Recent advances in engineering polyvalent biological interactions

Exploring Multivalency in the Development of Anti-PD-L1 Peptides for Cancer Immunotherapy

PURPOSE

The PD-1/PD-L1 pathway is one of the most effective immune checkpoint pathways utilized for cancer immunotherapy. Despite the success of anti-PD-1/PD-L1 mAbs, there is growing interest in developing low molecular weight anti-PD-1/PD-1 agents, such as peptides, because of their improved tumor penetration. We recently developed a small anti-PD-L1 peptide and demonstrated its promising anti-tumor activity. In this study, we investigate multivalency as a strategy to increase the binding avidity and blocking efficiency of the anti-PD-L1 peptide.

METHODS

Multivalent peptide inhibitors are designed with multiple copies of a peptide inhibitor in a single molecule. We synthesized peptides with different valences and examined their activity. We also investigated how spacer length affects the activity of these multivalent peptides.

RESULTS

Using this strategy, we developed a multivalent peptide that demonstrated approximately 40 times higher blocking efficiency and improved stability compared to the original peptide. Increasing the valency enhanced the peptide's specificity, which is essential for minimizing side effects.

CONCLUSIONS

Multivalency approach represents a promising platform for improving the efficacy of peptide-based checkpoint inhibitors.

Influence of Surface Chemistry on Host/Guest Interactions: A Model Study on Redox-Sensitive β-Cyclodextrin/Ferrocene Complexes

While host/guest interactions are widely used to control molecular assembly on surfaces, quantitative information on the effect of surface chemistry on their efficiency is lacking. To address this question, we combined electrochemical characterization with quartz crystal microbalance with dissipation monitoring to study host/guest interactions between surface-attached ferrocene (Fc) guests and soluble β-cyclodextrin (β-CD) hosts. We identified several parameters that influence the redox response, β-CD complexation ability, and repellent properties of Fc monolayers, including the method of Fc grafting, the linker connecting Fc with the surface, and the diluting molecule used to tune Fc surface density. The study on monovalent β-CD/Fc complexation was completed by the characterization of multivalent interactions between Fc monolayers and β-CD-functionalized polymers, with new insights being obtained on the interplay between the surface chemistry, binding efficiency, and reversibility under electrochemical stimulus. These results should facilitate the design of well-defined functional interfaces and their implementation in stimuli-responsive materials and sensing devices.

Multiple hydrogen bonding driven supramolecular architectures and their biomedical applications

Supramolecular chemistry combines the strength of molecular assembly via various molecular interactions. Hydrogen bonding facilitated self-assembly with the advantages of directionality, specificity, reversibility, and strength is a promising approach for constructing advanced supramolecules. There are still some challenges in hydrogen bonding based supramolecular polymers, such as complexity originating from tautomerism of the molecular building modules, the assembly process, and structure versatility of building blocks. In this review, examples are selected to give insights into multiple hydrogen bonding driven emerging supramolecular architectures. We focus on chiral supramolecular assemblies, multiple hydrogen bonding modules as stimuli responsive sources, interpenetrating polymer networks, multiple hydrogen bonding assisted organic frameworks, supramolecular adhesives, energy dissipators, and quantitative analysis of nano-adhesion. The applications in biomedical materials are focused with detailed examples including drug design evolution for myotonic dystrophy, molecular assembly for advanced drug delivery, an indicator displacement strategy for DNA detection, tissue engineering, and self-assembly complexes as gene delivery vectors for gene transfection. In addition, insights into the current challenges and future perspectives of this field to propel the development of multiple hydrogen bonding facilitated supramolecular materials are proposed.

Triblock copolymer–grafted restricted access materials with zwitterionic polymer outer layers for highly efficient extraction of fluoroquinolones and exclusion of proteins

High-selectivity and high-exclusion restricted access materials (RAMs) benefit the analysis of biological samples. Herein, triblock copolymer-functionalized poly(4-vinylbenzyl chloride-co-divinylbenzene) (P_VBC/DVB) microspheres were prepared via the sequential surface-initiated atom radical polymerization of hydrophobic styrene (St), ionic vinylimidazole (VIm), and zwitterionic sulfobetaine methacrylate (SBMA), affording RAMs with multiple interaction-adsorption sites and zwitterionic polymer exclusion sites on the internal and external surfaces of P_VBC/DVB. The preferential extraction of fluoroquinolones (FQs) is realized based on the hydrophobic/π-π/ion exchange interactions due to the grafted poly-St-VIm, and the zwitterionic poly-SBMA block in the triblock copolymers can efficiently exclude various proteins. A sensitive detection method for FQs in chicken was established by solid phase extraction with RAMs as adsorbent combined with UPLC-MS/MS, achieving wide linearity (2.0-200.0 ng mL^-1), low limit of detection (0.5 μg kg^-1) and limit of quantification (1.5 μg kg^-1), and good inter- and intraday precision with satisfactory recoveries (104.1%-117.7% and 115.3%-121.2% with RSDs < 12%).

