Rationalising drug delivery using nanoparticles: a combined simulation and immunology study of GnRH adsorbed to silica nanoparticles

Multivalent display of engineered HIV-1 envelope trimers on silica nanoparticles for targeting and in vitro activation of germline VRC01 B cells

Selective targeting of germline B cells with specifically designed germline-targeting HIV-1 envelope immunogens (GT-Env) is considered a feasible vaccination strategy to elicit broadly neutralizing antibodies (bnAbs). BnAbs are extremely valuable because they neutralize genetically distant viral strains at the same time. To overcome its inherently low affinity to germline B cells, the aim of the study was to present GT-Env via different immobilization strategies densely arrayed on the surface of nanoparticles. We engineered a prefusion-stabilized GT-Env trimer with affinity to VRC01 germline B cells using a bioinformatics-supported design approach. Distinct glycan modifications and amino acid substitutions yielded a GT-Env trimer which bound to the receptor with a K_D of 11.5 µM. Silica nanoparticles with 200 nm diameter (SiNPs) were used for the multivalent display of the novel GT-Env with a 15 nm mean centre-to-centre spacing either by site-specific, covalent conjugation or at random, non-specific adsorption. Oriented, covalent GT-Env conjugation revealed better binding of structure dependent bnAbs as compared to non-specifically adsorbed GT-Env. In addition, GT-Env covalently attached activated a B cell line expressing the germline VRC01 receptor at an EC₅₀ value in the nanomolar range (4 nM), while soluble GT-Env required 1,000-fold higher concentrations to induce signalling. The significantly lower GT-Env concentration was likely required due to avidity effects, which were in the picomolar range. Thus, low affinity antigens may particularly benefit from a particulate and multivalent delivery. In future, SiNPs are ideal to be modified in a modular design with various GT-Env variants that target different stages of germline and bnAb precursor B cells.

Biomolecular interactions with nanoparticles: applications for coronavirus disease 2019

Nanoparticles are small particles sized 1-100 nm, which have a large surface-to-volume ratio, allowing efficient adsorption of drugs, proteins, and other chemical compounds. Consequently, functionalized nanoparticles have potential diagnostic and therapeutic applications. A variety of nanoparticles have been studied, including those constructed from inorganic materials, biopolymers, and lipids. In this review, we focus on recent work targeting the severe acute respiratory syndrome coronavirus 2 virus that causes coronavirus disease (COVID-19). Understanding the interactions between coronavirus-specific proteins (such as the spike protein and its host cell receptor angiotensin-converting enzyme 2) with different nanoparticles paves the way to the development of new therapeutics and diagnostics that are urgently needed for the fight against COVID-19, and indeed for related future viral threats that may emerge.

Simulating Peptide Monolayer Formation: GnRH-I on Silica

Molecular dynamics (MD) simulations can provide a detailed view of molecule behaviour at an atomic level, which can be useful when attempting to interpret experiments or design new systems. The decapeptide gonadotrophin-releasing hormone I (GnRH-I) is known to control fertility in mammals for both sexes. It was previously shown that inoculation with silica nanoparticles (SiNPs) coated with GnRH-I makes an effective anti-fertility vaccine due to how the peptide adsorbs to the nanoparticle and is presented to the immune system. In this paper, we develop and employ a protocol to simulate the development of a GnRH-I peptide adlayer by allowing peptides to diffuse and adsorb in a staged series of trajectories. The peptides start the simulation in an immobile state in solution above the model silica surface, and are then released sequentially. This facile approach allows the adlayer to develop in a natural manner and appears to be quite versatile. We find that the GnRH-I adlayer tends to be sparse, with electrostatics dominating the interactions. The peptides are collapsed to the surface and are seemingly free to interact with additional solutes, supporting the interpretations of the GNRH-I/SiNP vaccine system.

