Nano drug delivery systems: Molecular dynamic simulation

Computational assessment of lipid facilitated membrane permeation of vancomycin using force-probe molecular dynamic simulation

In this study the efficacy of different edible lipids for drug permeation enhancement of vancomycin through biological membrane was investigated using molecular dynamic simulation. In this regard, at first the ability of the lipids for complex formation with the drug was evaluated for number of most common edible lipids including tripalmitin (TPA), trimyristin (TMY), labrafil (LAB), glycerol monostearate (GMS), glycerol monooleate (GMO), Distearoylphosphorylethanolamine (DSPE), dipalmitoylphosphatidylethanolamine (DPPE), Dipalmitoylphosphatidylcholine (DPPC), cholesterol (CL), stearic acid (SA), palmitic acid (PA) and oleic acid (OA). Then the complexes were pulled thorough a bilayer membrane while the changes in force were probed. The results showed that besides the SA, PA and OA the other examined lipids were able to perform a perfect molecular complex with the drug. Also the results of pulling simulation revealed that the least of force was needed for drug transmittance through the membrane when it was covered by LAB, TMY and DSPE. These results indicated that these lipids can be the excellent materials of choice as permeation enhancer for preparing a proper oral formulation of vancomycin.Communicated by Ramaswamy H. Sarma.

Advances in nano-preparations for improving tetrandrine solubility and bioavailability

Tetrandrine (TET) is a natural bis-benzylisoquinoline alkaloid isolated from Stephania species with a wide range of biological and pharmacologic activities; it mainly serves as an anti-inflammatory agent or antitumor adjuvant in clinical applications. However, limitations such as prominent hydrophobicity, severe off-target toxicity, and low absorption result in suboptimal therapeutic outcomes preventing its widespread adoption. Nanoparticles have proven to be efficient devices for targeted drug delivery since drug-carrying nanoparticles can be passively transported to the tumor site by the enhanced permeability and retention (EPR) effects, thus securing a niche in cancer therapies. Great progress has been made in nanocarrier construction for TET delivery due to their outstanding advantages such as increased water-solubility, improved biodistribution and blood circulation, reduced off-target irritation, and combinational therapy. Herein, we systematically reviewed the latest advancements in TET-loaded nanoparticles and their respective features with the expectation of providing perspective and guidelines for future research and potential applications of TET.

Monitoring of Isothermal Crystallization and Time-Temperature Transformation of Amorphous Felodipine: The Time-Domain Nuclear Magnetic Resonance Method

The isothermal crystallization process of felodipine has been investigated using the time-domain Nuclear Magnetic Resonance (NMR) method for amorphous bulk and ground samples. The obtained induction and crystallization times were then used to construct the time-temperature-transformation (TTT) diagram, both above and below the glass transition temperature (Tg). The Nose temperature was found equal to 363 K. Furthermore, the dynamics of crystalline and amorphous felodipine were compared across varying temperatures. Molecular dynamics simulations were also employed to explore the hydrogen-bond interactions and dynamic properties of both systems.

Navigating the neurological frontier: Macromolecular marvels in overcoming blood-brain barrier challenges for advanced drug delivery

The blood-brain interface poses formidable obstacles in addressing neurological conditions such as Alzheimer's, Multiple Sclerosis, brain cancers, and cerebrovascular accidents. Serving as a safeguard against potential threats in the blood, this barrier hinders direct drug delivery to affected cells, necessitating specialized transport mechanisms. Within the realm of nanotechnology, the creation of nanoscale carriers, including macromolecules such as polymers, lipids, and metallic nanoparticles, is gaining prominence. These carriers, tailored in diverse forms and sizes and enriched with specific functional groups for enhanced penetration and targeting, are capturing growing interest. This revised abstract explores the macromolecular dimension in understanding how nanoparticles interact with the blood-brain barrier. It re-evaluates the structure and function of the blood-brain barrier, highlighting macromolecular nanocarriers utilized in drug delivery to the brain. The discussion delves into the intricate pathways through which drugs navigate the blood-brain barrier, emphasizing the distinctive attributes of macromolecular nanocarriers. Additionally, it explores recent innovations in nanotechnology and unconventional approaches to drug delivery. Ultimately, the paper addresses the intricacies and considerations in developing macromolecular-based nanomedicines for the brain, aiming to advance the creation and evolution of nanomedicines for neurological ailments.

