Mechanistic insights into the role of glycosaminoglycans in delivery of polymeric nucleic acid nanoparticles by molecular dynamics simulations

Martini compatible coarse-grained model of polyethylenimine for pulmonary gene delivery

Pulmonary gene delivery has demonstrated high specificity for respiratory diseases, offering great control on dosage of therapeutics and side effects. On the other hand, intrinsic barriers in pulmonary systems impose new challenges such as crossing the pulmonary surfactant and evading mucus entrapment. Differences in hydrophobicity of plasma membrane and pulmonary surfactant require different chemistries of gene carriers to improve efficacy. Large-scale coarse-grained (CG) molecular dynamics simulations would facilitate the screening of gene carriers and understanding of the molecular mechanisms involved in pulmonary delivery. Among non-viral carriers, polyethyleneimine (PEI) has been a promising candidate that can be synthesized with various molecular weight, degree of branching, and functionalization. In this work, CG models are developed for PEI and its lipid-functionalized form, within the Martini framework, to provide a platform for exploring structure-function relationships of PEI-based pulmonary delivery systems. Special attention is focused on parameterizing the non-bonded interactions associated with CG PEI, to ensure compatibility with Martini proteins, short interfering RNA, and phospholipids that are essential components in pulmonary gene delivery. The non-bonded parameters are validated by comparing all-atom (AA) and CG potential of mean force (PMF) curves, where the root-mean-square deviations between the AA and CG PMF curves are shown to be comparable to or smaller than those reported in Martini literature.

Beyond Lipids: Exploring Advances in Polymeric Gene Delivery in the Lipid Nanoparticles Era

The recent success of gene therapy during the COVID-19 pandemic has underscored the importance of effective and safe delivery systems. Complementing lipid-based delivery systems, polymers present a promising alternative for gene delivery. Significant advances have been made in the recent past, with multiple clinical trials progressing beyond phase I and several companies actively working on polymeric delivery systems which provides assurance that polymeric carriers can soon achieve clinical translation. The massive advantage of structural tunability and vast chemical space of polymers is being actively leveraged to mitigate shortcomings of traditional polycationic polymers and improve the translatability of delivery systems. Tailored polymeric approaches for diverse nucleic acids and for specific subcellular targets are now being designed to improve therapeutic efficacy. This review describes the recent advances in polymer design for improved gene delivery by polyplexes and covalent polymer-nucleic acid conjugates. The review also offers a brief note on novel computational techniques for improved polymer design. The review concludes with an overview of the current state of polymeric gene therapies in the clinic as well as future directions on their translation to the clinic.

Salinity-Driven Interface Self-Assembly of a Biological Amphiphilic Emulsifier to Form Stable Janus Core-Shell Emulsion for Enhancing Agrichemical Delivery

Agrichemical losses are a severe threat to the ecological environment. Additionally, some agrichemical compounds contain abundant salt, which increases the instability of formulations, leading to a lower agrichemical utilization and soil hardening. Fortunately, the biological amphiphilic emulsifier sodium deoxycholate alleviates these problems by forming stable Janus core-shell emulsions through salinity-driven interfacial self-assembly. According to the interfacial behavior, dilational rheology, and molecular dynamics simulations, Janus-emulsion molecules are more closely arranged than traditional-emulsion molecules and generate an oil-water interfacial film that transforms into a gel film. In addition, at the same spray volume, the deposition area of the Janus emulsion increased by 37.70% compared with that of the traditional emulsion. Owing to the topology effect and deformation, the Janus emulsion adheres to rice micropapillae, achieving better flush resistance. Meanwhile, based on response of the Janus emulsion to stimulation by carbon dioxide (CO2), the emulsion lost to the soil can form a rigid shell for inhibiting the release of pesticides and metal ions from harming the soil. The pyraclostrobin release rate decreased by 50.89% at 4 h after the Janus emulsion was exposed to CO2. The Chao1 index of the Janus emulsion was increased by 12.49% as compared to coconut oil delivery in soil microbial community. The Janus emulsion ingested by harmful organisms can be effectively absorbed in the intestine to achieve better control effects. This study provides a simple and effective strategy, which turns waste into treasure, by combining metal ions in agrichemicals with natural amphiphilic molecules to prepare stable emulsions for enhancing agrichemical rainfastness and weakening environmental risk.