Design of Beta-2 Microglobulin Adsorbent Protein Nanoparticles

Beta-2 microglobulin (B2M) is an immune system protein that is found on the surface of all nucleated human cells. B2M is naturally shed from cell surfaces into the plasma, followed by renal excretion. In patients with impaired renal function, B2M will accumulate in organs and tissues leading to significantly reduced life expectancy and quality of life. While current hemodialysis methods have been successful in managing electrolyte as well as small and large molecule disturbances arising in chronic renal failure, they have shown only modest success in managing plasma levels of B2M and similar sized proteins, while sparing important proteins such as albumin. We describe a systematic protein design effort aimed at adding the ability to selectively remove specific, undesired waste proteins such as B2M from the plasma of chronic renal failure patients. A novel nanoparticle built using a tetrahedral protein assembly as a scaffold that presents 12 copies of a B2M-binding nanobody is described. The designed nanoparticle binds specifically to B2M through protein-protein interactions with nanomolar binding affinity (~4.2 nM). Notably, binding to the nanoparticle increases the effective size of B2M by over 50-fold, offering a potential selective avenue for separation based on size. We present data to support the potential utility of such a nanoparticle for removing B2M from plasma by either size-based filtration or by polyvalent binding to a stationary matrix under blood flow conditions. Such applications could address current shortcomings in the management of problematic mid-sized proteins in chronic renal failure patients.

Determinants of Superselectivity─Practical Concepts for Application in Biology and Medicine

ConspectusMultivalent interactions are common in biological systems and are also widely deployed for targeting applications in biomedicine. A unique feature of multivalent binding is "superselectivity". Superselectivity refers to the sharp discrimination of surfaces (e.g., on cells or cell compartments) by their comparative surface densities of a given receptor. This feature is different from the conventional "type" selectivity, which discriminates surfaces by their distinct receptor types. In a broader definition, a probe is superselective if it converts a gradual change in any one interaction parameter into a sharp on/off dependency in probe binding.This Account describes our systematic experimental and theoretical efforts over the past decade to analyze the determinants of superselective binding. It aims to offer chemical biologists, biophysicists, biologists, and biomedical scientists a set of guidelines for the interpretation of multivalent binding data, and design rules for tuning superselective targeting. We first provide a basic introduction that identifies multiple low-affinity interactions and combinatorial entropy as the minimal set of conditions required for superselective recognition. We then introduce the main experimental and theoretical tools and analyze how salient features of the multivalent probes (i.e., their concentration, size, ligand valency, and scaffold type), of the surface receptors (i.e., their affinity for ligands, surface density, and mobility), and of competitors and cofactors (i.e., their concentration and affinity for the ligands and/or receptors) influence the sharpness and the position of the threshold for superselective recognition.Emerging from this work are a set of relatively simple yet quantitative data analysis guidelines and superselectivity design rules that apply to a broad range of probe types and interaction systems. The key finding is the scaling variable x_S which faithfully predicts the influence of the surface receptor density, probe ligand valency, receptor-ligand affinity, and competitor/cofactor concentrations and affinities on superselective recognition. The scaling variable is a simple yet versatile tool to quantitatively tune the on/off threshold of superselective probes. We exemplify its application by reviewing and reinterpreting literature data for selected biological and biomedical interaction systems where superselectivity clearly is important.Our guidelines can be deployed to generate a new mechanistic understanding of multivalent recognition events inside and outside cells and the downstream physiological/pathological implications. Moreover, the design rules can be harnessed to develop novel superselective probes for analytical purposes in the life sciences and for diagnostic/therapeutic intervention in biomedicine.

Self-assembling peptides as immunomodulatory biomaterials

Self-assembling peptides are a type of biomaterial rapidly emerging in the fields of biomedicine and material sciences due to their promise in biocompatibility and effectiveness at controlled release. These self-assembling peptides can form diverse nanostructures in response to molecular interactions, making them versatile materials. Once assembled, the peptides can mimic biological functions and provide a combinatorial delivery of therapeutics such as cytokines and drugs. These self-assembling peptides are showing success in biomedical settings yet face unique challenges that must be addressed to be widely applied in the clinic. Herein, we describe self-assembling peptides' characteristics and current applications in immunomodulatory therapeutics.