Proposing of fungal endophyte secondary metabolites as a potential inhibitors of 2019-novel coronavirus main protease using docking and molecular dynamics

In this study, the inhibitory potential of 99 fungal derived secondary metabolites was predicted against SARS-CoV-2 main protease by using of computational approaches. This protein plays an important role in replication and is one of the important targets to inhibit viral reproduction. Among the 99 reported compounds, the 9 of them with the highest binding energy to Mpro obtained from the molecular docking method were selected for the molecular dynamic simulations. The compounds were then investigated by using the SwissADME serve to evaluate the compounds in terms of pharmacokinetic and druglikness properties. The overall results of different analysis show that the compound RKS-1778 is potentially more effective than others and form strong complexes with viral protease. It also had better pharmacokinetic properties than other metabolites, so predicted to be a suitable candidate as anti SARS-CoV-2 bioactive.Communicated by Ramaswamy H. Sarma.

In Silico Investigation on the Molecular Behavior and Structural Stability of the Rosette Nanotubes as the Drug Vehicles for Paclitaxel, an Anti-Cancer Drug

Most anticancer drugs affect healthy cells in addition to cancer cells, causing severe side effects. Targeted delivery by nano-based drug delivery systems (NDDS) can reduce these severe side effects while maintaining therapeutic efficacy. This work introduced rosette nanotube (RNT) as a potential drug vehicle for paclitaxel (PTX) due to its self-assembling property, biocompatibility, amphiphilicity, and low toxicity. Molecular dynamics (MD) simulations aided with molecular mechanics Poisson Boltzmann surface area (MMPBSA) analysis are used here to investigate the molecular behavior and the loading energetics of each type of RNT (K1, xK1, and iEt-xK1) with PTX. Analysis showed that the most probable configuration of PTX is on either end of each RNT. The binding free energies (-117.74 to -69.29 kJ/mol) when PTX is closer to one end were stronger than when it is in the inner channel (-53.51 to -40.88 kJ/mol). The latter alludes to the encapsulation of the PTX by each RNT. Thus, loading is possible by encapsulation during the self-assembly process given the favorable estimated binding free energies. Based on the results, RNT has potential as a drug vehicle for PTX, which warrants further investigation.

Computational Insight of Phase Transformation and Drug Release Behaviour of Doxycycline-Loaded Ibuprofen-Based In-Situ Forming Gel

This research investigates the gel formation behaviour and drug-controlling performance of doxycycline-loaded ibuprofen-based in-situ forming gels (DH-loaded IBU-based ISGs) for potential applications in periodontal treatment. The investigation begins by exploring the physical properties and gel formation behaviour of the ISGs, with a particular focus on determining their sustained release capabilities. To gain a deeper understanding of the molecular interactions and dynamics within the ISGs, molecular dynamic (MD) simulations are employed. The effects of adding IBU and DH on reducing surface tension and water tolerance properties, thus affecting molecular properties. The phase transformation phenomenon is observed around the interface, where droplets of ISGs move out to the water phase, leading to the precipitation of IBU around the interface. The optimization of drug release profiles ensures sustained local drug release over seven days, with a burst release observed on the first day. Interestingly, different organic solvents show varying abilities to control DH release, with dimethyl sulfoxide (DMSO) demonstrating superior control compared to N-Methyl-2-pyrrolidone (NMP). MD simulations using AMBER20 software provide valuable insights into the movement of individual molecules, as evidenced by root-mean-square deviation (RMSD) values. The addition of IBU to the system results in the retardation of IBU molecule movement, particularly evident in the DMSO series, with the diffusion constant value of DH reducing from 1.2452 to 0.3372 and in the NMP series from 0.3703 to 0.2245 after adding IBU. The RMSD values indicate a reduction in molecule fluctuation of DH, especially in the DMSO system, where it decreases from over 140 to 40 Å. Moreover, their radius of gyration is influenced by IBU, with the DMSO system showing lower values, suggesting an increase in molecular compactness. Notably, the DH-IBU configuration exhibits stable pairing through H-bonding, with a higher amount of H-bonding observed in the DMSO system, which is correlated with the drug retardation efficacy. These significant findings pave the way for the development of phase transformation mechanistic studies and offer new avenues for future design and optimization formulation in the ISG drug delivery systems field.

