Theoretical and Experimental Analyses of the Interfacial Mechanism of Dendrimer-Doxorubicin Complexes Formation

The work presents correlations between the physicochemical properties of the carrier and the active substance and optimization of the conditions for creating an active system based on PAMAM dendrimers and doxorubicin. The study monitored the influence of the ionized form of the doxorubicin molecule on the efficiency of complex formation. The deprotonated form of doxorubicin occurs under basic conditions in the pH range of 9.0-10.0. In the presence of doxorubicin, changes in the zeta potential of the complex concerning the initial system are observed. These changes result from electrostatic interactions between the drug molecules and external functional groups. Based on changes in the absorbance intensity of UV-vis spectra, the binding of the drug in the polymer structure is observed depending on the pH of the environment and the molar ratio. Optimal conditions for forming complexes occur under alkaline conditions. UV-vis, Fourier transform infrared spectroscopy, and circular dichroism spectroscopy confirmed the stability of the formed dendrimer-DOX complex. Molecular dynamics simulations were conducted to gain a deeper insight into the molecular mechanism of DOX adsorption on and within the G4.0 PAMAM dendrimers. It was observed that the protonation state of both the dendrimer and DOX significantly influences the adsorption stability. The system exhibited high stability at high pH values (∼9-10), with DOX molecules strongly adsorbed on the dendrimer surface and partially within its bulk. However, under lower pH conditions, a reduction in adsorption strength was observed, leading to the detachment of DOX clusters from the dendrimer structure.

Folic acid-functionalized and acetyl-terminated dendrimers as nanovectors for co-delivery of sorafenib and 5-fluorouracil

Molecular dynamics (MD) simulations were employed to investigate the simultaneous association of sorafenib (SF) and 5-fluorouracil (5-FU) with generation 4 (G4) acetyl-terminated poly(amidoamine) (PAMAM) dendrimers conjugated with folic acid (G4ACE-FA). Simulations were conducted under physiological (pH 7.4) and acidic (pH < 5) conditions, representing the environments of healthy and cancerous cells, respectively. The average radius of gyration (Rg) of G4ACE-FA was determined to be approximately 1.85 ± 0.01 nm and 2.31 ± 0.03 nm under physiological and acidic conditions, respectively. Drug loading did not exert a significant influence on the size and conformational compactness of G4ACE-FA at both neutral and low pH. However, a discernible increase in dendrimer size was observed upon simultaneous encapsulation and/or conjugation of both drug molecules. The relaxation times of G4ACE-FA were calculated to be 10.2 ns and 9.6 ns at neutral and low pH, respectively, indicating comparable equilibrium rates under both pH environments. The incorporation of small 5-FU molecules did not demonstrably alter the dendrimer's microstructure. The observed doubling of the relaxation time under acidic conditions can be attributed to the relatively compact structure of the dendrimer at neutral pH and the continuous intrastructural rearrangements occurring at acidic pH. The prolonged relaxation time observed in the G4ACE-FA:5-FU:SF complex is attributed to competitive interactions between 5-FU and SF molecules during simultaneous encapsulation by the dendrimer. Analysis of the unloaded and loaded structures of G4ACE-FA under varying pH conditions revealed a densely packed conformation at neutral pH and a more open, sponge-like structure at low pH. The solvent-accessible surface area (SASA) of the dendrimer was assessed at both pH conditions. At neutral pH, SASA values were approximately 124.0 ± 2.8 nm2, 127.5 ± 2.6 nm2, 131.3 ± 2.6 nm2, and 133.3 ± 2.6 nm2 for unloaded G4ACE-FA and the G4ACE-FA:5-FU, G4ACE-FA:SF, and G4ACE-FA:5-FU:SF complexes, respectively. Drug incorporation had a minimal effect on SASA at neutral pH. At low pH, the corresponding values were 198.2 ± 4.7 nm2, 195.8 ± 4.8 nm2, 212.5 ± 6.1 nm2, and 215.4 ± 4.2 nm2. These findings suggest that 5-FU encapsulation resulted in minimal changes to the dendrimer's surface exposure to the solvent, potentially due to its small size. In contrast, SF interaction led to a more pronounced increase in SASA, indicating structural expansion to accommodate SF conjugation. The equilibrium stoichiometry of the G4ACE-FA:5-FU complex was determined to be 1:11 and 1:3 at neutral and low pH, respectively. Similarly, the G4ACE-FA:SF complex exhibited equilibrium stoichiometries of 1:10 and 1:4 at neutral and low pH. The G4ACE-FA:5-FU:SF complex displayed stoichiometries of 1:11:10 at neutral pH and 1:3:3 at low pH. Collectively, these findings suggest that G4ACE-FA holds promise as a versatile nanovector capable of tightly binding drug molecules at neutral pH and facilitating their release within tumor cells, thereby enabling targeted drug delivery. Furthermore, the co-loading of 5-FU and SF did not compromise the loading capacity of G4ACE-FA. At neutral pH, 5-FU molecules were distributed evenly across the dendrimer surface and within its cavities, with 6 molecules encapsulated internally and 5 conjugated on the surface. At low pH, all bound 5-FU molecules were located at the dendrimer periphery. Similarly, at neutral pH, SF molecules were found both internally (6 molecules) and on the surface (4 molecules). At low pH, 2 SF molecules were found on the surface and 2 were internally complexed. The preferred binding sites of 5-FU and SF remained largely unchanged when co-loaded onto the dendrimer. This suggests that co-delivery of 5-FU and SF using G4ACE-FA could be a promising strategy for enhancing the therapeutic efficacy of these chemotherapeutic agents.

