Atomistic computer simulations on multi-loaded PAMAM dendrimers: a comparison of amine- and hydroxyl-terminated dendrimers

Exploring Polyol-Functionalized Dendrimers with Silsesquioxane Cores

Silsesquioxane dendrimers offer versatile structural potential, prompting our innovative synthesis of G1 and G2 polyol dendritic systems with diverse silsesquioxane cores, ranging from mono-T8 to difunctional and tetrafunctional double-decker silsesquioxanes. Through a strategic combination of hydrosilylation and O-silylation reactions, we have formed an extensive compound library. A major focus was directed toward investigating the reaction conditions of G1.5 dendrimers, as well as evaluating the stability and reactivity of the novel -O-Me2Si-H group. Notably, we unveiled solubility trends of these synthesized dendritic systems in basic organic solvents, offering vital information for potential applications. Our work advances dendrimer research by unraveling intricate synthesis, reactivity, and properties. We contribute to the broader understanding of these organic-inorganic complex interactions and envisage diverse applications in multiple domains.

Theoretical studies of phosphorene as a drug delivery nanocarrier for fluorouracil

The interactions between phosphorene nanosheets (PNSs) and 5-fluorouracil (FLU) were explored using the density functional theory (DFT) method and molecular dynamics (MD) simulations. DFT calculations were performed utilizing M06-2X functional and the 6-31G(d,p) basis set in both gas and solvent phases. Results showed that the FLU molecule is adsorbed horizontally on the PNS surface with an adsorption energy (Eads) of -18.64 kcal mol-1. The energy gap (Eg) between the highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO, respectively) of PNS remains constant after the adsorption process. The adsorption behavior of PNS is not affected by carbon and nitrogen doping. The dynamical behavior of PNS-FLU was studied at T = 298, 310, and 326 K reminiscent of room temperature, body temperature, and temperature of the tumor after exposure to 808 nm laser radiation, respectively. The D value decreases significantly after the equilibration of all systems so that the equilibrated value of D is about 1.1 × 10-6, 4.0 × 10-8, and 5.0 × 10-9 cm2 s-1 at T = 298, 310, and 326 K, respectively. About 60 FLU molecules can be adsorbed on both sides of each PNS, indicating its high loading capacity. PMF calculations demonstrated that the release of FLU from PNS is not spontaneous, which is favorable from a sustained drug delivery point of view.

A Dentin Biomimetic Remineralization Material with an Ability to Stabilize Collagen

The integrity of collagen matrix structure is a prerequisite for effectively inducing biomimetic remineralization. Repeated low pH stimulation activates matrix metalloproteinases (MMPs) in dental caries. Activated MMPs cause the breakdown of collagen fibrils. Collagen stabilization is a major obstacle to the clinical application of remineralization templates. Here, galardin-loaded poly(amido amine) (PAMAM)-NGV (PAMAM-NGV@galardin, PNG) is constructed to induce collagen stabilization and dentin biomimetic remineralization simultaneously, in order to combat early caries in dentin. PAMAM acts in the role of nucleation template for dentin remineralization, while galardin acts as the role of MMPs inhibitor. NGV peptides modified on the surface of dendrimer core can form small clusters with synergistic movement in short range, and those short-range clusters can form domain areas with different properties on the surface of PAMAM core and restrict the movement of collagen, favoring collagen crosslinking, which can be explained through the computational simulation analysis results. NGV peptides and galardin show a dual collagen-protective effect, laying the foundation for the dentin remineralization effect induced by PAMAM. PNG induces dentin remineralization in an environment with collagenase, meanwhile showsing anti-dentin caries efficacy in vivo. These findings indicate that PNG has great potential to combat early dentin caries for future clinical application.

Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide by molecular dynamics simulations

Angiotensin-(1-7) re-balance the Renin-Angiotensin system affected during several pathologies, including the new COVID-19; cardiovascular diseases; and cancer. However, one of the limiting factors for its therapeutic use is its short half-life, which might be overcome with the use of dendrimers as nanoprotectors. In this work, we addressed the following issues: (1) the capacity of our computational protocol to reproduce the experimental structural features of the (hydroxyl/amino)-terminated PAMAM dendrimers as well as the Angiotensin-(1-7) peptide; (2) the coupling of Angiotensin-(1-7) to (hydroxyl/amino)-terminated PAMAM dendrimers in order to gain insight into the structural basis of its molecular binding; (3) the capacity of the dendrimers to protect Angiotensin-(1-7); and (4) the effect of pH changes on the peptide binding and covering. Our Molecular-Dynamics/Metadynamics-based computational protocol well modeled the structural experimental features reported in the literature and our double-docking approach was able to provide reasonable initial structures for stable complexes. At neutral pH, PAMAM dendrimers with both terminal types were able to interact stably with 3 Angiotensin-(1-7) peptides through ASP1, TYR4 and PRO7 key amino acids. In general, they bind on the surface in the case of the hydroxyl-terminated compact dendrimer and in the internal zone in the case of the amino-terminated open dendrimer. At acidic pH, PAMAM dendrimers with both terminal groups are still able to interact with peptides either internalized or in its periphery, however, the number of contacts, the percentage of coverage and the number of hydrogen bonds are lesser than at neutral pH, suggesting a state for peptide release. In summary, amino-terminated PAMAM dendrimer showed slightly better features to bind, load and protect Angiotensin-(1-7) peptides.

Theoretical evaluation of poly(amidoamine) dendrimers with different peripheral groups as a purinethol drug delivery system in aqueous medium

In this work, density functional theory calculations were used to study the association of PUR with amine- and acetyl-terminated PAMAM dendrimers considering implicit solvent effect at neutral and low pH conditions. Frontier molecular orbitals' analysis indicates that the electronic properties of dendrimers are extremely sensitive to the presence of PUR molecule at both neutral and low pH conditions. Encapsulation of PUR molecule into the both amine- and acetyl-terminated PAMAM dendrimers leads to a Gibbs free energy of (ΔG) - 20.25 kcal.mol^-1 at physiological pH. The corresponding ΔG values reduce to the - 1.45 and - 0.91 kcal.mol^-1 at low pH, indicating that the drug molecule is released easily at low pH. The calculated recovery times for amine- (3.87 ×10² and 3.87 ×10², at neutral and low pH, respectively) and acetyl-terminated (5.34 ×10¹⁰ and 1.81 ×10^-1, at neutral and low pH, respectively) dendrimers suggest that acetylation can improve the release pattern of drug molecule.

Exploration of phosphorene as doxorubicin nanocarrier: An atomistic view from DFT calculations and MD simulations

Potential capability of phosphorene nanosheet (PNS) as doxorubicin (DOX) nanocarrier was investigated using density functional theory (DFT) method and molecular dynamics (MD) simulations. Both DFT calculations and MD simulations revealed that the DOX molecule is adsorbed horizontally onto the PNS surface with the nearest interaction distance of 2.5 Å. The binding energy of DOX is predicted to be about - 49.5 kcal.mol^-1, based on the DFT calculations. After DOX adsorption, the E_g value of PNS remains almost constant in both gas and solvent phases. The dynamical behavior of PNS-DOX was studied at T = 298, 310, and 326 K that reminiscent of room temperature, body temperature, and temperature of tumor after exposure to 808 nm laser radiation, respectively. The diffusion coefficient values of DOX molecule are proportional to temperature. We found that PNS can hold a high amount of DOX on both sides of its surface (66% in weight). MD simulations showed that the dynamical behavior of simulated systems are not affected by pH variances.