Target-Specific Delivery and Bioavailability of Pharmaceuticals via Janus and Dendrimer Particles

Nanosized Janus and dendrimer particles have emerged as promising nanocarriers for the target-specific delivery and improved bioavailability of pharmaceuticals. Janus particles, with two distinct regions exhibiting different physical and chemical properties, provide a unique platform for the simultaneous delivery of multiple drugs or tissue-specific targeting. Conversely, dendrimers are branched, nanoscale polymers with well-defined surface functionalities that can be designed for improved drug targeting and release. Both Janus particles and dendrimers have demonstrated their potential to improve the solubility and stability of poorly water-soluble drugs, increase the intracellular uptake of drugs, and reduce their toxicity by controlling the release rate. The surface functionalities of these nanocarriers can be tailored to specific targets, such as overexpressed receptors on cancer cells, leading to enhanced drug efficacy The design of these nanocarriers can be optimized by tuning the size, shape, and surface functionalities, among other parameters. The incorporation of Janus and dendrimer particles into composite materials to create hybrid systems for enhancing drug delivery, leveraging the unique properties and functionalities of both materials, can offer promising outcomes. Nanosized Janus and dendrimer particles hold great promise for the delivery and improved bioavailability of pharmaceuticals. Further research is required to optimize these nanocarriers and bring them to the clinical setting to treat various diseases. This article discusses various nanosized Janus and dendrimer particles for target-specific delivery and bioavailability of pharmaceuticals. In addition, the development of Janus-dendrimer hybrid nanoparticles to address some limitations of standalone nanosized Janus and dendrimer particles is discussed.

Target-Specific Delivery and Bioavailability of Pharmaceuticals via Janus and Dendrimer Particles

Nanosized Janus and dendrimer particles have emerged as promising nanocarriers for the target-specific delivery and improved bioavailability of pharmaceuticals. Janus particles, with two distinct regions exhibiting different physical and chemical properties, provide a unique platform for the simultaneous delivery of multiple drugs or tissue-specific targeting. Conversely, dendrimers are branched, nanoscale polymers with well-defined surface functionalities that can be designed for improved drug targeting and release. Both Janus particles and dendrimers have demonstrated their potential to improve the solubility and stability of poorly water-soluble drugs, increase the intracellular uptake of drugs, and reduce their toxicity by controlling the release rate. The surface functionalities of these nanocarriers can be tailored to specific targets, such as overexpressed receptors on cancer cells, leading to enhanced drug efficacy The design of these nanocarriers can be optimized by tuning the size, shape, and surface functionalities, among other parameters. The incorporation of Janus and dendrimer particles into composite materials to create hybrid systems for enhancing drug delivery, leveraging the unique properties and functionalities of both materials, can offer promising outcomes. Nanosized Janus and dendrimer particles hold great promise for the delivery and improved bioavailability of pharmaceuticals. Further research is required to optimize these nanocarriers and bring them to the clinical setting to treat various diseases. This article discusses various nanosized Janus and dendrimer particles for target-specific delivery and bioavailability of pharmaceuticals. In addition, the development of Janus-dendrimer hybrid nanoparticles to address some limitations of standalone nanosized Janus and dendrimer particles is discussed.

The effect of novel antihypertensive drug valsartan on lysozyme aggregation: A combined in situ and in silico study

Protein misfolding can result in amyloid fiber aggregation, which is associated with various types of diseases. Therefore, preventing or treating abnormally folded proteins may provide therapeutic intervention for these diseases. Valsartan (VAL) is an angiotensin II receptor blocker (ARB) that is used to treat hypertension. In this study, we examine the anti-aggregating effect of VAL against hen egg-white lysozyme (HEWL) amyloid fibrils through spectroscopy, docking, and microscopic analysis. In vitro formation of HEWL amyloid fibrils was indicated by increased turbidity, RLS (Rayleigh light scattering), and ThT fluorescence intensity. 10 μM VAL, amyloid/aggregation was inhibited up to 83% and 72% as measured by ThT and RLS respectively. In contrast, 100 μM VAL significantly increases the fibril aggregation of HEWL. CD spectroscopy results show a stabilization of HEWL α-helical structures in the presence of 10 μM VAL while the increase in β-sheet was detected at 100 μM concentration of VAL. The hydrophobicity of HEWL was increased at 100 μM VAL, suggesting the promotion of aggregation via its self-association. Steady-state quenching revealed that VAL and HEWL interact spontaneously via hydrogen bonds and van der Waals forces. Transmission electron microscopy (TEM) images illustrate that the needle-like fibers of HEWL amyloid were reduced at 10 μM VAL, while at 100 μM the fibrils of amyloid were increased. Additionally, our computational studies showed that VAL could bind to two binding sites within HEWL. In the BS-1 domain of HEWL, VAL binds to ASN⁵⁹, ILE⁹⁸, ILE⁵⁸, TRP¹⁰⁸, VAL¹⁰⁹, SER⁵⁰, ASP⁵², ASN⁵⁹, ALA¹⁰⁷, and TRP¹⁰⁸ residues with a binding energy of -9.72 kcal mol^-1. Also, it binds to GLU⁷, ALA¹⁰, ALA¹¹, CYS⁶, ARG¹²⁸, and ARG¹⁴ in the BS-2 domain with a binding energy of -5.89 kcal mol^-1. VAL, therefore, appears to have dual effect against HEWL aggregation. We suggest that VAL stabilizes HEWL's aggregation-prone region (APR) at 10 μM, preventing aggregation. Also, we assume that at 100 μM, VAL occupies BS-2 beside BS-1 and destabilizes the folding structure of HEWL, resulting in aggregation. Further studies are needed to investigate the mechanism of action and determine its potential side effects.

