Molecular Dynamics Studies of Liposomes as Carriers for Photosensitizing Drugs: Development, Validation, and Simulations with a Coarse-Grained Model

Unravelling the interactions between small molecules and liposomal bilayers via molecular dynamics and thermodynamic modelling

Lipid-based drug delivery systems hold immense promise in addressing critical medical needs, from cancer and neurodegenerative diseases to infectious diseases. By encapsulating active pharmaceutical ingredients - ranging from small molecule drugs to proteins and nucleic acids - these nanocarriers enhance treatment efficacy and safety. However, their commercial success faces hurdles, such as the lack of a systematic design approach and the issues related to scalability and reproducibility. This work aims to provide insights into the drug-phospholipid interaction by combining molecular dynamic simulations and thermodynamic modelling techniques. In particular, we have made a connection between the structural properties of the drug-phospholipid system and the physicochemical performance of the drug-loaded liposomal nanoformulations. We have considered two prototypical drugs, felodipine (FEL) and naproxen (NPX), and one model hydrogenated soy phosphatidylcholine (HSPC) bilayer membrane. Molecular dynamic simulations revealed which regions within the phospholipid bilayers are most and least favoured by the drug molecules. NPX tends to reside at the water-phospholipid interface and is characterized by a lower free energy barrier for bilayer membrane permeation. Meanwhile, FEL prefers to sit within the hydrophobic tails of the phospholipids and is characterized by a higher free energy barrier for membrane permeation. Flory-Huggins thermodynamic modelling, small angle X-ray scattering, dynamic light scattering, TEM, and drug release studies of these liposomal nanoformulations confirmed this drug-phospholipid structural difference. The naproxen-phospholipid system has a lower free energy barrier for permeation, higher drug miscibility with the bilayer, larger liposomal nanoparticle size, and faster drug release in the aqueous medium than felodipine. We suggest that this combination of molecular dynamics and thermodynamics approach may offer a new tool for designing and developing lipid-based nanocarriers for unmet medical applications.

Translational Challenges and Prospective Solutions in the Implementation of Biomimetic Delivery Systems

Biomimetic delivery systems (BDSs), inspired by the intricate designs of biological systems, have emerged as a groundbreaking paradigm in nanomedicine, offering unparalleled advantages in therapeutic delivery. These systems, encompassing platforms such as liposomes, protein-based nanoparticles, extracellular vesicles, and polysaccharides, are lauded for their targeted delivery, minimized side effects, and enhanced therapeutic outcomes. However, the translation of BDSs from research settings to clinical applications is fraught with challenges, including reproducibility concerns, physiological stability, and rigorous efficacy and safety evaluations. Furthermore, the innovative nature of BDSs demands the reevaluation and evolution of existing regulatory and ethical frameworks. This review provides an overview of BDSs and delves into the multifaceted translational challenges and present emerging solutions, underscored by real-world case studies. Emphasizing the potential of BDSs to redefine healthcare, we advocate for sustained interdisciplinary collaboration and research. As our understanding of biological systems deepens, the future of BDSs in clinical translation appears promising, with a focus on personalized medicine and refined patient-specific delivery systems.

Lipid-Based Nanoparticles for Drug/Gene Delivery: An Overview of the Production Techniques and Difficulties Encountered in Their Industrial Development

Over the past decade, the therapeutic potential of nanomaterials as novel drug delivery systems complementing conventional pharmacology has been widely acknowledged. Among these nanomaterials, lipid-based nanoparticles (LNPs) have shown remarkable pharmacological performance and promising therapeutic outcomes, thus gaining substantial interest in preclinical and clinical research. In this review, we introduce the main types of LNPs used in drug formulations such as liposomes, nanoemulsions, solid lipid nanoparticles, nanostructured lipid carriers, and lipid polymer hybrid nanoparticles, focusing on their main physicochemical properties and therapeutic potential. We discuss computational studies and modeling techniques to enhance the understanding of how LNPs interact with therapeutic cargo and to predict the potential effectiveness of such interactions in therapeutic applications. We also analyze the benefits and drawbacks of various LNP production techniques such as nanoprecipitation, emulsification, evaporation, thin film hydration, microfluidic-based methods, and an impingement jet mixer. Additionally, we discuss the major challenges associated with industrial development, including stability and sterilization, storage, regulatory compliance, reproducibility, and quality control. Overcoming these challenges and facilitating regulatory compliance represent the key steps toward LNP's successful commercialization and translation into clinical settings.