Surface Bio-engineered Polymeric Nanoparticles

Surface bio-engineering of polymeric nanoparticles (PNPs) has emerged as a cornerstone in contemporary biomedical research, presenting a transformative avenue that can revolutionize diagnostics, therapies, and drug delivery systems. The approach involves integrating bioactive elements on the surfaces of PNPs, aiming to provide them with functionalities to enable precise, targeted, and favorable interactions with biological components within cellular environments. However, the full potential of surface bio-engineered PNPs in biomedicine is hampered by obstacles, including precise control over surface modifications, stability in biological environments, and lasting targeted interactions with cells or tissues. Concerns like scalability, reproducibility, and long-term safety also impede translation to clinical practice. In this review, these challenges in the context of recent breakthroughs in developing surface-biofunctionalized PNPs for various applications, from biosensing and bioimaging to targeted delivery of therapeutics are discussed. Particular attention is given to bonding mechanisms that underlie the attachment of bioactive moieties to PNP surfaces. The stability and efficacy of surface-bioengineered PNPs are critically reviewed in disease detection, diagnostics, and treatment, both in vitro and in vivo settings. Insights into existing challenges and limitations impeding progress are provided, and a forward-looking discussion on the field's future is presented. The paper concludes with recommendations to accelerate the clinical translation of surface bio-engineered PNPs.

Development of nano-delivery systems for loaded bioactive compounds: using molecular dynamics simulations

Over the past decade, a remarkable surge in the development of functional nano-delivery systems loaded with bioactive compounds for healthcare has been witnessed. Notably, the demanding requirements of high solubility, prolonged circulation, high tissue penetration capability, and strong targeting ability of nanocarriers have posed interdisciplinary research challenges to the community. While extensive experimental studies have been conducted to understand the construction of nano-delivery systems and their metabolic behavior in vivo, less is known about these molecular mechanisms and kinetic pathways during their metabolic process in vivo, and lacking effective means for high-throughput screening. Molecular dynamics (MD) simulation techniques provide a reliable tool for investigating the design of nano-delivery carriers encapsulating these functional ingredients, elucidating the synthesis, translocation, and delivery of nanocarriers. This review introduces the basic MD principles, discusses how to apply MD simulation to design nanocarriers, evaluates the ability of nanocarriers to adhere to or cross gastrointestinal mucosa, and regulates plasma proteins in vivo. Moreover, we presented the critical role of MD simulation in developing delivery systems for precise nutrition and prospects for the future. This review aims to provide insights into the implications of MD simulation techniques for designing and optimizing nano-delivery systems in the healthcare food industry.