Recombinant Protein Micelles to Block Transduction by SARS-CoV-2 Pseudovirus

The continuing emergence of variants of the SARS-CoV-2 virus requires the development of modular molecular therapies. Here, we engineered a recombinant amphiphilic protein, oleosin, to spontaneously self-assemble into multivalent micellar nanostructures which can block the Spike S1 protein of SARS-CoV-2 pseudoviruses (PVs). Short recombinant proteins like oleosin can be formulated more easily than antibodies and can be functionalized with precision through genetic engineering. We cloned S1-binding mini-protein genes called LCBx, previously designed by David Baker's laboratory (UW Seattle), to the N-terminus of oleosin, expressing Oleo-LCBx proteins in E. coli. These proteins largely formed 10-100 nm micelles as verified by dynamic light scattering. Two proteins, Oleo-LCB1 and Oleo-LCB3, were seen to completely and irreversibly block transduction by both wild-type and delta variant PVs into 293T-hsACE2 cells at 10 μM. Presented in multivalent micelles, these proteins reduced transduction by PVs down to a functional protein concentration of 5 nM. Additionally, Oleo-LCB1 micelles outperformed corresponding synthetic LCB1 mini-proteins in reducing transduction by PVs. Tunable aqueous solubility of recombinant oleosin allowed incorporation of peptides/mini-proteins at high concentrations within micelles, thus enhancing drug loading. To validate the potential multifunctionality of the micelles, we showed that certain combinations of Oleo-LCB1 and Oleo-LCB3 performed much better than the individual proteins at the same concentration. These micelles, which we showed to be non-toxic to human cells, are thus a promising step toward the design of modular, multifunctional therapeutics that could bind to and inactivate multiple receptors and proteins necessary for the infection of the SARS-CoV-2 virus.

MVsim is a toolset for quantifying and designing multivalent interactions

Arising through multiple binding elements, multivalency can specify the avidity, duration, cooperativity, and selectivity of biomolecular interactions, but quantitative prediction and design of these properties has remained challenging. Here we present MVsim, an application suite built around a configurational network model of multivalency to facilitate the quantification, design, and mechanistic evaluation of multivalent binding phenomena through a simple graphical user interface. To demonstrate the utility and versatility of MVsim, we first show that both monospecific and multispecific multivalent ligand-receptor interactions, with their noncanonical binding kinetics, can be accurately simulated. Further, to illustrate the conceptual insights into multivalent systems that MVsim can provide, we apply it to quantitatively predict the ultrasensitivity and performance of multivalent-encoded protein logic gates, evaluate the inherent programmability of multispecificity for selective receptor targeting, and extract rate constants of conformational switching for the SARS-CoV-2 spike protein and model its binding to ACE2 as well as multivalent inhibitors of this interaction. MVsim and instructional tutorials are freely available at https://sarkarlab.github.io/MVsim/ .

Gigavalent Display of Proteins on Monodisperse Polyacrylamide Hydrogels as a Versatile Modular Platform for Functional Assays and Protein Engineering

The assembly of robust, modular biological components into complex functional systems is central to synthetic biology. Here, we apply modular "plug and play" design principles to a solid-phase protein display system that facilitates protein purification and functional assays. Specifically, we capture proteins on polyacrylamide hydrogel display beads (PHD beads) made in microfluidic droplet generators. These monodisperse PHD beads are decorated with predefined amounts of anchors, methacrylate-PEG-benzylguanine (BG) and methacrylate-PEG-chloroalkane (CA), that react covalently with SNAP-/Halo-tag fusion proteins, respectively, in a specific, orthogonal, and stable fashion. Anchors, and thus proteins, are distributed throughout the entire bead volume, allowing attachment of ∼10⁹ protein molecules per bead (⌀ 20 μm) -a higher density than achievable with commercial surface-modified beads. We showcase a diverse array of protein modules that enable the secondary capture of proteins, either noncovalently (IgG and SUMO-tag) or covalently (SpyCatcher, SpyTag, SnpCatcher, and SnpTag), in mono- and multivalent display formats. Solid-phase protein binding and enzymatic assays are carried out, and incorporating the photocleavable protein PhoCl enables the controlled release of modules via visible-light irradiation for functional assays in solution. We utilize photocleavage for valency engineering of an anti-TRAIL-R1 scFv, enhancing its apoptosis-inducing potency ∼50-fold through pentamerization.