Structure and interaction of therapeutic proteins in solution: a combined simulation and experimental study

The aggregation of therapeutic proteins in solution has attracted significant interest, driving efforts to understand the relationship between microscopic structural changes and protein-protein interactions determining aggregation processes in solution. Additionally, there is substantial interest in being able to predict aggregation based on protein structure as part of molecular developability assessments. Molecular Dynamics provides theoretical tools to complement experimental studies and to interrogate and identify the microscopic mechanisms determining aggregation. Here we perform all-atom MD simulations to study the structure and inter-protein interaction of the Fab and Fc fragments of the monoclonal antibody (mAb) COE3. We unravel the role of ion-protein interactions in building the ionic double layer and determining effective inter-protein interaction. Further, we demonstrate, using various state-of-the-art force fields (charmm, gromos, amber, opls/aa), that the protein solvation, ionic structure and protein-protein interaction depend significantly on the force field parameters. We perform SANS and Static Light Scattering experiments to assess the accuracy of the different forcefields. Comparison of the simulated and experimental results reveal significant differences in the forcefields' performance, particularly in their ability to predict the protein size in solution and inter-protein interactions quantified through the second virial coefficients. In addition, the performance of the forcefields is correlated with the protein hydration structure.

Predicting liposome formulations by the integrated machine learning and molecular modeling approaches

Liposome is one of the most widely used carriers for drug delivery because of the great biocompatibility and biodegradability. Due to the complex formulation components and preparation process, formulation screening mostly relies on trial-and-error process with low efficiency. Here liposome formulation prediction models have been built by machine learning (ML) approaches. The important parameters of liposomes, including size, polydispersity index (PDI), zeta potential and encapsulation, are predicted individually by optimal ML algorithm, while the formulation features are also ranked to provide important guidance for formulation design. The analysis of key parameter reveals that drug molecules with logS [-3, -6], molecular complexity [500, 1000] and XLogP3 (≥2) are priority for preparing liposome with higher encapsulation. In addition, naproxen (NAP) and palmatine HCl (PAL) represented the insoluble and water-soluble molecules are prepared as liposome formulations to validate prediction ability. The consistency between predicted and experimental value verifies the satisfied accuracy of ML models. As the drug properties are critical for liposome particles, the molecular interactions and dynamics of NAP and PAL liposome are further investigated by coarse-grained molecular dynamics simulations. The modeling structure reveals that NAP molecules could distribute into lipid layer, while most PAL molecules aggregate in the inner aqueous phase of liposome. The completely different physical state of NAP and PAL confirms the importance of drug properties for liposome formulations. In summary, the general prediction models are built to predict liposome formulations, and the impacts of key factors are analyzed by combing ML with molecular modeling. The availability and rationality of these intelligent prediction systems have been proved in this study, which could be applied for liposome formulation development in the future.

In silico modeling and empirical study of 4-n-Butylresorcinol nanoliposome formulation

A study to incorporate in silico modeling with an empirical experiment has been carried out to formulate nanoliposome containing 4-n-butylresorcinol as the active ingredient. The in silico modeling was performed using molecular dynamics simulation followed by radius of gyration observation to provide insight into the mechanisms of 4-n-butylresorcinol stabilization by liposome due to their nano-size. The empirical experiment was conducted by formulating the nanoliposome using soy lecithin phospholipid formula as suggested by the in silico modeling followed by determining its particle size as well as its shape. From their incorporation, it was found that 3200 phospholipid molecules were selected in formulating nanoliposome containing 4-n-butylresorcinol. The results of the nanoliposomes size observation in the modeling of 3200 lipid molecules was 87.01 (± 0.59) nm, whereas the size from the empirical study was 87.57 (± 0.06) nm. Communicated by Ramaswamy H. Sarma.

Fluorescent Multifunctional Organic Nanoparticles for Drug Delivery and Bioimaging: A Tutorial Review

Fluorescent organic nanoparticles (FONs) are a large family of nanostructures constituted by organic components that emit light in different spectral regions upon excitation, due to the presence of organic fluorophores. FONs are of great interest for numerous biological and medical applications, due to their high tunability in terms of composition, morphology, surface functionalization, and optical properties. Multifunctional FONs combine several functionalities in a single nanostructure (emission of light, carriers for drug-delivery, functionalization with targeting ligands, etc.), opening the possibility of using the same nanoparticle for diagnosis and therapy. The preparation, characterization, and application of these multifunctional FONs require a multidisciplinary approach. In this review, we present FONs following a tutorial approach, with the aim of providing a general overview of the different aspects of the design, preparation, and characterization of FONs. The review encompasses the most common FONs developed to date, the description of the most important features of fluorophores that determine the optical properties of FONs, an overview of the preparation methods and of the optical characterization techniques, and the description of the theoretical approaches that are currently adopted for modeling FONs. The last part of the review is devoted to a non-exhaustive selection of some recent biomedical applications of FONs.

