In particular, we examine the influence of polymers which are slow relative to the colloids-a scenario for which both DDFT and simulation show a significant peak forming at r  =  0 in the colloid-colloid distribution function, akin to experimental findings involving gelation of colloidal suspensions. Moreover, we observe that, in the presence of slow polymers, the long-time self diffusivity of the colloids displays a maximum at an intermediate colloid packing fraction. This behavior is captured by a simple semi-empirical formula, which provides an excellent description of the data.

We study structural relaxation of colloidal hard spheres undergoing Brownian motion using dynamical density functional theory. Contrary to the partial linearization route [D. Stopper et al., Phys. Rev. E 92, 022151 (2015)] which amounts to using different free energy functionals for the self and distinct part of the van Hove function G(r, t), we put forward a unified description employing a single functional for both components. To this end, interactions within the self part are removed via the zero-dimensional limit of the functional with a quenched self component. In addition, we make use of a theoretical result for the long-time mobility in hard-sphere suspensions, which we adapt to the inhomogeneous fluid. Our results for G(r, t) are in excellent agreement with numerical simulations even in the dense liquid phase. In particular, our theory accurately yields the crossover from free diffusion at short times to the slower long-time diffusion in a crowded environment.

We study the dynamics of colloidal suspensions of hard spheres that are subject to Brownian motion in the overdamped limit. We obtain the time evolution of the self- and distinct parts of the van Hove function by means of dynamical density functional theory. The free-energy model for the hard-sphere fluid that we use is the very accurate White Bear II version of Rosenfeld's fundamental measure theory. However, in order to remove interactions within the self-part of the van Hove function, a nontrivial modification has to be applied to the free-energy functional. We compare our theoretical results with data that we obtain from dynamical Monte Carlo simulations, and we find that the latter are well described by our approach even for colloid packing fractions as large as 40%.