Red-Absorbing Ru(II) Polypyridyl Complexes with Biotin Targeting Spontaneously Assemble into Nanoparticles in Biological Media

Four new ruthenium(II) polypyridyl complexes were synthesized to study the effect of poly(ethylene glycol) and/or biotin conjugation on their physical and biological properties, including their hydrophilicity, their cellular uptake, and their phototoxicity. Unexpectedly, these complexes self-assembled into nanoparticles upon dilution in biological media. This behavior leads to their accumulation in lysosomes following their internalization by cells. While a significant increase in cellular uptake was observed for the biotin-conjugated complexes, it did not result in an increase in their phototoxicity. However, their high phototoxicity upon irradiation at long wavelengths (645-670 nm) and their self-assembling behavior make them a promising backbone for the development of new lysosome-targeted photosensitizers for photodynamic therapy.

Structure-Guided Designing Pre-Organization in Bivalent Aptamers

Multivalent interaction is often used in molecular design and leads to engineered multivalent ligands with increased binding avidities toward target molecules. The resulting binding avidity relies critically on the rigid scaffold that joins multiple ligands as the scaffold controls the relative spatial positions and orientations toward target molecules. Currently, no general design rules exist to construct a simple and rigid DNA scaffold for properly joining multiple ligands. Herein, we report a crystal structure-guided strategy for the rational design of a rigid bivalent aptamer with precise control over spatial separation and orientation. Such a pre-organization allows the two aptamer moieties simultaneously to bind to the target protein at their native conformations. The bivalent aptamer binding has been extensively characterized, and an enhanced binding has been clearly observed. This strategy, we believe, could potentially be generally applicable to design multivalent aptamers.

Toward Glycomaterials with Selectivity as Well as Affinity

Multivalent glycosylated materials (polymers, surfaces, and particles) often show high affinity toward carbohydrate binding proteins (e.g., lectins) due to the nonlinear enhancement from the cluster glycoside effect. This affinity gain has potential in applications from diagnostics, biosensors, and targeted delivery to anti-infectives and in an understanding of basic glycobiology. This perspective highlights the question of selectivity, which is less often addressed due to the reductionist nature of glycomaterials and the promiscuity of many lectins. The use of macromolecular features, including architecture, heterogeneous ligand display, and the installation of non-natural glycans, to address this challenge is discussed, and examples of selectivity gains are given.

Avidity observed between a bivalent inhibitor and an enzyme monomer with a single active site

Although myriad protein–protein interactions in nature use polyvalent binding, in which multiple ligands on one entity bind to multiple receptors on another, to date an affinity advantage of polyvalent binding has been demonstrated experimentally only in cases where the target receptor molecules are clustered prior to complex formation. Here, we demonstrate cooperativity in binding affinity (i.e., avidity) for a protein complex in which an engineered dimer of the amyloid precursor protein inhibitor (APPI), possessing two fully functional inhibitory loops, interacts with mesotrypsin, a soluble monomeric protein that does not self-associate or cluster spontaneously. We found that each inhibitory loop of the purified APPI homodimer was over three-fold more potent than the corresponding loop in the monovalent APPI inhibitor. This observation is consistent with a suggested mechanism whereby the two APPI loops in the homodimer simultaneously and reversibly bind two corresponding mesotrypsin monomers to mediate mesotrypsin dimerization. We propose a simple model for such dimerization that quantitatively explains the observed cooperativity in binding affinity. Binding cooperativity in this system reveals that the valency of ligands may affect avidity in protein–protein interactions including those of targets that are not surface-anchored and do not self-associate spontaneously. In this scenario, avidity may be explained by the enhanced concentration of ligand binding sites in proximity to the monomeric target, which may favor rebinding of the multiple ligand binding sites with the receptor molecules upon dissociation of the protein complex.

MVsim : a toolset for quantifying and designing multivalent interactions

Arising through multiple binding elements, multivalency can specify the avidity, duration, cooperativity, and selectivity of biomolecular interactions, but quantitative prediction and design of these properties has remained challenging. Here we present MVsim , an application suite built around a configurational network model of multivalency to facilitate the quantification, design, and mechanistic evaluation of multivalent binding phenomena through a simple graphical user interface. To demonstrate the utility and versatility of MVsim , we first show that both monospecific and multispecific multivalent ligand-receptor interactions, with their noncanonical binding kinetics, can be accurately simulated. We then quantitatively predict the ultrasensitivity and performance of multivalent-encoded protein logic gates, evaluate the inherent programmability of multispecificity for selective receptor targeting, and extract rate constants of conformational switching for the SARS-CoV-2 spike protein and model its binding to ACE2 as well as multivalent inhibitors of this interaction. MVsim is freely available at https://sarkarlab.github.io/MVsim/ .