Drug-dendrimer complexes and conjugates: Detailed furtherance through theory and experiments

Dendritic nanovectors-based drug delivery has gained significant attention in the past couple of decades. Dendrimers play a crucial role in deciding the solubility of sparingly soluble drug molecules and help in improving pharmacokinetics. A few important steps in drug delivery through dendrimers, such as drug encapsulation, formulation, and target-specific delivery, play an important role in deciding the fate of a drug molecule. It is also of prime importance to understand the interactions between a drug molecule and dendrimers at atomistic levels to decode the mechanism of action of drug-dendrimer complexes and their reliability in terms of drug delivery. Colossal progress in current experimental and computational approaches in the field has resulted in a vast amount of data that needs to be curated to be further implemented efficiently. Improved computational power has led to greater accuracy and prompt predictions of properties of drug-dendrimer complexes and their mechanism of action. The current review encapsulates the pioneering work in the field, experimental achievements in terms of drug delivery, and newer computational techniques employed in the advancement of the field.

PAMAM and polyester dendrimers as favipiravir nanocarriers: a comparative study using DFT method

The electronic sensitivity and reactivity of polyamidoamine (PAMAM) and polyester dendrimers toward favipiravir (T705) were inspected using density functional theory method. The T705 drug is adsorbed on the surface of PAMAM and polyester dendrimers with the binding energy of -27.26 and -26.80 kcal mol-1, respectively, in the solvent phase. The energy gap of PAMAM and polyester dendrimers reduced by about 32% and 27%, indicating that the electrical conductance of carriers become 8.16 × 1023 and 4.41 × 1022 times higher, upon T705 adsorption. The work function (Φ) value of PAMAM and polyester is changed about 1.53 and 0.71 eV, respectively. Thus, PAMAM dendrimer is about 2.5 times stronger Φ-type sensor than polyester dendrimer. The recovery time for T705 desorption from the PAMAM and polyester surface is predicted to be 9.2 × 103 and 4.2 × 103 s, respectively, at physiological environment.

Application of borophene as catechol sensor: a computational study

The efficacy of borophene (BP) as catechol (CC) sensor was explored using density functional theory (DFT) method. All calculations were performed at B3LYP level of theory and 6-31 + G(d) basis set employing the dispersion correction term of Grimme to consider dispersion interactions. The CC molecule is adsorbed on top of BP horizontally with the adsorption energy (E_ads) of about - 13.5 kcal·mol^-1. The HOMO and LUMO levels of nanosheet destabilize by about 0.36 and 0.14 eV, respectively, going from bare BP to BP-CC complex. Therefore, the E_g value decreases by about 10.5% upon adsorption process, which is a reasonable energy gap change for detection of CC. The negligible difference between the work function values (Φ, defined as the minimum amount of the energy needed to remove an electron from a solid to a point in the vacuum immediately outside the solid surface) of BP and its complex with CC indicates that the BP sheet is not an appropriate Φ-type sensor (in these sensors, adsorption of a chemical changes the gate voltage and produces an electrical signal that leads to the detection of chemical agent) for CC detection. The electrical conductivity of BP becomes 72 times higher after CC adsorption. The time needed for CC desorption from BP sheet is 7.6 ns, based on conventional transition state theory, showing that BP benefits from a short recovery time. The effect of CC concentration was explored by adsorption of 2 and 3 CC molecules on top of BP nanosheet and the results showed that the sensor response does not change by increasing the CC concentration. Also, the effect of lateral dimensions of BP on the adsorption energy was explored and it was shown that E_ads increases by enlargement of the nanosheet.

Exploration of interaction behavior between spiro[indene-2,2'-[1,3,5]oxathiazine]-1,3-diones and DNA with the help of DFT, molecular docking, and MD simulations