How can machine learning and multiscale modeling benefit ocular drug development?

The eyes possess sophisticated physiological structures, diverse disease targets, limited drug delivery space, distinctive barriers, and complicated biomechanical processes, requiring a more in-depth understanding of the interactions between drug delivery systems and biological systems for ocular formulation development. However, the tiny size of the eyes makes sampling difficult and invasive studies costly and ethically constrained. Developing ocular formulations following conventional trial-and-error formulation and manufacturing process screening procedures is inefficient. Along with the popularity of computational pharmaceutics, non-invasive in silico modeling & simulation offer new opportunities for the paradigm shift of ocular formulation development. The current work first systematically reviews the theoretical underpinnings, advanced applications, and unique advantages of data-driven machine learning and multiscale simulation approaches represented by molecular simulation, mathematical modeling, and pharmacokinetic (PK)/pharmacodynamic (PD) modeling for ocular drug development. Following this, a new computer-driven framework for rational pharmaceutical formulation design is proposed, inspired by the potential of in silico explorations in understanding drug delivery details and facilitating drug formulation design. Lastly, to promote the paradigm shift, integrated in silico methodologies were highlighted, and discussions on data challenges, model practicality, personalized modeling, regulatory science, interdisciplinary collaboration, and talent training were conducted in detail with a view to achieving more efficient objective-oriented pharmaceutical formulation design.

Nanoparticles loaded with pharmacologically active plant-derived natural products: Biomedical applications and toxicity

Pharmacologically active natural products have played a significant role in the history of drug development. They have acted as sources of therapeutic drugs for various diseases such as cancer and infectious diseases. However, most natural products suffer from poor water solubility and low bioavailability, limiting their clinical applications. The rapid development of nanotechnology has opened up new directions for applying natural products and numerous studies have explored the biomedical applications of nanomaterials loaded with natural products. This review covers the recent research on applying plant-derived natural products (PDNPs) nanomaterials, including nanomedicines loaded with flavonoids, non-flavonoid polyphenols, alkaloids, and quinones, especially their use in treating various diseases. Furthermore, some drugs derived from natural products can be toxic to the body, so the toxicity of them is discussed. This comprehensive review includes fundamental discoveries and exploratory advances in natural product-loaded nanomaterials that may be helpful for future clinical development.

Mucus adhesion vs. mucus penetration? Screening nanomaterials for nasal inhalation by MD simulation

Nanocarrier-aided drug delivery techniques have improved the absorption and permeability of drugs in nose-to-brain delivery. However, the molecular properties of nanocarriers during the delivery process are of great interest; in particular, the characteristics when penetrating barriers in vivo are crucial for the screening and optimization of materials for nasal inhalation. In this study, we have focused on two types of delivery systems: mucoadhesive nanoparticles (MAPs) and mucopenetrating nanoparticles (MPPs); both have been widely used for mucosal delivery, although a method for selecting the more effective type of drug carriers for mucosal delivery has not been established. Molecular dynamics (MD) simulations were used to reveal the all-atom dynamic characteristics of the interaction between different delivery systems and the nasal mucus protein MUC5AC. Among the systems tested, hydroxypropyltrimethyl ammonium chloride chitosan (HTCC) had the strongest interaction with mucin, suggesting it had better mucoadhesive performance, and that it interacted with MUC5AC more strongly than unmodified chitosan. In contrast, the mucus-penetrating material polyethylene glycol-poly lactic acid-co-glycolic acid (PEG-PLGA), had almost no interaction with MUC5AC. The results of the MD simulations were verified by in vitro experiments on nanoparticles (NPs) and mucin binding. The drug delivery performance of the four types of NPs, analyzed by in vitro and ex vivo mucosal penetration, were all generally consistent with the properties of the material predicted from the MD simulation. These clues to the molecular mechanism of MAPs and MPPs may provide useful insight into the screening and optimization of nanomaterials suitable for nasal inhalation.

