Machine Learning-Based Prediction of Reduction Potentials for PtIV Complexes

Some of the well-known drawbacks of clinically approved PtII complexes can be overcome using six-coordinate PtIV complexes as inert prodrugs, which release the corresponding four-coordinate active PtII species upon reduction by cellular reducing agents. Therefore, the key factor of PtIV prodrug mechanism of action is their tendency to be reduced which, when the involved mechanism is of outer-sphere type, is measured by the value of the reduction potential. Machine learning (ML) models can be used to effectively capture intricate relationships within PtIV complex data, leading to highly accurate predictions of reduction potentials and other properties, and offering significant insights into their electrochemical behavior and potential applications. In this study, a machine learning-based approach for predicting the reduction potentials of PtIV complexes based on relevant molecular descriptors is presented. Leveraging a data set of experimentally determined reduction potentials and a diverse range of molecular descriptors, the proposed model demonstrates remarkable predictive accuracy (MSE = 0.016 V2, RMSE = 0.13 V, R2 = 0.92). Ab initio calculations and a set of different machine learning algorithms and feature engineering techniques have been employed to systematically explore the relationship between molecular structure and similarity and reduction potential. Specifically, it has been investigated whether the reduction potential of these compounds can be described by combining ML models across different combinations of constitutional, topological, and electronic molecular descriptors. Our results not only provide insights into the crucial factors influencing reduction potentials but also offer a rapid and effective tool for the rational design of PtIV complexes with tailored electrochemical properties for pharmaceutical applications. This approach has the potential to significantly expedite the development and screening of novel PtIV prodrug candidates. The analysis of principal components and key features extracted from the model highlights the significance of structural descriptors of the 2D Atom Pairs type and the lowest unoccupied molecular orbital energy. Specifically, with just 20 appropriately selected descriptors, a notable separation of complexes based on their reduction potential value is achieved.

DNA-based nanoscaffolds as vehicles for 5-fluoro-2'-deoxyuridine oligomers in colorectal cancer therapy

Fluoropyrimidines, such as 5-fluorouracil (5-FU) and related prodrugs, are considered one of the most successful agents in the treatment of colorectal cancer, yet poor specificity and tumor cell resistance remain the major limiting bottlenecks. Here, we exploited for the first time the ability of two DNA nanoscaffolds, a DNA tetrahedron (Td) and rectangle DNA origami, to incorporate 5-fluoro-2'-deoxyuridine (FdUn) oligomers. In addition, cholesterol moieties were synthetically attached to Td and DNA origami staples to enhance cellular uptake. DNA nanostructures functionalized with FdUn exhibited an enhanced cytotoxicity and higher ability to trigger apoptosis in colorectal cancer cells relative to conventional 5-FU and FdU, especially having cholesterol as an internalization helper. The cholesterol content mostly correlates with the increase of the FdUn nanostructure cytotoxicity. DNA nanoscaffolds bearing FdUn were able to circumvent the low sensitivity of colorectal cancer cells towards 5-FU. Both DNA nanostructures attained a comparable cytotoxic effect yet Td displays higher antiproliferative action. The ability to reduce the proliferation of cancer cells is mainly related to the concentration of DNA nanostructures. The present work suggests that self-assembled DNA nanoparticles are privileged vehicles for delivering fluoropyrimidines, opening new avenues to the development of promising therapeutics for cancer treatment.

Fluorescence Enhancement of a Cationic Fluorene-Phenylene Conjugated Polyelectrolyte Induced by Nonionic n-Alkyl Polyoxyethylene Surfactants