The role of peptide-based therapeutics in oncotherapy

Cancer is the second leading cause of death worldwide, and the search for specialised therapy options has been a challenge for decades. The emergence of active targeted therapies provides the opportunity to treat cancerous tissues without harming healthy ones due to peculiar physiological changes. Herein, peptides and peptide analogs have been gaining a lot of attention over the last decade, especially for the on-site delivery of therapeutics to target tissues in order to achieve efficient and reliable cancer treatment. Combining peptides with highly efficient drug delivery platforms could potentially eliminate off-target adverse effects encountered during active targeting of conventional chemotherapeutics. Small size, ease of production and characterisation, low immunogenicity and satisfactory binding affinity of peptides offer some advantages over other complex targeting moiety, no wonder the market of peptide-based drugs continues to expand expeditiously. It is estimated that the global peptide drug market will be worth around USD 48.04 billion by 2025, with a compound annual growth rate of 9.4%. In this review, the current state of art of peptide-based therapeutics with special interest on tumour targeting peptides has been discussed. Moreover, various active targeting strategies such as the use functionalised peptides or peptide analogs are also elaborated.

Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.

On the Role of Silica Carrier Curvature for the Unloading of Small Drug Molecules: A Molecular Dynamics Simulation Study

We present atomic scale models of differently shaped silica surfaces loaded by gemcitabine and ibuprofene molecules. Despite the dissimilar nature of the drug molecules, their association to silica carriers shows quite similar characteristics. We identify a well-defined contact layer that is stabilized by silica-molecule salt-bridges/hydrogen bonding in parallel to interactions among the drug molecules. Additional loading of the carriers leads to rough films with dynamically evolving asperities rather than layer-by-layer ordering. To elucidate the role of differently shaped silica surfaces, we compared planar slab models and spherical nanoparticles as 2 limiting cases. Despite the strong difference in the curvature of the silica surfaces, our molecular dynamics simulations show only small changes of the unloading characteristics. This suggests that the design of different pore shapes in mesoporous silica-based drug carriers mainly affects the migration kinetics rather than the energetics of drug loading and release.

Continuous-Flow Synthesis of ZIF-8 Biocomposites with Tunable Particle Size

Zeolitic imidazolate framework (ZIF) biocomposites show the capacity to protect and deliver biotherapeutics. To date, the progress in this research area is based on laboratory batch methods. Now, the first continuous flow synthetic method is presented for the encapsulation of a model protein (bovine serum albumin, BSA) and a clinical therapeutic (α1-antitrypsin, AAT) in ZIF-8. The in situ kinetics of nucleation, growth, and crystallization of BSA@ZIF-8 were studied by small-angle X-ray scattering. By controlling the injection time of ethanol, the particle growth could be quenched by ethanol-induced crystallization from amorphous particles to ZIF-8 crystals. The particle size of the biocomposite was tuned in the 40-100 nm range by varying residence time prior to introduction of ethanol. As a proof-of-concept, this procedure was used for the encapsulation of AAT in ZIF-8. Upon release of the biotherapeutic from the composite, the trypsin inhibitor function of AAT was preserved.

Phase dependent encapsulation and release profile of ZIF-based biocomposites

Biocomposites composed of Zeolitic Imidazolate Frameworks (ZIFs) are generating significant interest due to their facile synthesis, and capacity to protect proteins from harsh environments. Here we systematically varied the composition (i.e. relative amounts of ligand (2-methylimidazole), metal precursor (Zn(OAc)2·2H2O), and protein) and post synthetic treatments (i.e. washes with water or water/ethanol) to prepare a series of protein@ZIF biocomposites. These data were used to construct two ternary phase diagrams that showed the synthesis conditions employed gave rise to five different phases including, for the first time, biocomposites based on ZIF-CO3-1. We examined the influence of the different phases on two properties relevant to drug delivery applications: encapsulation efficiency and release profile. The encapsulation efficiencies of bovine serum albumin and insulin were phase dependent and ranged from 75% to 100%. In addition, release profiles showed that 100% protein release varied between 40 and 300 minutes depending on the phase. This study provides a detailed compositional map for the targeted preparation of ZIF-based biocomposites of specific phases and a tool for the straightforward analysis of the crystalline phases of ZIF based materials (web application named "ZIF phase analysis"). These data will facilitate the progress of ZIF bio-composites in the fields of biomedicine and biotechnology.