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.

Investigating the Orientation of an Interfacially Adsorbed Monoclonal Antibody and Its Fragments Using Neutron Reflection.

Interfacial adsorption is a molecular process occurring during the production, purification, transport, and storage of antibodies, with a direct impact on their structural stability and subsequent implications on their bioactivities. While the average conformational orientation of an adsorbed protein can be readily determined, its associated structures are more complex to characterize. Neutron reflection has been used in this work to investigate the conformational orientations of the monoclonal antibody COE-3 and its Fab and Fc fragments at the oil/water and air/water interfaces. Rigid body rotation modeling was found to be suitable for globular and relatively rigid proteins such as the Fab and Fc fragments but less so for relatively flexible proteins such as full COE-3. Fab and Fc fragments adopted a 'flat-on' orientation at the air/water interface, minimizing the thickness of the protein layer, but they adopted a substantially tilted orientation at the oil/water interface with increased layer thickness. In contrast, COE-3 was found to adsorb in tilted orientations at both interfaces, with one fragment protruding into the solution. This work demonstrates that rigid-body modeling can provide additional insights into protein layers at various interfaces relevant to bioprocess engineering.

Understanding the Stabilizing Effect of Histidine on mAb Aggregation: A Molecular Dynamics Study.

Histidine, a widely used buffer in monoclonal antibody (mAb) formulations, is known to reduce antibody aggregation. While experimental studies suggest a nonelectrostatic, nonstructural (relating to secondary structure preservation) origin of the phenomenon, the underlying microscopic mechanism behind the histidine action is still unknown. Understanding this mechanism will help evaluate and predict the stabilizing effect of this buffer under different experimental conditions and for different mAbs. We have used all-atom molecular dynamics simulations and contact-based free energy calculations to investigate molecular-level interactions between the histidine buffer and mAbs, which lead to the observed stability of therapeutic formulations in the presence of histidine. We reformulate the Spatial Aggregation Propensity index by including the buffer-protein interactions. The buffer adsorption on the protein surface leads to lower exposure of the hydrophobic regions to water. Our analysis indicates that the mechanism behind the stabilizing action of histidine is connected to the shielding of the solvent-exposed hydrophobic regions on the protein surface by the buffer molecules.

What happens when pesticides are solubilised in binary ionic/zwitterionic-nonionic mixed micelles?

HYPOTHESIS: Surfactants have been widely used as adjuvants in agri-sprays to enhance the solubility of pesticides in foliar spray deposits and their mobility through leaf cuticles. Previously, we have characterised pesticide solubilisation in nonionic surfactant micelles, but what happens when pesticides become solubilised in anionic, cationic and zwitterionic and their mixtures with nonionic surfactants remain poorly characterised. EXPERIMENTS: To facilitate characterisations by SANS and NMR, we used nonionic surfactant hexaethylene glycol monododecyl ether (C12E6), anionic sodium dodecylsulphate (SDS), cationic dodecyltrimethylammonium bromide (DTAB) and zwitterionic dodecylphosphocholine (C12PC) as model adjuvant systems to solubilise 3 pesticides, Cyprodinil (CP), Azoxystrobin (AZ) and Difenoconazole (DF), representing different structural features. The investigation focused on the influence of solubilisates in driving changes to the micellar nanostructures in the absence or presence of electrolytes. NMR and NOESY were applied to investigate the solubility and location of each pesticide in the micelles. SANS was used to reveal subtle changes to the micellar structures due to pesticide solubilisation with and without electrolytes. FINDINGS: Unlike nonionic surfactants, the ionic and zwitterionic surfactant micellar structures remain unchanged upon pesticide solubilisation. Electrolytes slightly elongate the ionic surfactant micelles but have no effect on nonionic and zwitterionic surfactants. Pesticide solubilisation could alter the structures of the binary mixtures of ionic/zwitterionic and ionic/nonionic micelles by causing elongation, shell shrinkage and dehydration, with the exact alteration being determined by the molar ratio in the mixture.

How do Self-Assembling Antimicrobial Lipopeptides Kill Bacteria?

Antimicrobial peptides are promising alternatives to traditional antibiotics. A group of self-assembling lipopeptides was formed by attaching an acyl chain to the N-terminus of α-helix-forming peptides with the sequence Cx-G(IIKK)yI-NH2 (CxGy, x = 4-12 and y = 2). CxGy self-assemble into nanofibers above their critical aggregation concentrations (CACs). With increasing x, the CACs decrease and the hydrophobic interactions increase, promoting secondary structure transitions within the nanofibers. Antimicrobial activity, determined by the minimum inhibition concentration (MIC), also decreases with increasing x, but the MICs are significantly smaller than the CACs, suggesting effective bacterial membrane-disrupting power. Unlike conventional antibiotics, both C8G2 and C12G2 can kill Staphylococcus aureus and Escherichia coli after only minutes of exposure under the concentrations studied. C12G2 nanofibers have considerably faster killing dynamics and lower cytotoxicity than their nonaggregated monomers. Antimicrobial activity of peptide aggregates has, to date, been underexploited, and it is found to be a very promising mechanism for peptide design. Detailed evidence for the molecular mechanisms involved is provided, based on superresolution fluorescence microscopy, solid-state nuclear magnetic resonance, atomic force microscopy, neutron scattering/reflectivity, circular dichroism, and Brewster angle microscopy.

Aggregated Amphiphilic Antimicrobial Peptides Embedded in Bacterial Membranes.