The modulation of conjugated polyelectrolyte fluorescence response by nonionic surfactants is dependent on the structures of the surfactant and polymer, polymer average molecular weight, and polyelectrolyte-surfactant interactions. In this paper, we study the effect of nonionic n-alkyl polyoxyethylene surfactants (C_iE_j) with different alkyl chain lengths (C_iE₅ with i = 6, 8, 10, and 12) and number of oxyethylene groups (C₁₂E_j with j = 5, 7, and 9) on the photophysics and ionic conductivity of poly{[9,9-bis(6'-N,N,N-trimethylammonium)-hexyl]-2,7-fluorene-alt-1,4-phenylene}bromide (HTMA-PFP) in dimethyl sulfoxide-water 4% (v/v). Molecular dynamics simulations show that HTMA-PFP chains tend to approach as the simulation evolves. However, the minimum distance between the polymer centers of mass increases upon addition of the surfactant and grows with both the surfactant alkyl chain length and the number of oxyethylene groups, although there are no specific polymer-surfactant interactions. A significant increase in the polymer emission intensity has been observed at surfactant concentrations around their critical micelle concentrations (cmcs), which is attributed to polymer aggregate disruption. However, an increase in the solution conductivity for concentrations above the C₁₂E₅ cmc has only been observed for the HTMA-PFP/C₁₂E₅ system. The enhancement of fluorescence emission intensity and conductivity upon surfactant addition increases with polymer average molecular weights and seems to be controlled by the polymer-surfactant proximity, which is maximum for C₁₀E₅ and C₁₂E₅.

From molecular modelling to photophysics of neutral oligo- and polyfluorenes incorporated into phospholipid bilayers

The combination of various experimental techniques with theoretical simulations has allowed elucidation of the mode of incorporation of fluorene based derivatives into phospholipid bilayers. Molecular dynamics (MD) simulations on a fully hydrated 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) bilayer, with benzene (B), biphenyl (BP), fluorene (F) and tri-(9,9-di-n-octylfluorenyl-2,7-diyl), TF, have provided insights into the topography of these molecules when they are present in the phospholipid bilayer, and suggest marked differences between the behavior of the small molecules and the oligomer. Further information on the interaction of neutral fluorenes within the phospholipid bilayer was obtained by an infrared (IR) spectroscopic study of films of DMPC and of the phospholipid with PFO deuterated specifically on its alkyl chains (DMPC-PFO-d34). This was complemented by measurements of the effect of F, TF and two neutral polymers: polyfluorene poly(9,9-di-n-octylfluorenyl-2,7-diyl), PFO, and poly(9,9-di-n-dodecylfluorenyl-2,7-diyl), PFD, on the phospholipid phase transition temperature using differential scanning calorimetry (DSC). Changes in liposome size upon addition of F and PFO were followed by dynamic light scattering. In addition, the spectroscopic properties of F, TF, PFO and PFD solubilised in DMPC liposomes (absorption, steady-state and time-resolved fluorescence) were compared with those of the same probes in typical organic solvents (chloroform, cyclohexane and ethanol). Combining the insight from MD simulations with the results at the molecular level from the various experimental techniques suggests that while the small molecules have a tendency to be located in the phospholipid head group region, the polymers are incorporated within the lipid bilayers, with the backbone predominantly orthogonal to the phospholipid alkyl chains and with interdigitation of them and the PFO alkyl chains.

Nonrandom adsorption of polyelectrolyte chains on finite regularly charged surfaces

Adsorption phenomena are relevant in a wide variety of subjects, from biophysics to technological applications. Different aspects, such as molecular recognition, multilayer deposition, and dynamics of polymer adsorption have been addressed. The methodologies used range from analytical and numerical methods to molecular dynamics or Monte Carlo simulations. In this work, a coarse-grained model is used to explore the adsorption of charged backbones to oppositely charged regions of a surface. These regions encompass those small enough to prevent complete adsorption, but extend to surfaces sufficiently large to promote adsorption with minimal effect on the three-dimensional conformation in bulk. Apart from the different surface areas explored, variations on the surface charge density, polyelectrolyte chain length, and chain stiffness were also considered. The degree of compaction of the polyelectrolyte, on adsorption, is different from that found in the bulk. Also, results indicate an nonuniform adsorption pattern on regularly charged surfaces.