Design and simulation of the liposomal model by using a coarse-grained molecular dynamics approach towards drug delivery goals

The simulated liposome models provide events in molecular biological science and cellular biology. These models may help to understand the cell membrane mechanisms, biological cell interactions, and drug delivery systems. In addition, the liposomes model may resolve specific issues such as membrane transports, ion channels, drug penetration in the membrane, vesicle formation, membrane fusion, and membrane protein function mechanism. One of the approaches to investigate the lipid membranes and the mechanism of their formation is by molecular dynamics (MD) simulations. In this study, we used the coarse-grained MD simulation approach and designed a liposome model system. To simulate the liposome model, we used phospholipids that are present in the structure of natural cell membranes (1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)). Simulation conditions such as temperature, ions, water, lipid concentration were performed based on experimental conditions. Our results showed a liposome model (ellipse vesicle structure) during the 2100 ns was formed. Moreover, the analysis confirmed that the stretched and ellipse structure is the best structure that could be formed. The eukaryotic and even the bacterial cells have elliptical and flexible structures. Usually, an elliptical structure is more stable than other assembled structures. The results indicated the assembly of the lipids is directed through short-range interactions (electrostatic interactions and, van der Waals interactions). Total energy (Van der Waals and electrostatic interaction energy) confirmed the designed elliptical liposome structure has suitable stability at the end of the simulation process. Our findings confirmed that phospholipids DOPC and DOPE have a good tendency to form bilayer membranes (liposomal structure) based on their geometric shapes and chemical-physical properties. Finally, we expected the simulated liposomal structure as a simple model to be useful in understanding the function and structure of biological cell membranes. Furthermore, it is useful to design optimal, suitable, and biocompatible liposomes as potential drug carriers.

Photophysical characterization of Hypericin-loaded in micellar, liposomal and copolymer-lipid nanostructures based F127 and DPPC liposomes

Hypericin (Hy) compound presents a high photoactivity in photodynamic therapy (PDT), photodiagnosis and theranostics applications. The maintenance of this compound in monomeric form could undermine the potential benefits of its photophysical and photodynamic activity. In this study, we demonstrated that the Hy formulated in a system based on the use of the F127 copolymer and the 1,2-dipalmitoyl-sn-3-glycerol-phosphatidylcholine (DPPC) as micelles, liposomal vesicles and Copolymer-Lipid coated systems, have improved its photophysical properties for many clinical modalities. Based on the results of the triplet state lifetime values (τ_t), the singlet oxygen quantum yield (Φ_Δ¹O₂), the fluorescence lifetime (τ_F) and the fluorescence quantum yield (Φ_F), all Hy formulations had its photophysical properties described in different models of drug delivery systems (DDS). In addition, the transient spectra profile of those formulations was unaffected by the Hy incorporation process, except for the liposomal system, which demonstrated to be the less stable one by flash photolysis technique. The cytotoxic effects of those formulations were also investigated for CaCo-2 and HaCat cells line. The cytotoxic concentrations for 50% (CC₅₀) were 0.56, 1.05, 1.33 and 4.80 µmol L^-1 for Copolymer-Lipid/Hy, DPPC/Hy, F127/Hy and ethanol/Hy for CaCo-2 cells, respectively, and 0.69, 2.02, 1.45 and 1.16 µmol L^-1 for Copolymer-Lipid/Hy, DPPC/Hy, F127/Hy and ethanol/Hy for HaCat cells, respectively. The F127 copolymer had a significant role in many photophysical parameters determined for Copolymer-Lipid/Hy coated system. Although all those formulations had shown satisfactory results, Copolymer-Lipid/Hy proved to be superior in many aspects, being the most promising formulation for PDT, photodiagnosis and theranostics applications.

