Unraveling the Microscopic Mechanism of Molecular Ion Interaction with Monoclonal Antibodies: Impact on Protein Aggregation.

Understanding and predicting protein aggregation represents one of the major challenges in accelerating the pharmaceutical development of protein therapeutics. In addition to maintaining the solution pH, buffers influence both monoclonal antibody (mAb) aggregation in solution and the aggregation mechanisms since the latter depend on the protein charge. Molecular-level insight is necessary to understand the relationship between the buffer-mAb interaction and mAb aggregation. Here, we use all-atom molecular dynamics simulations to investigate the interaction of phosphate (Phos) and citrate (Cit) buffer ions with the Fab and Fc domains of mAb COE3. We demonstrate that Phos and Cit ions feature binding mechanisms, with the protein that are very different from those reported previously for histidine (His). These differences are reflected in distinctive ion-protein binding modes and adsorption/desorption kinetics of the buffer molecules from the mAb surface and result in dissimilar effects of these buffer species on mAb aggregation. While His shows significant affinity toward hydrophobic amino acids on the protein surface, Phos and Cit ions preferentially bind to charged amino acids. We also show that Phos and Cit anions provide bridging contacts between basic amino acids in neighboring proteins. The implications of such contacts and their connection to mAb aggregation in therapeutic formulations are discussed.

Mechanistic Insights into the Adsorption of Monoclonal Antibodies at the Water/Vapor Interface.

Monoclonal antibodies (mAbs) are active components of therapeutic formulations that interact with the water-vapor interface during manufacturing, storage, and administration. Surface adsorption has been demonstrated to mediate antibody aggregation, which leads to a loss of therapeutic efficacy. Controlling mAb adsorption at interfaces requires a deep understanding of the microscopic processes that lead to adsorption and identification of the protein regions that drive mAb surface activity. Here, we report all-atom molecular dynamics (MD) simulations of the adsorption behavior of a full IgG1-type antibody at the water/vapor interface. We demonstrate that small local changes in the protein structure play a crucial role in promoting adsorption. Also, interfacial adsorption triggers structural changes in the antibody, potentially contributing to the further enhancement of surface activity. Moreover, we identify key amino acid sequences that determine the adsorption of antibodies at the water-air interface and outline strategies to control the surface activity of these important therapeutic proteins.

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.

Antibacterial effects in blood irradiated with a polychromatic device mediated through reactive oxygen species: possible involvement of haem.

The antibacterial effects of a polychromatic light device designed for intravenous application were assessed in vitro. Staphylococcus aureus, Klebsiella pneumoniae, or Escherichia coli were exposed to a 60-min sequential light cycle comprising 365, 530, and 630 nm wavelengths in circulated sheep blood. Bacteria were quantified by viable counting. The potential involvement of reactive oxygen species in the antibacterial effect was assessed using the antioxidant N-acetylcysteine-amide. A modified device was then used to determine the effects of the individual wavelengths. Exposure of blood to the standard wavelength sequence caused small (c. 0.5 Log 10 CFU) but statistically significant reductions in viable counts for all three bacteria, which were prevented by the addition of N-acetylcysteine-amide. Bacterial inactivation did not occur in blood-free medium, but supplementation with haem restored the moderate bactericidal effect. In single-wavelength experiments, bacterial inactivation occurred only with red (630 nm) light. Concentrations of reactive oxygen species were significantly higher under light stimulation than in unstimulated controls. In summary, exposure of bacteria within blood to a cycle of visible light wavelengths resulted in small but statistically significant bacterial inactivation apparently mediated by a 630 nm wavelength only, via reactive oxygen species possibly generated by excitation of haem groups.

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.

Assessing the risk of resistance to cationic biocides incorporating realism-based and biophysical approaches.