Improving Breast Cancer Treatment Specificity Using Aptamers Obtained by 3D Cell-SELEX

Three-dimensional spheroids of non-malignant MCF10A and malignant SKBR3 breast cells were used for subsequent 3D Cell-SELEX to generate aptamers for specific binding and treatment of breast cancer cells. Using 3D Cell-SELEX combined with Next-Generation Sequencing and bioinformatics, ten abundant aptamer families with specific structures were identified that selectively bind to SKBR3, and not to MCF10A cells. Multivalent aptamer polymers were synthesized by co-polymerization and analyzed for binding performance as well as therapeutic efficacy. Binding performance was determined by confocal fluorescence imaging and revealed specific binding and efficient internalization of aptamer polymers into SKBR3 spheroids. For therapeutic purposes, DNA sequences that intercalate the cytotoxic drug doxorubicin were co-polymerized into the aptamer polymers. Viability tests show that the drug-loaded polymers are specific and effective in killing SKBR3 breast cancer cells. Thus, the 3D-selected aptamers enhanced the specificity of doxorubicin against malignant over non-malignant breast cells. The innovative modular DNA aptamer platform based on 3D Cell SELEX and polymer multivalency holds great promise for diagnostics and treatment of breast cancer.

PEGylated sequence-controlled macromolecules using supramolecular binding to target the Taspase1/Importin α interaction

A novel strategy to inhibit the oncologically relevant protease Taspase1 is explored by developing PEGylated macromolecular ligands presenting the supramolecular binding motif guanidiniocarbonylpyrrole (GCP). Taspase1 requires interaction of its nuclear localization signal (NLS) with import receptor Importin α. We show the synthesis and effective interference of PEGylated multivalent macromolecular ligands with Taspase1-Importin α-complex formation.

Control of Superselectivity by Crowding in Three-Dimensional Hosts

Motivated by the fine compositional control observed in membraneless droplet organelles in cells, we investigate how a sharp binding-unbinding transition can occur between multivalent client molecules and receptors embedded in a porous three-dimensional structure. In contrast to similar superselective binding previously observed at surfaces, we have identified that a key effect in a three-dimensional environment is that the presence of inert crowding agents can significantly enhance or even introduce superselectivity. In essence, molecular crowding initially suppresses binding via an entropic penalty, but the clients can then more easily form many bonds simultaneously. We demonstrate the robustness of the superselective behavior with respect to client valency, linker length, and binding interactions in Monte Carlo simulations of an archetypal lattice polymer model.

First-order 'hyper-selective' binding transition of multivalent particles under force

Multivalent particles bind to targets via many independent ligand-receptor bonding interactions. This microscopic design spans length scales in both synthetic and biological systems. Classic examples include interactions between cells, virus binding, synthetic ligand-coated micrometer-scale vesicles or smaller nano-particles, functionalised polymers, and toxins. Equilibrium multivalent binding is a continuous yet super-selective transition with respect to the number of ligands and receptors involved in the interaction. Increasing the ligand or receptor density on the two particles leads to sharp growth in the number of bound particles at equilibrium. Here we present a theory and Monte Carlo simulations to show that applying mechanical force to multivalent particles causes their adsorption/desorption isotherm on a surface to become sharper and more selective, with respect to variation in the number of ligands and receptors on the two objects. When the force is only applied to particles bound to the surface by one or more ligands, then the transition can become infinitely sharp and first-order-a new binding regime which we term 'hyper-selective'. Force may be imposed by, e.g. flow of solvent around the particles, a magnetic field, chemical gradients, or triggered uncoiling of inert oligomers/polymers tethered to the particles to provide a steric repulsion to the surface. This physical principle is a step towards 'all or nothing' binding selectivity in the design of multivalent constructs.

How the avidity of polymerase binding to the -35/-10 promoter sites affects gene expression

Although the key promoter elements necessary to drive transcription in Escherichia coli have long been understood, we still cannot predict the behavior of arbitrary novel promoters, hampering our ability to characterize the myriad sequenced regulatory architectures as well as to design new synthetic circuits. This work builds upon a beautiful recent experiment by Urtecho et al. [G. Urtecho, et al, Biochemistry, 68, 1539-1551 (2019)] who measured the gene expression of over 10,000 promoters spanning all possible combinations of a small set of regulatory elements. Using these data, we demonstrate that a central claim in energy matrix models of gene expression-that each promoter element contributes independently and additively to gene expression-contradicts experimental measurements. We propose that a key missing ingredient from such models is the avidity between the -35 and -10 RNA polymerase binding sites and develop what we call a multivalent model that incorporates this effect and can successfully characterize the full suite of gene expression data. We explore several applications of this framework, namely, how multivalent binding at the -35 and -10 sites can buffer RNA polymerase (RNAP) kinetics against mutations and how promoters that bind overly tightly to RNA polymerase can inhibit gene expression. The success of our approach suggests that avidity represents a key physical principle governing the interaction of RNA polymerase to its promoter.