Computer simulation of the structural properties of fatty-acid modified PAMAM dendrimers at pH 5 and 7

In this work, we performed coarse-grained molecular dynamics (CGMD) simulations of G3, G4, and G5 polyamidoamine (PAMAM) dendrimers grafting with fatty acid (FTA) chains. The FTA chains of varying length and grafting densities (50% and 100% of surface terminals) correspond to pH 7 and 5, respectively. Our findings suggested that the structural properties of dendrimers were determined by dendrimer generation, polymerization degrees, and pH. With one exception, the size of the FTA grafting dendrimer shrank after fatty acid attachment. Because of the protonation of the dendrimer's interior amines at low pH, the FTA chains are distributed at the dendrimer's surface group. At pH 7, the FTA chains that have aggregated in the interior of the dendrimer cause chain crowding. Our research provided references on drug encapsulation and the lower toxicity of these hydrophobically modified nanoparticles.

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.

Adsorption of Molnupiravir anti-COVID-19 drug over B12N12 and Al12N12 nanocarriers: a DFT study

The potentiality of B12N12 and Al12N12 nanocarriers to adsorb Molnupiravir anti-COVID-19 drug, for the first time, was herein elucidated using a series of quantum mechanical calculations. Density function theory (DFT) was systematically utilized. Interaction (Eint) and adsorption (Eads) energies showed higher negative values for Molnupiravir···Al12N12 complexes compared with Molnupiravir···B12N12 analogs. Symmetry-adapted perturbation theory (SAPT) results proclaimed that the adsorption process was predominated by electrostatic forces. Notably, the alterations in the distributions of the molecular orbitals ensured that the B12N12 and Al12N12 nanocarriers were efficient candidates for delivering the Molnupiravir drug. From the thermodynamic perspective, the adsorption process of Molnupiravir drug over B12N12 and Al12N12 nanocarriers had spontaneous and exothermic nature. The ESP, QTAIM, NCI, and DOS observations exposed the tendency of BN and Al12N12 to adsorb the Molnupiravir drug. Overall, these findings proposed that the B12N12 and Al12N12 nanocarriers are efficient aspirants for the development of the Molnupiravir anti-COVID-19 drug delivery process.Communicated by Ramaswamy H. Sarma.

Peripherally “tertiary butyl ester” functionalized bipyridine cored dendrons: from synthesis and characterization to molecular dynamic simulation study

In this study, we report the design, synthesis, characterization and solvent dependent behaviour of series of new bipyridine cored poly(benzyl-ether) dendrons functionalized with tertiary butyl esters.

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.

Phase equilibria and conformational behavior of dendrimers in porous media: Towards chromatographic analysis of dendrimers

HYPOTHESIS

The intricate entropy-enthalpy interplay of dendrimers confined in pores affects their conformation and retention in the porous stationary phase. This work aims at providing important insights into its impacts on partitioning and chromatographic separation in both size-exclusion chromatography (SEC) and interaction chromatography (IC) regimes.

SIMULATIONS

Using Monte Carlo (MC) simulations, we investigated the bulk-pore phase equilibria and the conformational behavior of flexible dendrimers differing in generation, in spacer length and in fraction of modified terminal groups interacting differently with pore walls than the majority building units.