The control of microorganisms is a key objective in disease prevention and in medical, industrial, domestic, and food-production environments. Whilst the effectiveness of biocides in these contexts is well-evidenced, debate continues about the resistance risks associated with their use. This has driven an increased regulatory burden, which in turn could result in a reduction of both the deployment of current biocides and the development of new compounds and formulas. Efforts to balance risk and benefit are therefore of critical importance and should be underpinned by realistic methods and a multi-disciplinary approach, and through objective and critical analyses of the literature. The current literature on this topic can be difficult to navigate. Much of the evidence for potential issues of resistance generation by biocides is based on either correlation analysis of isolated bacteria, where reports of treatment failure are generally uncommon, or laboratory studies that do not necessarily represent real biocide applications. This is complicated by inconsistencies in the definition of the term resistance. Similar uncertainties also apply to cross-resistance between biocides and antibiotics. Risk assessment studies that can better inform practice are required. The resulting knowledge can be utilised by multiple stakeholders including those tasked with new product development, regulatory authorities, clinical practitioners, and the public. This review considers current evidence for resistance and cross-resistance and outlines efforts to increase realism in risk assessment. This is done in the background of the discussion of the mode of application of biocides and the demonstrable benefits as well as the potential risks.

Ordered Nanofibers Fabricated from Hierarchical Self-Assembling Processes of Designed α-Helical Peptides.

Peptide self-assembly is fast evolving into a powerful method for the development of bio-inspired nanomaterials with great potential for many applications, but it remains challenging to control the self-assembling processes and nanostrucutres because of the intricate interplay of various non-covalent interactions. A group of 28-residue α-helical peptides is designed including NN, NK, and HH that display distinct hierarchical events. The key of the design lies in the incorporation of two asparagine (Asn) or histidine (His) residues at the a positions of the second and fourth heptads, which allow one sequence to pack into homodimers with sticky ends through specific interhelical Asn-Asn or metal complexation interactions, followed by their longitudinal association into ordered nanofibers. This is in contrast to classical self-assembling helical peptide systems consisting of two complementary peptides. The collaborative roles played by the four main non-covalent interactions, including hydrogen-bonding, hydrophobic interactions, electrostatic interactions, and metal ion coordination, are well demonstrated during the hierarchical self-assembling processes of these peptides. Different nanostructures, for example, long and short nanofibers, thin and thick fibers, uniform metal ion-entrapped nanofibers, and polydisperse globular stacks, can be prepared by harnessing these interactions at different levels of hierarchy.

Interfacial Assembly Inspired by Marine Mussels and Antifouling Effects of Polypeptoids: A Neutron Reflection Study.

Polypeptoid-coated surfaces and many surface-grafted hydrophilic polymer brushes have been proven efficient in antifouling-the prevention of nonspecific biomolecular adsorption and cell attachment. Protein adsorption, in particular, is known to mediate subsequent cell-surface interactions. However, the detailed antifouling mechanism of polypeptoid and other polymer brush coatings at the molecular level is not well understood. Moreover, most adsorption studies focus only on measuring a single adsorbed mass value, and few techniques are capable of characterizing the hydrated in situ layer structure of either the antifouling coating or adsorbed proteins. In this study, interfacial assembly of polypeptoid brushes with different chain lengths has been investigated in situ using neutron reflection (NR). Consistent with past simulation results, NR revealed a common two-step structure for grafted polypeptoids consisting of a dense inner region that included a mussel adhesive-inspired oligopeptide for grafting polypeptoid chains and a highly hydrated upper region with very low polymer density (molecular brush). Protein adsorption was studied with human serum albumin (HSA) and fibrinogen (FIB), two common serum proteins of different sizes but similar isoelectric points (IEPs). In contrast to controls, we observed higher resistance by grafted polypeptoid against adsorption of the larger FIB, especially for longer chain lengths. Changing the pH to close to the IEPs of the proteins, which generally promotes adsorption, also did not significantly affect the antifouling effect against FIB, which was corroborated by atomic force microscopy imaging. Moreover, NR enabled characterization of the in situ hydrated layer structures of the polypeptoids together with proteins adsorbed under selected conditions. While adsorption on bare SiO2 controls resulted in surface-induced protein denaturation, this was not observed on polypeptoids. Our current results therefore highlight the detailed in situ view that NR may provide for characterizing protein adsorption on polymer brushes as well as the excellent antifouling behavior of polypeptoids.

Development of a novel in vitro 3D intestinal model for permeability evaluations.