Computational approach to elucidate the formation and stabilization mechanism of amorphous formulation using molecular dynamics simulation and fragment molecular orbital calculation

α-Glycosyl rutin (Rutin-G) consists of a flavonol skeleton and sugar groups and is a promising additive for amorphous formulations. In our previous study, experimental approaches suggested an interaction between the model drug carbamazepine (CBZ) and flavonol skeleton of Rutin-G that stabilizes amorphous formulations. In the present study, the formation and stabilization mechanisms of CBZ/Rutin-G amorphous formulation were investigated using a computational approach. The CBZ/Rutin-G amorphous formulation was obtained via molecular dynamics (MD) simulation, which mimicked the melt-quenching method. Root mean square deviation analysis revealed that the translational motion of CBZ during the cooling process was suppressed by adding Rutin-G. Monitoring the atomic distance during the cooling process revealed that hydrogen bonds via carboxamide oxygen of CBZ with hydroxyl hydrogen of Rutin-G were preferentially formed with flavonol skeletons than sugar groups. The simulated amorphous formulation was then calculated using fragment molecular orbital (FMO) method. The quantitative evaluation of multiple interactions revealed that the hydrogen bond energy was higher in CBZ-sugar groups than in CBZ-flavonol skeleton, while the π-type of interaction energy was higher in CBZ-flavonol skeleton than in CBZ-sugar groups. The computational approach combining MD simulation and FMO calculation provides information on various interactions that are difficult to detect using experimental approaches, which helps understand the formation and stabilization mechanism of amorphous formulations.

New insight into the structural changes of apoferritin pores in the process of doxorubicin loading at an acidic pH: Molecular dynamics simulations

Apoferritin (APO-Fr) is one of the most investigated proteins proposed as an advanced structure for drug delivery systems. Herein, molecular dynamics simulation was employed to compare the opening of 3-fold and 4-fold pores in APO-Fr during the partial disassembly process at an acidic pH. We showed that more hydrophilic residues in the surface of 3-fold pores compared to 4-fold pores facilitate increased flexibility and a higher tendency to open. In particular, dissociation is induced by the presence of Doxorubicin (DOX) close to 3-fold pores. Our simulations showed loaded DOXs on the APO-Fr surface were mainly involved in the hydrogen bond interactions with the hydrophilic residues, suggesting the difficulty of hydrophobic drugs loading in APO-Fr with the partial disassembly process. However, π-π interactions as well as hydrogen bonds between protein and DOXs were mediated by the basic and acidic amino acids such as HIP128, GLU17, and LYS143 at the open pores, providing penetration of DOXs into the H-Apo-Fr. We conclude that increased drug encapsulations and loading capacity of hydrophobic drugs into the cavity of APO-Fr are feasible by further disassembly of openings to access the internal hydrophobic portions of the protein.

Key Points in Remote-Controlled Drug Delivery: From the Carrier Design to Clinical Trials

The increased research activity aiming at improved delivery of pharmaceutical molecules indicates the expansion of the field. An efficient therapeutic delivery approach is based on the optimal choice of drug-carrying vehicle, successful targeting, and payload release enabling the site-specific accumulation of the therapeutic molecules. However, designing the formulation endowed with the targeting properties in vitro does not guarantee its selective delivery in vivo. The various biological barriers that the carrier encounters upon intravascular administration should be adequately addressed in its overall design to reduce the off-target effects and unwanted toxicity in vivo and thereby enhance the therapeutic efficacy of the payload. Here, we discuss the main parameters of remote-controlled drug delivery systems: (i) key principles of the carrier selection; (ii) the most significant physiological barriers and limitations associated with the drug delivery; (iii) major concepts for its targeting and cargo release stimulation by external stimuli in vivo. The clinical translation for drug delivery systems is also described along with the main challenges, key parameters, and examples of successfully translated drug delivery platforms. The essential steps on the way from drug delivery system design to clinical trials are summarized, arranged, and discussed.