Computational and Experimental Approaches to Investigate Lipid Nanoparticles as Drug and Gene Delivery Systems

Lipid nanoparticles (LNPs) have been widely applied in drug and gene delivery. More than twenty years ago, DoxilTM was the first LNPs-based drug approved by the US Food and Drug Administration (FDA). Since then, with decades of research and development, more and more LNP-based therapeutics have been used to treat diverse diseases, which often offer the benefits of reduced toxicity and/or enhanced efficacy compared to the active ingredients alone. Here, we provide a review of recent advances in the development of efficient and robust LNPs for drug/gene delivery. We emphasize the importance of rationally combining experimental and computational approaches, especially those providing multiscale structural and functional information of LNPs, to the design of novel and powerful LNP-based delivery systems.

Coarse-Grained Molecular Dynamics (CG-MD) Simulation of the Encapsulation of Dexamethasone in PSS/PDDA Layer-by-Layer Assembled Polyelectrolyte Nanocapsules

Experimental studies have reported the fundamental and applied science aspects of polyelectrolyte (PE) layer-by-layer (LbL) self-assembly. LbL nanocoating is a simple and robust technique that can be used to modify the surface properties of nearly any material. These modifications take place by adsorption of mere nanometers of PE to impart previously absent properties to the nanocoated substrate. Paper manufacturing, drug delivery, and antimicrobial applications have since been developed. LbL self-assembly has become a very lucrative field of research. Computational modeling of LbL nanocoating has received limited attention. PE simulations often require significant computational resources and make computational modeling studies challenging. In this study, atomic-level PE and dexamethasone models are developed and then converted into coarse-grained (CG) models. This modeling study is based on experimental results that were previously reported. The CG models showed the effect of salt concentration and the number of PE layers on the LbL drug nanocapsule. The suitability of the model was evaluated and showed that this model can serve as a predictive tool for an LbL-nanocoated drug delivery system. It is suggested that this model can be used to simulate LbL drug delivery systems before the experimental evaluation of the real systems take place.

Liposome Drug Delivery System across Endothelial Plasma Membrane: Role of Distance between Endothelial Cells and Blood Flow Rate

This paper discusses specific features of the interactions of small-diameter liposomes with the cytoplasmic membrane of endothelial cells using in silico methods. The movement pattern of the liposomal drug delivery system was modeled in accordance with the conditions of the near-wall layer of blood flow. Our simulation results show that the liposomes can become stuck in the intercellular gaps and even break down when the gap is reduced. Liposomes stuck in the gaps are capable of withstanding a shell deformation of ~15% with an increase in liposome energy by 26%. Critical deformation of the membrane gives an impetus to drug release from the liposome outward. We found that the liposomes moving in the near-wall layer of blood flow inevitably stick to the membrane. Liposome sticking on the membrane is accompanied by its gradual splicing with the membrane bilayer. This leads to a gradual drug release inside the cell.

Hypericin photodynamic activity in DPPC liposomes - part II: stability and application in melanoma B16-F10 cancer cells

Hypericin (Hyp) is considered a promising photosensitizer for Photodynamic Therapy (PDT), due to its high hydrophobicity, affinity for cell membranes, low toxicity and high photooxidation activity. In this study, Hyp photophysical properties and photodynamic activity against melanoma B16-F10 cells were optimized using DPPC liposomes (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) as a drug delivery system. This nanoparticle is used as a cell membrane biomimetic model and solubilizes hydrophobic drugs. Hyp oxygen singlet lifetime (τ) in DPPC was approximately two-fold larger than that in P-123 micelles (Pluronic™ surfactants), reflecting a more hydrophobic environment provided by the DPPC liposome. On the other hand, singlet oxygen quantum yield values (Φ_Δ¹O₂) in DPPC and P-123 were similar; Hyp molecules were preserved as monomers. The Hyp/DPPC liposome aqueous dispersion was stable during fluorescence emission and the liposome diameter remained stable for at least five days at 30 °C. However, the liposomes collapsed after the lyophilization/rehydration process, which was resolved by adding the lyoprotectant Trehalose to the liposome dispersion before lyophilization. Cell viability of the Hyp/DPPC formulation was assessed against healthy HaCat cells and high-metastatic melanoma B16-F10 cells. Hyp incorporated into the DPPC carrier presented a higher selectivity index than the Hyp sample previously solubilized in ethanol under the illumination effect. Moreover, the IC₅₀ was lower for Hyp in DPPC than for Hyp pre-solubilized in ethanol. These results indicate the potential of the formulation of Hyp/DPPC for future biomedical applications in PDT treatment.