Co-encapsulating nanostructured lipid carriers for transdermal application: from experimental design to the molecular detail

Co-encapsulation of drugs directed at commonly associated diseases provides a convenient means for administration, especially if transdermally delivered. In this work, a comprehensive study for the co-encapsulation of drugs with a differential lipophilicity, olanzapine and simvastatin, and their transdermal delivery in a formulation containing nanostructured lipid carriers (NLC) is presented. Focus is given to the evaluation of a strategy in which NLC and chemical permeation enhancers are combined. It comprises in vitro, in silico and cellular viability approaches. The optimization and rationalization of the systems are carried out using a two-step factorial design. It is shown that the external medium in the NLC dispersion strongly influences permeation. It is also seen that the use of NLC determines a synergistic effect with selected permeation enhancers, thus promoting marked flux enhancement ratios (48 and 21, respectively for olanzapine and simvastatin) relative to the drugs in solution. The developed formulations can be considered non-irritant. A correlation between enhancer positioning in a lipid bilayer, partially governed by a H-bonding phenomenon, and enhancement effect is suggested from molecular dynamics studies and experimental observations.

Polyelectrolyte condensation in bulk, at surfaces, and under confinement

In this review we discuss recent results from computer simulations based on coarse-grained polyion models representing aqueous solutions of polyelectrolytes. The focus will be directed to the conformation of the polyions and, in particular, their condensation in bulk, induced by multivalent ions and oppositely charged polyelectrolytes, at responsive surfaces and under confinement.

Structure of microemulsion-ABA triblock copolymer networks

Structural equilibrium properties of transient networks formed by microemulsion droplets and ABA triblock copolymers in solution have been studied by Monte Carlo simulation. The droplets were represented by soft spheres, and the polymers were represented by junctions connected by harmonic bonds with an angular potential regulating the intrinsic chain stiffness. The interaction parameters were selected such that the end A-blocks were localized inside the droplets and the middle B-block in the continuous phase. The influence of (i) the polymer concentration, (ii) the polymer stiffness, and (iii) the contour length of the middle B-block on the formation and the structure of the microemulsion-polymer network were investigated using polymer end-to-end separation probability distribution functions, droplet radial distribution functions, droplet-droplet nearest-neighbor probability distribution functions, and network connectivity indicators. An increase of the polymer-droplet number ratio had a strong impact on the network formation. Under typical conditions and at an intermediate polymer-droplet number ratio, (i) the fraction of polymers forming bridges between droplets increased from essentially zero to unity and (ii) the fraction of polymers that were forming loops decreased as the ratio of the polymer end-to-end separation and the surface-to-surface separation between neighboring droplets for a hypothetical homogeneous droplet distribution was increased from 0.5 to 2. For long and flexible polymers, a mesoscopic segregation triggered by a depletion attraction between droplets appeared, and, furthermore, for sufficiently stiff chains, only bridge conformations occurred. The percolation probability could be represented as a function of the average droplet cluster size only, across all systems.

Interaction of Omeprazole with a Methylated Derivative of β-Cyclodextrin: Phase Solubility, NMR Spectroscopy and Molecular Simulation

PURPOSE

Cyclodextrins are known to be good solubility enhancers for several drugs, improving bioavailability when incorporated in pharmaceutical formulations. In this work we intend to assess and characterize the formation of inclusion complexes between omeprazole (OME) and a methylated derivative of beta-cyclodextrin, methyl-beta-cyclodextrin (MbetaCD). A comparison with results obtained from the most commonly used natural cyclodextrin, beta-cyclodextrin (betaCD) is also presented in most cases.

MATERIALS AND METHODS

The interaction of OME with the mentioned cyclodextrins in aqueous solutions was studied by phase solubility studies, 1D (1)H and 2D rotating frame nuclear overhauser effect NMR spectroscopy (ROESY) and Molecular Dynamics.