Responsive and Synergistic Antibacterial Coatings: Fighting against Bacteria in a Smart and Effective Way

Antibacterial coatings that eliminate initial bacterial attachment and prevent subsequent biofilm formation are essential in a number of applications, especially implanted medical devices. Although various approaches, including bacteria-repelling and bacteria-killing mechanisms, have been developed, none of them have been entirely successful due to their inherent drawbacks. In recent years, antibacterial coatings that are responsive to the bacterial microenvironment, that possess two or more killing mechanisms, or that have triggered-cleaning capability have emerged as promising solutions for bacterial infection and contamination problems. This review focuses on recent progress on three types of such responsive and synergistic antibacterial coatings, including i) self-defensive antibacterial coatings, which can "turn on" biocidal activity in response to a bacteria-containing microenvironment; ii) synergistic antibacterial coatings, which possess two or more killing mechanisms that interact synergistically to reinforce each other; and iii) smart "kill-and-release" antibacterial coatings, which can switch functionality between bacteria killing and bacteria releasing under a proper stimulus. The design principles and potential applications of these coatings are discussed and a brief perspective on remaining challenges and future research directions is presented.

Mechanisms of PDZ domain scaffold assembly illuminated by use of supported cell membrane sheets

PDZ domain scaffold proteins are molecular modules orchestrating cellular signalling in space and time. Here, we investigate assembly of PDZ scaffolds using supported cell membrane sheets, a unique experimental setup enabling direct access to the intracellular face of the cell membrane. Our data demonstrate how multivalent protein-protein and protein-lipid interactions provide critical avidity for the strong binding between the PDZ domain scaffold proteins, PICK1 and PSD-95, and their cognate transmembrane binding partners. The kinetics of the binding were remarkably slow and binding strength two-three orders of magnitude higher than the intrinsic affinity for the isolated PDZ interaction. Interestingly, discrete changes in the intrinsic PICK1 PDZ affinity did not affect overall binding strength but instead revealed dual scaffold modes for PICK1. Our data supported by simulations suggest that intrinsic PDZ domain affinities are finely tuned and encode specific cellular responses, enabling multiplexed cellular functions of PDZ scaffolds.

Inside a cell, many different signals carry information that is essential for the cell to remain healthy and perform its role in the body. It is, therefore, very important that the signals are sent to the right places at the right times. Scaffold proteins play an essential role in organizing these signals by bringing specific proteins and other molecules into close contact at particular times and locations within the cell. Defects in scaffolding proteins can lead to cancer, psychiatric disorders and other diseases, so these proteins represent potential new targets for medicinal drugs.

Many scaffolding proteins assemble groups of proteins on the surface of the membrane that surrounds the cell. Previous studies have shown that scaffolding proteins are able to bind to several other proteins as well as the membrane itself at the same time. However, the precise way in which scaffolding proteins assemble such groups is not clear because it is technically challenging to study this process in living cells. To overcome this challenge, Erlendsson, Thorsen et al. used a new experimental setup known as supported cell membrane sheets – which provides direct access to the side of the cell membrane that usually faces into the cell – to study two scaffolding proteins known as PICK1 and PSD-95.

The experiments show that PICK1 and PSD-95 bind to their partner proteins up to 100 times more strongly than previously observed using other approaches. This is due to the scaffolding proteins binding more strongly to both their partners and the membrane.

Unexpectedly, the experiments show that the shape and physical characteristics of the partner protein have no effect on the increase in the strength of the binding. Further experiments suggest that altering the ability of the PDZ domain of PICK1 to bind to partner proteins changes the mode of action of the PICK1 protein so that it can activate different responses in the cell. Together these findings imply that the ability of scaffolding proteins to bind to their partner proteins is finely tuned to encode specific responses in cells in different situations – a hypothesis that Erlendsson, Thorsen et al. are planning to test in intact cells.