Nanovesicles Versus Nanoparticle-Supported Lipid Bilayers: Massive Differences in Bilayer Structures and in Diffusivities of Lipid Molecules and Nanoconfined Water

We carry out molecular dynamics (MD) simulations to compare the equilibrium architecture and properties of nanoparticle-supported lipid bilayers (NPSLBLs) with the free vesicles of similar dimensions. Three key differences emerge. First, we witness that for a free vesicle, a much larger number of lipid molecules occupy the outer layer as compared to the inner layer; on the other hand, for the NPSLBL the number of lipid molecules occupying the inner and outer layers is identical. Second, we witness that the diffusivities of the lipid molecules occupying both the inner and the outer layers of the free vesicles are identical, whereas for the NPSLBLs the diffusivity of the lipid molecules in the outer layer is more than twice the diffusivity of the lipid molecules in the inner layer. Finally, the NPSLBLs entrap nanoscopic thin water film between the inner lipid layer and the NP and the diffusivity of this water film is nearly 1 order of magnitude smaller than the diffusivity of the bulk water; on the other hand, the water inside the free vesicles has a diffusivity that is only slightly lower than that of the bulk water. Our findings, possibly the first probing the atomistic details of the NPSLBLs, are anticipated to shed light on the properties of this important nanomaterial with applications in a large number of disciplines ranging from drug and gene delivery to characterizing curvature-sensitive molecules.

Photodynamic opening of the blood-brain barrier to high weight molecules and liposomes through an optical clearing skull window

The photodynamic (PD) effect has been reported to be efficient for the opening of the blood-brain barrier (BBB), which provides a new informative platform for developing perspective strategies towards brain disease therapy and drug delivery. However, this method is usually performed via craniotomy due to high scattering of the turbid skull. In this work, we employed a newly-developed optical clearing skull window for investigating non-invasive PD-induced BBB opening to high weight molecules and 100-nm fluid-phase liposomes containing ganglioside GM1. The results demonstrated that the BBB permeability to the Evans blue albumin complex is related to laser doses. By in vivo two-photon imaging and ex vivo confocal imaging with specific markers of the BBB, we noticed PD-related extravasation of rhodamine-dextran and liposomes from the vessels into the brain parenchyma. The PD induced an increase in oxidative stress associated with mild hypoxia and changes in the expression of tight junction (CLND-5 and ZO-1) and adherens junction (VE-cadherin) proteins, which might be one of the mechanisms underlying the PD-related BBB opening for liposomes. Our experiments indicate that optical clearing skull window will be a promising tool for non-invasive PD-related BBB opening for high weight molecules and liposomes that provides a novel useful tool for brain drug delivery and treatment of brain diseases.

Hydrogen Bonding Regulates the Rigidity of Liposome-Encapsulated Chlorin Photosensitizers

Liposomal formulations facilitate the administration of hydrophobic drugs, avoiding precipitation and aggregation phenomena when injected in polar solvents. The integration of the photosensitizer into the liposome may alter the fluidity of the system and, thus, modify the delivery process of the drug. Such a change has been observed for the liposomal formulation of Temoporfin, which is one of the most potent chlorin photosensitizers employed in photodynamic therapy. Here, all-atom molecular dynamics simulations have been performed to identify the nature of the intermolecular interactions that might be responsible of the different lipids freedom of motion when the drug is introduced in the bilayer. It is found that Temoporfin participates as a hydrogen donor in strong hydrogen-bonding interactions with the polar groups of the phospholipids. The theoretical analysis suggests that the rigidity of drug/liposome complexes can be modulated by considering the different hydrogen-bond ability of the photosensitizer and the carrier material.

Rational Design of Cholesterol Derivative for Improved Stability of Paclitaxel Cationic Liposomes

PURPOSE

This work explores synthesis of novel cholesterol derivative for the preparation of cationic liposomes and its interaction with Paclitaxel (PTX) within liposome membrane using molecular dynamic (MD) simulation and in-vitro studies.

METHODS

Cholesteryl Arginine Ethylester (CAE) was synthesized and characterized. Cationic liposomes were prepared using Soy PC (SPC) at a molar ratio of 77.5:15:7.5 of SPC/CAE/PTX. Conventional liposomes were composed of SPC/cholesterol/PTX (92:5:3 M ratio). The interaction between paclitaxel, ligand and the membrane was studied using 10 ns MD simulation. The interactions were studied using Differential Scanning Calorimetry (DSC) and Small Angle Neutron Scattering analysis. The efficacy of liposomes was evaluated by MTT assay and endothelial cell migration assay on different cell lines. The safety of the ligand was determined using the Comet Assay.