FINDINGS

With increasing interaction strength, a distinct transition from a roughly spherical shape caused by simultaneous interactions with two walls to an ellipsoidal (or even disklike) conformation tenaciously adhering to only one wall was observed for moderately confined dendrimers. The strongly deformed dendrimers subjected to severe confinement gain high energy and the samples differing in the degree of modification become chromatographically discernable thanks to large energy differences. Consequently, our results suggest that the column fillings with fairly narrow pores which are ineffective in SEC, are highly efficient separation media for dendrimer studies by IC above the critical adsorption point (CAP). Overall, our simulations reveal useful information for advancing and optimizing experimental liquid chromatography studies of dendrimers.

New Insights into the Binding Site and Affinity of the Interaction between Biotin and PAMAMs-NH2 via NMR Studies

Biotin-dendrimer conjugates (such as biotin-PAMAMs-NH₂) are important macromolecules in the field of host-guest chemistry and widely used systems for delivery. The similar chemical structures of the inner and outer layers of PAMAM-NH₂ make it difficult to illuminate the interaction and the binding affinity of biotin-PAMAMs-NH₂. By utilizing NMR techniques including ¹H NMR titration, CSSF-TOCSY, STDD methods, and 2D DOSY analysis, we demonstrate a method to sort out these interactions. The methylene protons of the inner and outer layers of PAMAM-NH₂ are successfully identified and accurately positioned so that the carboxylic acid groups of biotins are having ionic interactions with the outermost amine groups of PAMAM-NH₂. The inner PAMAM-NH₂ is protonated when reaching the isoelectric point of PAMAM-NH₂, increasing the hydrodynamic radius. On the basis of the NMR experiments, a model is proposed, where the carboxylic acid groups and heterocyclic skeleton of biotin arched over the outer layers of PAMAM-NH₂ like a bridge. Furthermore, using STDD epitope mapping, the binding affinity between biotin and PAMAM-NH₂ was quantified. The diffusion behavior of biotin-G5 PAMAM-NH₂ complex is more complicated than that of biotin-G3 PAMAM-NH₂ complex due to steric hindrance. The results provide a theoretical basis for understanding these complicated drug delivery systems.

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.

Structure optimization of dendritic lipopeptide based gene vectors with the assistance from molecular dynamic simulation

Disulfide modified lipopeptide assemblies with an arginine-rich dendritic periphery provide a promising platform for effective gene transfer. Dendritic arginine peptides that mimic the cell-penetrating peptides of a virus envelope are vital for complexation, interaction with physical barriers, and final gene release. Here, we report three lipopeptides with different-generation dendritic peripheries (R₁LS, R₂LS and R₃LS), each of which contains a dioleoyl-l-lysinate hydrophobic tail. Such molecules were proven to self-assemble in aqueous solution with different morphologies, sizes, and surface zeta potentials. R₂LS and R₃LS assemblies showed spherical and spindle shapes with zeta potentials of 27.2 and 32.8 mV, respectively. They exhibited complete condensation of pDNA at a low N/P ratio, while R₁LS assemblies displayed a fiber pattern with a relatively low electric potential of 10.9 mV with poor DNA binding ability. In a cellular viability experiment, R₁LS and R₂LS have no significant cytotoxicity even at high dosage, while R₃LS showed conspicuous toxicity. As a gene vector, R₂LS presented high gene transfection efficiency either in the presence or the absence of serum, which was 58.7% greater than liposome 2000 and PEI in the condition of 10% fetal bovine serum for HeLa cells. While R₃LS showed good results just without serum and R₁LS was unserviceable in all situations. Moreover, molecular dynamic simulation was exploited to analyze the kinestate of the signal molecule and the interactions of multiple molecules, which could assist us in better understanding the experimental phenomena. The simulation results indicated that the R₂LS molecule has better flexibility, which was favorable for interaction with the cell membrane. And it could generate tight integration in self-assembly while R₁LS and R₃LS assemblies have a large molecular interval, which led to a controllable release of cargos for R₂LS in a reductive environment. In summary, the generation of the dendrimer in lipopeptides is vital for the gene transfer effect. For optimization, it is necessary to study the structure-function relationship, and molecular dynamic simulation is an effective strategy for screening the molecular structure and even for predicting experimental results.