Self-Assembly of Antigen Proteins into Nanowires Greatly Enhances the Binding Affinity for High-Efficiency Target Capture

High-efficiency target capture is an essential prerequisite for sensitive immunoassays. However, the current available immunoassay approaches are subject to deficient binding affinities between predator-prey molecules that greatly restrict the target capture efficiency and immunoassay sensitivity. Herein, we present a new strategy through the self-assembly of antigen proteins into nanowires to enhance the binding affinity between an antigen and antibody. Through the genetic fusion of antigen proteins (e.g., HIV p24) with the yeast amyloid protein Sup35 self-assembly domain, specific antigen nanowires (Ag nanowires) were constructed and demonstrated a remarkable enhancement in binding affinity compared with that of the monomeric antigen molecule. The Ag nanowires were further combined with magnetic beads to form a 3D magnetic probe based on a seed-induced self-assembly strategy. Taking advantage of both the strong binding affinity and the rapid magnetic separation and enrichment capacity, the specific 3D magnetic probe achieved a 100-fold improvement in detection sensitivity within a significantly shorter period of 20 min over that of the conventional enzyme-linked immunosorbent assay method.

Multivalent nanosystems: targeting monocytes/macrophages

Among all the cellular partners involved in inflammatory processes, monocytes and macrophages are the master regulators of inflammation. They are found in almost all the tissues and are nearly the only cells capable of performing each step of inflammation. Consequently, they stand as major relevant therapeutic targets to treat inflammatory disorders and diseases. The physiological phagocytic activity of macrophages prompts them to detect, to recognize, and eventually to engulf any nanosystem cruising in their neighborhood. Interestingly, nanosystems can be rationally engineered to afford multivalent, and multifunctional if needed, entities with multiplexed and/or reinforced biological activities. Indeed, engineered nanosystems bearing moieties specifically targeting macrophages, and loaded with or bound to drugs are promising candidates to modulate, or even eradicate, deleterious macrophages in vivo. In this review we highlight recent articles and concepts of multivalent nanosystems targeting monocytes and macrophages to treat inflammatory disorders.

Synthesis of multivalent polymer-aptamer conjugates with enhanced inhibitory potency

PURPOSE

We are interested in designing a modular strategy for creating potent multivalent ligands, which frequently can be used as effective inhibitors of undesired biomolecular interactions. For example, such inhibitors might prevent the self-assembly of bacterial toxins or the attachment of a virus to its host cell receptors.

METHODS

We used a biocompatible polyamino acid polymer as a scaffold for grafting multiple copies of an oligonucleotide aptamer (OA). Specifically, the carboxylates on the side chains of polyglutamic acid (PGA) were modified with a thiol-reactive linker, N-aminoethyl maleimide (AEM), and thiol-functionalized OAs were attached to the maleimide moieties. The resulting conjugates were tested for their ability to compete with and inhibit the binding of unconjugated monovalent OAs to the target cell receptor.

RESULTS

Multivalent PGA-OA conjugates with low, medium, and high valency were successfully prepared. The varying valency and successful purification to remove unconjugated OAs were confirmed by polyacrylamide gel electrophoresis. The resulting purified conjugates inhibited the binding of unconjugated monovalent OAs, and the measured half maximal inhibitory concentration (IC50) values corresponded to a 38-88-fold enhancement of potency on a per-aptamer basis, relative to OA alone.

CONCLUSION

Multivalent conjugation of OA ligands has potential as a generally useful way to improve the potency of the interaction between the ligand and its target receptor. We have demonstrated this principle with a known OA as a proof of concept as well a synthetic strategy that can be used to synthesize multivalent conjugates of other OAs.

Polyvalent C-glycomimetics based on l-fucose or d-mannose as potent DC-SIGN antagonists

The C-type lectin DC-SIGN expressed on immature dendritic cells is a promising target for antiviral drug development. Previously, we have demonstrated that mono- and divalent C-glycosides based on d-manno and l-fuco configurations are promising DC-SIGN ligands. Here, we described the convergent synthesis of C-glycoside dendrimers decorated with 4, 6, 9, and 12 α-l-fucopyranosyl units and with 9 and 12 α-d-mannopyranosyl units. Their affinity against DC-SIGN was assessed by surface plasmon resonance (SPR) assays. For comparison, parent O-glycosidic dendrimers were synthesized and tested, as well. A clear increase of both affinity and multivalency effect was observed for C-glycomimetics of both types (mannose and fucose). However, when dodecavalent C-glycosidic dendrimers were compared, there was no difference in affinity regarding the sugar unit (l-fuco, IC₅₀ 17 μM; d-manno, IC₅₀ 12 μM). For the rest of glycodendrimers with l-fucose or d-mannose attached by the O- or C-glycosidic linkage, C-glycosidic dendrimers were significantly more active. These results show that in addition to the expected physiological stability, the biological activity of C-glycoside mimetics is higher in comparison to the corresponding O-glycosides and therefore these glycomimetic multivalent systems represent potentially promising candidates for targeting DC-SIGN.