Current Advancement and Future Prospects: Biomedical Nanoengineering

Recent advancements in biomedicine have seen a significant reliance on nanoengineering, as traditional methods often fall short in harnessing the unique attributes of biomaterials. Nanoengineering has emerged as a valuable approach to enhance and enrich the performance and functionalities of biomaterials, driving research and development in the field. This review emphasizes the most prevalent biomaterials used in biomedicine, including polymers, nanocomposites, and metallic materials, and explores the pivotal role of nanoengineering in developing biomedical treatments and processes. Particularly, the review highlights research focused on gaining an in-depth understanding of material properties and effectively enhancing material performance through molecular dynamics simulations, all from a nanoengineering perspective.

In silico prediction of the in vitro behavior of polymeric gene delivery vectors

Non-viral gene delivery vectors have increasingly come under the spotlight, but their performaces are still far from being satisfactory. Therefore, there is an urgent need for forecasting tools and screening methods to enable the development of ever more effective transfectants. Here, coarse-grained (CG) models of gold standard transfectant poly(ethylene imine)s (PEIs) have been profitably used to investigate and highlight the effect of experimentally-relevant parameters, namely molecular weight (2 vs. 10 kDa) and topologies (linear vs. branched), protonation state, and ammine-to-phosphate ratios (N/Ps), on the complexation and the gene silencing efficiency of siRNA molecules. The results from the in vitro screening of cationic polymers and conditions were used to validate the in silico platform that we developed, such that the hits which came out of the CG models were of high practical relevance. We show that our in silico platform enables to foresee the most suitable conditions for the complexation of relevant siRNA-polycation assemblies, thereby providing a reliable predictive tool to test bench transfectants in silico, and foster the design and development of gene delivery vectors.

How can molecular dynamics simulations assist with gene medicines?

Molecular Dynamics (MD) simulations can provide a glimpse of complex atomistic and molecular events at the interface of biomaterials and biosystems. Gene therapy efforts that deploy biomaterial mediated delivery of nucleic acids could benefit immensely from such MD simulations. These efforts most commonly employ supramolecular assembly whose structure is highly dynamic and influential in the final outcomes. By careful analysis of the behavior of constituting elements, one can visualize the assembly as it makes its way though biosystems. We highlight the beneficial information to be gained from MD studies in this short perspective and outline a vision for future activity in the field.

Membrane lipids destabilize short interfering ribonucleic acid (siRNA)/polyethylenimine nanoparticles

Cell entry of polymeric nanoparticles (NPs) bearing polynucleotides is an important stage for successful gene delivery. In this work, we addressed the influence of cell membrane lipids on the integrity and configurational changes of NPs composed of short interfering ribonucleic acid (siRNA) and polyethylenimine. We focused on NPs derived from two different PEIs, unmodified low molecular weight PEI and linoleic acid (LA)-substituted PEI, and their interactions with two membrane lipids (zwitterionic 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC) and anionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS)). Our experiments showed that POPS liposomes interacted strongly with both types of NPs, which caused partial dissociation of the NPs. POPC liposomes, however, did not induce any dissociation. Consistent with the experiments, steered molecular dynamics simulations showed a stronger interaction between the NPs and the POPS membrane than between the NPs and the POPC membrane. Lipid substitution on the PEIs enhanced the stability of the NPs during membrane crossing; lipid association between PEIs of the LA-bearing NPs as well as parallel orientation of the siRNAs provided protection against their dissociation (unlike NPs from native PEI). Our observations provide valuable insight into the integrity and structural changes of PEI/siRNA NPs during membrane crossing which will help in the design of more effective carriers for nucleic acid delivery.

Steered molecular dynamics simulations reveal a self-protecting configuration of nanoparticles during membrane penetration

Cell entry of polynucleotide-based therapeutic agents can be facilitated by nanoparticle (NP) mediated delivery. In this work, using steered molecular dynamics simulations, we simulated the membrane penetration process of a NP formed by 2 short interfering RNA (siRNA) and 6 polyethylenimine (PEI) molecules. To the best of our knowledge, this is the first set of simulations that explore the direct penetration of an siRNA/PEI NP through a membrane at an all-atom scale. Three types of PEI molecules were used for NP formation: a native PEI, a PEI modified with caprylic acids and a PEI modified with linoleic acids. We found that hydrogen bond formation between the PEIs and the membrane did not lead to instability of the siRNA/PEI NPs during the internalization process. Instead, our results suggested adoption of a "self-protecting" configuration by the siRNA/PEI NP during membrane penetration, where the siRNA/PEI NP becomes more compact and siRNAs become aligned, leading to more stable configurations while detaching from the membrane. The siRNA/PEI NP modified with linoleic acid showed the smallest structural change due to its strong intra-particle lipid associations and the resulting rigidity, while NP modified with caprylic acid showed the largest structural changes. Our observations provide unique insight into the structural changes of siRNA/PEI NPs when crossing the cell membrane, which can be important for the design of new NP carriers for nucleic acid delivery.