Molecular dynamics (MD) simulations, stochastic optical reconstruction microscopy (STORM), and neutron reflection (NR) were combined to explore how antimicrobial peptides (AMPs) can be designed to promote the formation of nanoaggregates in bacterial membranes and impose effective bactericidal actions. Changes in the hydrophobicity of the designed AMPs were found to have a strong influence on their bactericidal potency and cytotoxicity. G(IIKK)3I-NH2 (G3) achieved low minimum inhibition concentrations (MICs) and effective dynamic kills against both antibiotic-resistant and -susceptible bacteria. However, a G3 derivative with weaker hydrophobicity, KI(KKII)2I-NH2 (KI), exhibited considerably lower membrane-lytic activity. In contrast, the more hydrophobic G(ILKK)3L-NH2 (GL) peptide achieved MICs similar to those observed for G3 but with worsened hemolysis. Both the model membranes studied by Brewster angle microscopy, zeta potential measurements, and NR and the real bacterial membranes examined with direct STORM contained membrane-inserted peptide aggregates upon AMP exposure. These structural features were well supported by MD simulations. By revealing how AMPs self-assemble in microbial membranes, this work provides important insights into AMP mechanistic actions and allows further fine-tuning of antimicrobial potency and cytotoxicity.

How does substrate hydrophobicity affect the morphological features of reconstituted wax films and their interactions with nonionic surfactant and pesticide?

HYPOTHESIS: Surfactants are widely used in agri-sprays to improve pesticide efficiency, but the mechanism underlying their interactions with the surface wax film on plants remains poorly understood. To facilitate physical characterisations, we have reconstituted wheat cuticular wax films onto an optically flat silicon substrate with and without octadecyltrimethoxysilane modification to control surface hydrophobicity. EXPERIMENTS: Imaging techniques including scanning electron microscopy (SEM) unravelled morphological features of the reconstituted wax films similar to those on leaves, showing little impact from the different substrates used. Neutron reflection (NR) established that reconstituted wax films were comprised of an underlying wax film decorated with top surface wax protrusions, a common feature irrespective of substrate hydrophobicity and highly consistent with what was observed from natural wax films. NR measurements, with the help of isotopic H/D substitutions to modify the scattering contributions of the wax and solvent, revealed different wax regimes within the wax films, illustrating the impact of surface hydrophilicity on the nanostructures within the wax films. FINDINGS: It was observed from both spectroscopic ellipsometry and NR measurements that wax films formed on the hydrophobic substrate were more robust and durable against attack by nonionic surfactant C12E6 solubilised with pesticide Cyprodinil (CP) than films coated on the bare hydrophilic silica. Thus, the former could be a more feasible model for studying the wax-surfactant-pesticide interactions.

Recent Advances in Studying Interfacial Adsorption of Bioengineered Monoclonal Antibodies.

Monoclonal antibodies (mAbs) are an important class of biotherapeutics; as of 2020, dozens are commercialized medicines, over a hundred are in clinical trials, and many more are in preclinical developmental stages. Therapeutic mAbs are sequence modified from the wild type IgG isoforms to varying extents and can have different intrinsic structural stability. For chronic treatments in particular, high concentration (≥ 100 mg/mL) aqueous formulations are often preferred for at-home administration with a syringe-based device. MAbs, like any globular protein, are amphiphilic and readily adsorb to interfaces, potentially causing structural deformation and even unfolding. Desorption of structurally perturbed mAbs is often hypothesized to promote aggregation, potentially leading to the formation of subvisible particles and visible precipitates. Since mAbs are exposed to numerous interfaces during biomanufacturing, storage and administration, many studies have examined mAb adsorption to different interfaces under various mitigation strategies. This review examines recent published literature focusing on adsorption of bioengineered mAbs under well-defined solution and surface conditions. The focus of this review is on understanding adsorption features driven by distinct antibody domains and on recent advances in establishing model interfaces suitable for high resolution surface measurements. Our summary highlights the need to further understand the relationship between mAb interfacial adsorption and desorption, solution aggregation, and product instability during fill-finish, transport, storage and administration.

How does solubilisation of plant waxes into nonionic surfactant micelles affect pesticide release?

HYPOTHESIS: Nonionic surfactants are used as adjuvants in agri-sprays to stabilise pesticides, but what happens when pesticide-loaded micelles are brought into direct contact with plant leaves? As pesticide solubilisation dehydrates the micellar shell and increases the effective hydrophobicity of the surfactant, we hypothesise that these micelles would uptake plant waxes and alter the amount of pesticide solubilized as a result of the re-equilibrating process. EXPERIMENTS: The solubility of the pesticide cyprodinil (CP) and its effect on the shape of hexaethylene glycol monododecyl ether (C12E6) micelles were studied using changes in cloud point, nuclear magnetic resonance (NMR), cryogenic transmission electron microscopy (Cryo-TEM) and small-angle neutron scattering (SANS). Similarly, the solubility of wheat leaf waxes was examined, as was the effect of adding leaf waxes to pre-dissolved cyprodinil in micellar C12E6. FINDINGS: Wax solubilisation caused pesticide release and shell hydration, and shortened the length of the cylindrical micelles of the CP loaded C12E6. Temperature increase led to a significant rise in the amount of the dissolved waxes, increased pesticide release, increased micellar length, and caused shrinkage and dehydration of the shell. This study indicates that agrochemical sprays are capable of dissolving leaf waxes, and may trigger pesticide release from surfactant micelles upon contact with plant surfaces.