RESULTS

The cationic liposomes improved loading efficiency and stability compared to conventional liposomes. The increased PTX loading could be attributed to the hydrogen bond between CAE and PTX and deeper penetration of PTX in the bilayer. The DSC study suggested that inclusion of CAE in the DPPC bilayer eliminates T_g. SANS data showed that CAE has more pronounced membrane thickening effect as compared to cholesterol. The cationic liposomes showed slightly improved cytotoxicity in three different cell lines and improved endothelial cell migration inhibition compared to conventional liposomes. Furthermore, the COMET assay showed that CAE alone does not show any genotoxicity.

CONCLUSIONS

The novel cationic ligand (CAE) retains paclitaxel within the phospholipid bilayer and helps in improved drug loading and physical stability. Graphical Abstract ᅟ.

Formation of Large Hypericin Aggregates in Giant Unilamellar Vesicles-Experiments and Modeling

The incorporation of hypericin (Hyp) from aqueous solutions into giant unilamellar vesicle (GUV) membranes has been studied experimentally and by means of kinetic Monte Carlo modeling. The time evolution of Hyp fluorescence originating from Hyp monomers dissolved in the GUV membrane has been recorded by confocal microscopy and while trapping individual GUVs in optical tweezers. It was shown that after reaching a maximum, the fluorescence intensity gradually decreased toward longer times. Formation of oversized Hyp clusters has been observed on the GUV surface at prolonged time. A simplified kinetic Monte Carlo model is presented to follow the aggregation/dissociation processes of Hyp molecules in the membrane. The simulation results reproduced the basic experimental observations: the scaling of the characteristic fluorescence decay time with the vesicle diameter and the buildup of large Hyp clusters in the GUV membrane.

Physical properties and biological interactions of liposomes developed as a drug carrier in the field of regenerative medicine

Liposomes are used for encapsulation of the active compounds in different therapies, with the increasing frequency. The important areas of clinical applications of liposomes are cancer targeted treatment, antibiotic delivery or regenerative medicine. The liposomes can transfer both hydrophilic and hydrophobic compounds and have the lipid bilayer which imitates the cell membrane. Liposomes additionally may extend half-live period of drugs and protect them against the elimination in different ways, such as phagocytosis, enzymatic cleavage or exclusion by detoxification. The size and charge of liposomes play an important role in drug distribution and absorption into the cell. Limited data is available on the effects of liposomes on stem cells and progenitor cells. In this article, we examined the effect of charged conventional liposomes on growth of mesenchymal and blood stem cells isolated from umbilical cord. The data suggest a likelihood, that positively charged liposomes could impair stem cell growth and metabolism. Different methodological approaches allowed for the selection of negatively charged liposomes for further experiments, as the only type of liposomes which has the lowest cytotoxicity and does not affect hematopoietic cell proliferation.

Combining Immune Checkpoint Inhibitors and Kinase-Inhibiting Supramolecular Therapeutics for Enhanced Anticancer Efficacy

A major limitation of immune checkpoint inhibitors is that only a small subset of patients achieve durable clinical responses. This necessitates the development of combinatorial regimens with immunotherapy. However, some combinations, such as MEK- or PI3K-inhibitors with a PD1-PDL1 checkpoint inhibitor, are pharmacologically challenging to implement. We rationalized that such combinations can be enabled using nanoscale supramolecular targeted therapeutics, which spatially home into tumors and exert temporally sustained inhibition of the target. Here we describe two case studies where nanoscale MEK- and PI3K-targeting supramolecular therapeutics were engineered using a quantum mechanical all-atomistic simulation-based approach. The combinations of nanoscale MEK- and PI3K-targeting supramolecular therapeutics with checkpoint PDL1 and PD1 inhibitors exert enhanced antitumor outcome in melanoma and breast cancers in vivo, respectively. Additionally, the temporal sequence of administration impacts the outcome. The combination of supramolecular therapeutics and immunotherapy could emerge as a paradigm shift in the treatment of cancer.