A detailed computational study covering density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulations of some spirocyclic compounds interacting with a B-DNA has been performed. DFT calculations were performed using the B3LYP functional with 6-311++G(d,p) basis set and were used to identify the electrophilic and nucleophilic centers in electrostatic forces. NMR results were in agreement with previous experimental data and approved the reliability of the used method and basis set. The in silico screening results showed that spirocyclic compounds fulfill the Lipinski's rule of five and can be developed as potential oral bioavailable drug candidates. Based on molecular docking results, the binding affinities follow the 4c < 4d < 4a = 4b < 4e < 4g < 4f order and ranged from -8.6 to -9.7 kcal/mol indicating a reasonably favorable interaction between DNA and investigated compounds. The adducts were stabilized by hydrophobic and hydrogen bonding interactions. The MD simulations performed for 100 ns and the results are reported in terms of variables such as root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), center of mass (COM) separation distance between DNA and ligands, intermolecular hydrogen bonds, and radial distribution functions (RDF). The MD simulations demonstrated that compounds 4a and 4d bind into the minor groove of 1BNA and may act as potential biological probes for B-DNA.Communicated by Ramaswamy H. Sarma.

Drug-Loading Capacity of PAMAM Dendrimers Encapsulating Quercetin Molecules: A Molecular Dynamics Study with the 2016H66 Force Field

The complexation of quercetin molecules with poly(amidoamine) (PAMAM) dendrimers of generation 0-3 was studied by molecular dynamics simulations. Three main points were addressed: (i) the effect of starting from different initial structures; (ii) the performance of the 2016H66 force field (recently validated in the context of dendrimer simulations) in predicting the experimental drug(quercetin)-loading capacity of PAMAM dendrimers; and (iii) the stability of quercetin-PAMAM complexes and their interactions. Initial structures generated by different restraint protocols led to faster convergence compared to initial structures generated by randomly placing the drug molecules in the simulation box. The simulations yielded meta-stable complexes where the loading numbers have converged to average values and were compared to experimentally obtained values. Once the first meta-stable state was reached, the drug-dendrimer complexes did not deviate significantly throughout the simulation. They were characterized in terms of structural properties, such as the radius of gyration and radial distribution functions. The results suggest that quercetin molecules interact mostly with the internal dendrimer monomers rather than to their surface.

Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery

In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.

Cheminformatics-driven discovery of polymeric micelle formulations for poorly soluble drugs

Many drug candidates fail therapeutic development because of poor aqueous solubility. We have conceived a computer-aided strategy to enable polymeric micelle-based delivery of poorly soluble drugs. We built models predicting both drug loading efficiency (LE) and loading capacity (LC) using novel descriptors of drug-polymer complexes. These models were employed for virtual screening of drug libraries, and eight drugs predicted to have either high LE and high LC or low LE and low LC were selected. Three putative positives, as well as three putative negative hits, were confirmed experimentally (implying 75% prediction accuracy). Fortuitously, simvastatin, a putative negative hit, was found to have the desired micelle solubility. Podophyllotoxin and simvastatin (LE of 95% and 87% and LC of 43% and 41%, respectively) were among the top five polymeric micelle-soluble compounds ever studied experimentally. The success of the strategy described herein suggests its broad utility for designing drug delivery systems.

Multivalency in a Dendritic Host-Guest System

Multivalency is an important instrument in the supramolecular chemistry toolkit for the creation of strong specific interactions. In this paper we investigate the multivalency effect in a dendritic host–guest system using molecular dynamics simulations. Specifically, we consider urea–adamantyl decorated poly(propyleneimine) dendrimers that together with compatible mono-, bi-, and tetravalent ureidoacetic acid guests can form dynamic patchy nanoparticles. First, we simulate the self-assembly of these particles into macromolecular nanostructures, showing guest-controlled reduction of dendrimer aggregation. Subsequently, we systematically study guest concentration dependent multivalent binding. At low guest concentrations multivalency of the guests clearly increases relative binding as tethered headgroups bind more often than free guests’ headgroups. We find that despite an abundance of binding sites, most of the tethered headgroups bind in close proximity, irrespective of the spacer length; nevertheless, longer spacers do increase binding. At high guest concentrations the dendrimer becomes saturated with bound headgroups, independent of guest valency. However, in direct competition the tetravalent guests prevail over the monovalent ones. This demonstrates the benefit of multivalency at high as well as low concentrations.