In this work, a new three-dimensional (3D) in vitro cell model was described, which was comprised of an epithelium, a subepithelial fibroblast network and an extracellular matrix, thereby more closely mimicking the morphology of the small intestine. Transmission electron microscopy studies clearly revealed the complex structure of the new in vitro model. In a comparative study of drug absorption in the 3D model and a conventional Caco-2 mono-culture cell model, the 3D model provided more physiological observations of transepithelial electrical resistance and alkaline phosphatase activity. The activities of two major intestinal xenobiotic efflux transporters, namely ABCB1 (P-glycoprotein, P-gp) and ABCG2 (Breast Cancer Resistance Protein, BCRP), were also studied, with the decreased ABCB1 activity and increased ABCG2 activity observed in the 3D model closer to the physiological characteristics of the human small intestine. A better correlation between drug permeability and human drug absorption was also observed from the 3D model, consistent with the better modelling of human intestine in structure and physiology.

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.

Interfacial Adsorption of a Monoclonal Antibody and Its Fab and Fc Fragments at the Oil/Water Interface.

The physical stability of a monoclonal antibody (mAb) solution for injection in a prefilled syringe may in part depend on its behavior at the silicone oil/water interface. Here, the adsorption of a mAb (termed COE-3) and its fragment antigen-binding (Fab) and crystallizable (Fc) at the oil/water interface was measured using neutron reflection. A 1.4 ± 0.1 µm hexadecane oil film was formed on a sapphire block by a spin-freeze-thaw process, retaining its integrity upon contact with the protein solutions. Measurements revealed that adsorbed COE-3 and its Fab and Fc fragments retained their globular structure, forming layers that did not penetrate substantially into the oil phase. COE-3 and Fc were found to adsorb flat-on to the interface, with denser 45 and 42 Å inner layers, respectively, in contact with the oil and a more diffuse 17-21 Å outer layer caused by fragments adsorbing in a tilted manner. In contrast, Fab fragments formed a uniform 60 Å monolayer. Monolayers were formed under all conditions studied (10-200 ppm, using three isotopic contrasts), although changes in packing density across the COE-3 and Fc layers were observed. COE-3 had a higher affinity to the interface than either of its constituent fragments, while Fab had a lower interfacial affinity consistent with its higher net surface charge. This study extends the application of high-resolution neutron reflection measurements to the study of protein adsorption at the oil/water interface using an experimental setup mimicking the protein drug product in a siliconized prefilled syringe.

Active Modulation of States of Prestress in Self-Assembled Short Peptide Gels.

Peptide hydrogels are excellent candidates for medical therapeutics due to their tuneable viscoelastic properties, however, in vivo they will be subject to various osmotic pressures, temperature changes, and biological co-solutes, which could alter their performance. Peptide hydrogels formed from the synthetic peptide I3K have a temperature-induced hardening of their shear modulus by a factor of 2. We show that the addition of uncross-linked poly( N-isopropylacrylamide) chains to the peptide gels increases the gels' temperature sensitivity by 3 orders of magnitude through the control of osmotic swelling and cross-linking. Using machine learning combined with single-molecule fluorescence microscopy, we measured the modulation of states of prestress in the gels on the level of single peptide fibers. A new self-consistent mixture model was developed to simultaneously quantify the energy and the length distributions of the states of prestress. Switching the temperature from 20 to 40 °C causes 6-fold increases in the number of states of prestress. At the higher temperature, many of the fibers experience constrained buckling with characteristic small wavelength oscillations in their curvature.

Controlling the Diameters of Nanotubes Self-Assembled from Designed Peptide Bolaphiles.

Controlling the diameters of nanotubes represents a major challenge in nanostructures self-assembled from templating molecules. Here, two series of bolaform hexapeptides are designed, with Set I consisting of Ac-KI4 K-NH2 , Ac-KI3 NleK-NH2 , Ac-KI3 LK-NH2 and Ac-KI3 TleK-NH2 , and Set II consisting of Ac-KI3 VK-NH2 , Ac-KI2 V2 K-NH2 , Ac-KIV3 K-NH2 and Ac-KV4 K-NH2 . In Set I, substitution for Ile in the C-terminal alters its side-chain branching, but the hydrophobicity is retained. In Set II, the substitution of Val for Ile leads to the decrease of hydrophobicity, but the side-chain ß-branching is retained. The peptide bolaphiles tend to form long nanotubes, with the tube shell being composed of a peptide monolayer. Variation in core side-chain branching and hydrophobicity causes a steady shift of peptide nanotube diameters from more than one hundred to several nanometers, thereby achieving a reliable control over the underlying molecular self-assembling processes. Given the structural and functional roles of peptide tubes with varying dimensions in nature and in technological applications, this study exemplifies the predictive templating of nanostructures from short peptide self-assembly.