RESULTS

The solubility of OME was significantly increased by formation of inclusion complexes with each cyclodextrin. Phase solubility studies and continuous variation plots revealed that OME forms an inclusion complex in a stoichiometry of 1:1 with both cyclodextrins. (1)H NMR and ROESY spectra of the inclusion complexes indicated that the benzimidazole moiety is included within the cyclodextrins cavities. Molecular dynamics showed that OME is more deeply included in the MbetaCD than in betaCD cavity, in agreement with a larger apparent stability constant (K (S)) obtained for the inclusion complex with MbetaCD.

CONCLUSIONS

MbetaCD proved to be an efficient enhancer of OME solubility, thus possessing characteristics for being an useful excipient in pharmaceutical formulations of this drug.

Coil-globule coexistence and compaction of DNA chains

In this work we discuss different factors governing coil-globule coexistence in the compaction process of DNA. We initially analyse the role played by fluctuations in the degree of binding of an external compacting agent in the conformational behavior of the chain backbone. The analysis relies both on Monte Carlo simulation results and simple statistical approaches. Compacting agents of various binding characteristics are taken into consideration and the degree of charge neutralization upon the chain is related to conformational indicators. Selected model systems comprising stiff chains in the presence of multivalent ions are employed to assess intrinsic single-chain conformational fluctuation, in the presence of external agents but not resulting from differences in binding. It is shown that trends found for a variety of compacting agents, including the extension of the coil-globule coexistence regions, can be rationalised on the basis of this analysis.

Thermal Behaviour of Human Stratum Corneum

PURPOSE

To use high-speed differential scanning calorimetry (DSC) in the identification of transitions in human stratum corneum (SC). Several scanning rates (100 degrees C/min to 400 degrees C/min) are used.

RESULTS

Eight transitions from 0 to 120 degrees C are detected in a significant number of samples. Most of these transitions have already been identified in previous studies, but have been labeled considering essentially that only four are present. Results also indicate some degree of reversibility for transitions occurring at temperatures above 90 degrees C. Dehydrated SC samples displayed slightly more defined transition peaks and a less frequent presence of the transitions below 50 degrees C. In turn, the delipidised SC matrix showed two major endothermic signals, centered around 55 and 100 degrees C, in conjunction with other much less marked features.

CONCLUSIONS

The interpretation of DSC traces in terms of four main transition temperatures must be complemented having in mind the occurrence of other transitions, some of them at physiological temperatures. This work further suggests that transitions at temperatures above 90 degrees C may to a large degree be associated to lipids, while transition at approx. 55 degrees C is probably related to lipids covalently linked to proteins, as previously suggested.

Study of human stratum corneum and extracted lipids by thermomicroscopy and DSC

A study on the thermal behavior of human stratum corneum and lipids is described. The use of high scanning rate DSC for both SC and extracted lipids allows the consistent determination of transition temperatures, including those of lower energy. Changes are found both at physiological and higher temperatures. There is a clear correspondence between the thermotropic behavior of these two systems. However, one of the transitions found in human SC (approximately 55 degrees C) is absent in extracted lipids and may be ascribed to those covalently-linked to corneocytes. Lipidic thermotropic behavior is clearly found above 100 degrees C, in which proteins do not play an exclusive role. Changes related to most transitions are observed directly by polarized light thermal microscopy in extracted lipids. This technique also allowed for the observation of large segregated domains in the extracted lipids. A drastic change is observed at approximately 60 degrees C, corresponding to the disruption of the lamellar structure.

Polyelectrolytes in solutions with multivalent salt. Effects of flexibility and contour length

It has been experimentally observed that trivalent ions are capable of promoting compaction of semi-flexible polyelectrolyte chains. In this work we perform Monte Carlo simulations on single chain model systems with varying chain size and stiffness and evaluate the action of multivalent salt on the chain conformation. It is observed that longer chains tend to achieve relatively more compact conformations than shorter ones, and the dimensions of the collapsed structures do not significantly vary with contour length. The influence of contour length and intrinsic stiffness in the process of ion condensation is studied by analysis of the ion-ion nearest-neighbor distribution. The general trend is an increase of the degree of ion condensation as the chain length increases, in accordance with experimental evidence. A decreased importance of end-effects and, especially, larger volume charge densities are responsible for such behavior. The influence of chain stiffness is nontrivial, and depends on salt concentration. The results emphasize the complex nature of ion-correlation phenomena in flexible or semi-flexible chains and call for the development of more sophisticated analytical theories.