Algorithm for Designing Nanoscale Supramolecular Therapeutics with Increased Anticancer Efficacy

In the chemical world, evolution is mirrored in the origin of nanoscale supramolecular structures from molecular subunits. The complexity of function acquired in a supramolecular system over a molecular subunit can be harnessed in the treatment of cancer. However, the design of supramolecular nanostructures is hindered by a limited atomistic level understanding of interactions between building blocks. Here, we report the development of a computational algorithm, which we term Volvox after the first multicellular organism, that sequentially integrates quantum mechanical energy-state- and force-field-based models with large-scale all-atomistic explicit water molecular dynamics simulations to design stable nanoscale lipidic supramolecular structures. In one example, we demonstrate that Volvox enables the design of a nanoscale taxane supramolecular therapeutic. In another example, we demonstrate that Volvox can be extended to optimizing the ratio of excipients to form a stable nanoscale supramolecular therapeutic. The nanoscale taxane supramolecular therapeutic exerts greater antitumor efficacy than a clinically used taxane in vivo. Volvox can emerge as a powerful tool in the design of nanoscale supramolecular therapeutics for effective treatment of cancer.

Facilitating the Clinical Integration of Nanomedicines: The Roles of Theoretical and Computational Scientists

Since the launch of multiple research initiatives on nanotechnology applied to medicine in the early 2000s, a plethora of nanomedicines have been developed that exhibit great therapeutic efficacy in preclinical models but yet minimal impact in daily clinical practice. The successful and complete clinical fruition of nanomedicines requires addressing three major technical challenges: improving loading efficacy and on-command release, modulating recognition and sequestration by immune cells, and maximizing accumulation at biological targets. In this Perspective, I describe how theoretical and computational models can help address each of these challenges. This armamentarium represents an ideal tool for maximizing the therapeutic efficacy of nanomedicines, thus facilitating their integration into daily clinical operations.

Estimation of Liposome Penetration Barriers of Drug Molecules with All-Atom and Coarse-Grained Models

Liposomes are common carriers of drug molecules, providing enhanced delivery and accumulation of hydrophilic agents or larger biomolecules. Molecular simulations can be used to estimate key features of the drug molecules upon interaction with the liposomes, such as penetration barriers and localization. Herein, we investigate several aspects of the computational estimation of penetration barriers, viz. the potential of mean force (PMFs) along a vector spanning the membrane. First, we provide an evaluation of the all-atom (AA) and coarse-grained (CG) parametrization of 5-aminolevulinic acid (5-ALA) and two of its alkyl esters by computing n-octanol/water partition coefficients. We find that the CG parametrization of the esters performs significantly better than the CG model of 5-ALA, highlighting the difficulty to coarse-grain small, polar molecules. However, the expected trend in partition coefficients is reproduced also with the CG models. Second, we compare PMFs in a small membrane slab described with either the AA or CG models. Here, we are able to reproduce the all-atom PMF of 5-ALA with CG. However, for the alkyl esters it is unfortunately not possible to correctly reproduce both the depth and the penetration barrier of the PMF seen in the AA simulations with any of the tested CG models. We argue that it is more important to choose a CG parametrization that reproduces the depth of the PMF. Third, we compare, using the CG model, PMFs in the membrane slab with PMFs in a large, realistic liposome. We find similar depths but slightly different penetration barriers most likely due to differences in the lipid density along the membrane axis. Finally, we compute PMFs in liposomes with three different lipid compositions. Unfortunately, differences in the PMFs could not be quantified, and it remains to be investigated to what extent liposome simulations can fully reproduce experimental findings.

Computational and experimental approaches for investigating nanoparticle-based drug delivery systems

Most therapeutic agents suffer from poor solubility, rapid clearance from the blood stream, a lack of targeting, and often poor translocation ability across cell membranes. Drug/gene delivery systems (DDSs) are capable of overcoming some of these barriers to enhance delivery of drugs to their right place of action, e.g. inside cancer cells. In this review, we focus on nanoparticles as DDSs. Complementary experimental and computational studies have enhanced our understanding of the mechanism of action of nanocarriers and their underlying interactions with drugs, biomembranes and other biological molecules. We review key biophysical aspects of DDSs and discuss how computer modeling can assist in rational design of DDSs with improved and optimized properties. We summarize commonly used experimental techniques for the study of DDSs. Then we review computational studies for several major categories of nanocarriers, including dendrimers and dendrons, polymer-, peptide-, nucleic acid-, lipid-, and carbon-based DDSs, and gold nanoparticles. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.