Single-Molecule Study of Peptide Gel Dynamics Reveals States of Prestress.

De novo peptide surfactant (I3K) gels provide an ideal system to study the complex dynamics of lightly cross-linked semiflexible fibers because of their large contour lengths, simple chemistry, and slow dynamics. We used single-molecule fluorescence microscopy to record individual fibers and Fourier decomposition of the fiber dynamics to separate thermal contributions to the persistence length from compressive states of prestress (SPS). Our results show that SPS in the network depend strongly on peptide concentration, buffer, and pH and that the fibril energies in SPS follow a Lévy distribution. The presence of SPS in the network imply that collective states of self-stress are also present. Therefore, semiflexible polymer gels need to be considered as complex load-bearing structures and the mean field models for polymer gel elasticity and dynamics often applied to them will not be fully representative of the behavior at the nanoscale. We quantify the impact of cross-links on reptation tube dynamics, which provides a second population of tube fluctuations in addition to those expected for uncross-linked entangled solutions.

Determination of PMMA Residues on a Chemical-Vapor-Deposited Monolayer of Graphene by Neutron Reflection and Atomic Force Microscopy.

Chemical vapor deposition (CVD) is now a well-established method for creating monolayer graphene films. In this method, poly(methyl methacrylate) (PMMA) films are often coated onto monolayer graphene films to make them mechanically robust enough for transfer and further handling. However, it is found that PMMA is hard to remove entirely, and any residual polymers remaining can affect graphene's properties. We demonstrate here a method to determine the amount of PMMA remaining on the graphene sheet fabricated from CVD by a combined study of Raman scattering, atomic force microscopy, and neutron reflection. Neutron reflectivity is a powerful technique which is particularly sensitive to any interfacial structure, so it is able to investigate the density profile of the residual PMMA in the direction perpendicular to the graphene film surface. After the standard process of PMMA removal by acetone-IPA cleaning, we found that the remaining PMMA film could be represented as a two-layer model: an inner layer with a thickness of 17 Å and a roughness of 1 Å mixed with graphene and an outer diffuse layer with an average thickness of 31 Å and a roughness of 4 Å well mixed with water. On the basis of this model analysis, it was demonstrated that the remaining PMMA still occupied a significant fraction of the graphene film surface.

Temperature Resistant Binary SLES/Nonionic Surfactant Mixtures at the Air/Water Interface.

Surface compositions of adsorbed monolayers at the air/water interface, formed from binary surfactant mixtures in equilibrium, have been studied using neutron reflectivity at three discrete temperatures: 10, 25, and 40 °C. The binary compositions studied are sodium lauryl dodecyl ether sulfate (SLES EO3)/C12E n, where n = 6 and 8, at a fixed concentration of 2 mM with and without the addition of 0.1 M NaCl. Without NaCl, the nonionic surfactant dominates at the interface and nonideal mixing behavior is observed. This is modeled using the pseudophase approximation with a quadratic expansion of the free energy of mixing. The addition of 0.1 M NaCl screens the charge interaction between the surfactants and drives the surface composition of each system closer to that of the bulk composition. However, model fits to both the micelles and surface layers suggest that nonideal mixing is still taking place, although it is difficult to establish the extent of nonideality due to the limited data quality. The effect of temperature changes on the surface adsorption and composition of the surfactant mixtures is minimal and within error, with and without NaCl, but the critical micelle concentrations are significantly affected. This indicates the dominant influence of steric hindrances and surfactant charge interactions in determining interfacial behavior for these surfactants, relative to the temperature changes. The study also highlights the delicate effect of a relatively small change in the number of EO groups on mixing behavior.

Structural Features of Reconstituted Cuticular Wax Films upon Interaction with Nonionic Surfactant C12E6.