Polymer distribution in connected spherical domains

The distribution of neutral and charged polymers with different flexibilities between two spheres of varying volume connected by a short and narrow cylinder has been investigated by Monte Carlo simulations. The uncharged chain displayed mostly a single-sphere occupancy due to the high conformational entropy penalty of crossing the cylindrical domain, whereas for the charged polymer a double-sphere occupancy was obtained, except for very different spherical volumes. The origin of this different occupancy behavior stems from the counterion entropy. At increasing stiffness, a stronger preference for double-sphere occupancy was predicted.

Polyion Adsorption onto Catanionic Surfaces. A Monte Carlo Study

The adsorption of a single and negatively charged polyion with varying flexibility onto a surface carrying both negative and positive charges representing a charged membrane surface has been investigated by using a simple model employing Monte Carlo simulations. The polyion was represented by a sequence of negatively charged hard spheres connected with harmonic bonds. The charged surface groups were also represented by charged hard spheres, and they were positioned on a hard surface slightly protruding into the solution. The surface charges were either frozen in a liquidlike structure or laterally mobile. With a large excess of positive surface charges, the classical picture of a strongly adsorbed polyion with an extended and flat configuration emerged. However, adsorption also appeared at a net neutral surface or at a weakly negatively charged surface, and at these conditions the adsorption was stronger with a flexible polyion as compared to a semiflexible one, two features not appearing in simpler models containing homogeneously charged surfaces. The presence of charged surface patches (frozen surface charges) and the ability of polarization of the surface charges (mobile surface charges) are the main reasons for the enhanced adsorption. The stronger adsorption with the flexible chain is caused by its greater ability to spatially correlate with the surface charges.

Analysis of formulation effects in the dissolution of ibuprofen pellets

In this work the effects of citric acid and of two common fillers, lactose (soluble) and tricalcium phosphate (insoluble) are examined on the release profiles from pellets, using ibuprofen as a model drug with pH-dependent solubility. Also studied is the dependence of these profiles on the specific surface area, bulk density, apparent density, porosity and porosity parameters (pore size distribution, total pore surface area, mean pore diameter and pore shape), as determined by mercury intrusion porosimetry. Pellets with high porosity and total pore surface area but small median pore diameter (tricalcium phosphate pellets-IPM) are found to produce similar dissolution results to those of low porosity and low total pore surface area, but having a high median pore diameter (lactose pellets-ILM), irrespective of the solubility of excipients. Addition of citric acid causes a delay in the initial dissolution for both formulations. During dissolution, however, citric acid reduces the median pore diameter of lactose-based pellets. In contrast, in tricalcium phosphate/citric acid pellets (CIPM), this parameter increases considerably during dissolution, when compared to the IPM formulation. These findings may justify the contrasting dissolution behaviors of CIPM and CILM (lactose/citric acid) pellets, after their common behavior in the initial stages, and show that porosity and its related parameters, along with physical properties of excipients such as solubility, density and specific surface area, are helpful to predict pellet behavior in drug release profiles.

Comparison of dissolution profiles of Ibuprofen pellets

In this work we use both model dependent and independent techniques to assess the difference between dissolution profiles in which ibuprofen, in the form of uncoated pellets, is used as a model drug. The choice of a proper regression function, the relevance of the estimated parameters and the influence of the choice of dissolution points in the assessment of differences is discussed. The results obtained via mean dissolution times (MDT) and fit-factors (f(1) and f(2)) are also discussed and a non-quantitative method based on profiles correlation with graphical representation (concentration vs. concentration and rate vs. rate) presented. The tested methods discriminate similarly between curves, although not in all cases, but those based on modeling, MDT and fit-factors have shown to be less informative than the correlation approach.