The interaction of nonionic surfactant hexaethylene glycol monododecyl ether (C12E6) with a reconstituted cuticular wheat wax film has been investigated by spectroscopic ellipsometry and neutron reflection (NR) to help understand the role of the leaf wax barrier during pesticide uptake, focusing on the mimicry of the actions adjuvants impose on the physical integrity and transport of the cuticular wax films against surfactant concentration. As the C12E6 concentration was increased up to the critical micelle concentration (CMC = 0.067 mM), an increasing amount of surfactant mass was deposited onto the wax film. Alongside surface adsorption, C12E6 was also observed to penetrate the wax film, which is evident from the NR measurements using fully protonated and chain-deuterated surfactants. Furthermore, surfactant action upon the model wax film was found to be physically reversible below the CMC, as water rinsing could readily remove the adsorbed surfactant, leaving the wax film in its original state. Above the CMC, the detergency action of the surfactant became dominant, and a significant proportion of the wax film was removed, causing structural damage. The results thus reveal that both water and C12E6 could easily penetrate the wax film throughout the concentration range measured, indicating a clear pathway for the transport of active ingredients while the removal of the wax components above the CMC must have enhanced the transport process. As the partial removal of the wax film could also expose the underlying cutaneous substrate to the environment and undermine the plant's health, this study has a broad implication to the roles of surfactants in crop care.

Left or Right: How Does Amino Acid Chirality Affect the Handedness of Nanostructures Self-Assembled from Short Amphiphilic Peptides?

Peptide and protein fibrils have attracted an enormous amount of interests due to their relevance to many neurodegenerative diseases and their potential applications in nanotechnology. Although twisted fibrils are regarded as the key intermediate structures of thick fibrils or bundles of fibrils, the factors determining their twisting tendency and their handedness development from the molecular to the supramolecular level are still poorly understood. In this study, we have designed three pairs of enantiomeric short amphiphilic peptides: LI3LK and DI3DK, LI3DK and DI3LK, and LaI3LK and DaI3DK, and investigated the chirality of their self-assembled nanofibrils through the combined use of atomic force microscopy (AFM), circular dichroism (CD) spectroscopy, scanning electron microscopy (SEM), and molecular dynamic (MD) simulations. The results indicated that the twisted handedness of the supramolecular nanofibrils was dictated by the chirality of the hydrophilic Lys head at the C-terminal, while their characteristic CD signals were determined by the chirality of hydrophobic Ile residues. MD simulations delineated the handedness development from molecular chirality to supramolecular handedness by showing that the ß-sheets formed by LI3LK, LaI3LK, and DI3LK exhibited a propensity to twist in a left-handed direction, while the ones of DI3DK, DaI3DK, and LI3DK in a right-handed twisting orientation.

Self-Assembly of Mesoscopic Peptide Surfactant Fibrils Investigated by STORM Super-Resolution Fluorescence Microscopy.

Super-resolution fluorescence microscopy, specifically stochastic reconstruction microscopy (STORM), and atomic force microscopy (AFM) were used to image the self-assembly processes of the peptide surfactant I3K. The peptide surfactants self-assembled into giant helical fibrils with diameters between 5 and 10 nm with significant helical twisting. The resolution of the STORM images was 30 nm, calculated using the Fourier ring correlation method. STORM compares favorably with AFM for the calculation of contour lengths (∼6 µm) and persistence lengths (10.1 ± 1.2 µm) due to its increased field of view (50 µm), and its ability to image bulk morphologies away from surfaces under ambient solution conditions. Two-color STORM experiments were performed to investigate the dynamic process of self-assembly after mixing of two separately labeled samples, and the results revealed the formation of long nanofibers via end-to-end connections of short ones. No evidence was found for significant monomer exchange between the samples, and the self-assembled structures were very stable and long-lived.

Tuning One-Dimensional Nanostructures of Bola-Like Peptide Amphiphiles by Varying the Hydrophilic Amino Acids.

By combining experimental measurements and computer simulations, we here show that for the bola-like peptide amphiphiles XI4 X, where X=K, R, and H, the hydrophilic amino acid substitutions have little effect on the ß-sheet hydrogen-bonding between peptide backbones. Whereas all of the peptides self-assemble into one dimensional (1D) nanostructures with completely different morphologies, that is, nanotubes and helical nanoribbons for KI4 K, flat and multilayered nanoribbons for HI4 H, and twisted and bilayered nanoribbons for RI4 R. These different 1D morphologies can be explained by the distinct stacking degrees and modes of the three peptide ß-sheets along the x-direction (width) and the z-direction (height), which microscopically originate from the hydrogen-bonding ability of the sheets to solvent molecules and the pairing of hydrophilic amino acid side chains between ß-sheet monolayers through stacking interactions and hydrogen bonding. These different 1D nanostructures have distinct surface chemistry and functions, with great potential in various applications exploiting the respective properties of these hydrophilic amino acids.