Three-Dimensional Directionality Is a Pivotal Structural Feature for the Bioactivity of Azabisphosphonate-Capped Poly(PhosphorHydrazone) Nanodrug Dendrimers

Dendrimers are nanosized, nonlinear, hyperbranched polymers whose overall 3D shape is key for their biological activity. Poly(PhosphorHydrazone) (PPH) dendrimers capped with aza-bisphosphonate (ABP) end groups are known to have anti-inflammatory properties enabling the control of inflammatory diseases in different mouse models. Here we screen the anti-inflammatory activity of a series of PPH dendrimers bearing between 2 and 16 ABP end groups in a mouse model of arthritis and confront the biological results with atomistic simulations of the dendrimers. We show that only the PPH dendrimers capped with 10 and 12 ABP end groups can control the flare of the inflammatory disease. All-atom accelerated molecular dynamics simulations show that dendrimers with a low number of ABP end groups are directional but highly flexible/dynamic and have thereby limited efficiency in establishing multivalent interactions. The largest dendrimer appears as nondirectional, having 16 ABP end groups forming patches all over the dendrimer surface. Conversely, intermediate dendrimers having 10 or 12 ABP end groups reach the best compromise between the number of surface groups and their stable directional gathering, a real maximization of multivalency.

Reversible control of cell membrane receptor function using DNA nano-spring multivalent ligands

Chemically functionalized and nanostructured materials, which mimic the features of the natural extracellular matrix, provide a tool to organize cell surface receptors into nanoscale clusters and manipulate cell functions. However, the existing materials are mainly based on static structures. Herein, we developed a DNA based structure-switchable and multivalent material that acts as a 'nano-spring', enabling reversible control of membrane receptor function at the cell surface. This 'nano-spring' can be easily synthesized by rolling circle amplification and finely tuned by changing the circular template design. Using this 'nano-spring' to interact with cells, we have demonstrated that the movement of the DNA nanostructure is sufficient to direct a cell morphology change from the normal morphology to having numerous cell protrusions and affect the mRNA expression level of integrin related genes. This DNA nano-spring structure can be a competitive material for actively manipulating cell receptor function and may help us to understand the role of receptor mediated signalling cascades.

Pro-Inflammatory Versus Anti-Inflammatory Effects of Dendrimers: The Two Faces of Immuno-Modulatory Nanoparticles

Dendrimers are soft matter, hyperbranched, and multivalent nanoparticles whose synthesis theoretically affords monodisperse compounds. They are built from a core on which one or several successive series of branches are engrafted in an arborescent way. At the end of the synthesis, the tunable addition of surface groups gives birth to multivalent nano-objects which are generally intended for a specific use. For these reasons, dendrimers have received a lot of attention from biomedical researchers. In particular, some of us have demonstrated that dendrimers can be intrinsically drug-candidate for the treatment of inflammatory disorders, amongst others, using relevant preclinical animal models. These anti-inflammatory dendrimers are innovative in the pharmaceutical field. More recently, it has appeared that some dendrimers (even among those which have been described as anti-inflammatory) can promote inflammatory responses in non-diseased animals. The main corpus of this concise review is focused on the reports which describe anti-inflammatory properties of dendrimers in vivo, following which we review the few recent articles that show pro-inflammatory effects of our favorite molecules, to finally discuss this duality in immuno-modulation which has to be taken into account for the preclinical and clinical developments of dendrimers.

Controlling Multivalent Binding through Surface Chemistry: Model Study on Streptavidin

Although multivalent binding to surfaces is an important tool in nanotechnology, quantitative information about the residual valency and orientation of surface-bound molecules is missing. To address these questions, we study streptavidin (SAv) binding to commonly used biotinylated surfaces such as supported lipid bilayers (SLBs) and self-assembled monolayers (SAMs). Stability and kinetics of SAv binding are characterized by quartz crystal microbalance with dissipation monitoring, while the residual valency of immobilized SAv is quantified using spectroscopic ellipsometry by monitoring binding of biotinylated probes. Purpose-designed SAv constructs having controlled valencies (mono-, di-, trivalent in terms of biotin-binding sites) are studied to rationalize the results obtained on regular (tetravalent) SAv. We find that divalent interaction of SAv with biotinylated surfaces is a strict requirement for stable immobilization, while monovalent attachment is reversible and, in the case of SLBs, leads to the extraction of biotinylated lipids from the bilayer. The surface density and lateral mobility of biotin, and the SAv surface coverage are all found to influence the average orientation and residual valency of SAv on a biotinylated surface. We demonstrate how the residual valency can be adjusted to one or two biotin binding sites per immobilized SAv by choosing appropriate surface chemistry. The obtained results provide means for the rational design of surface-confined supramolecular architectures involving specific biointeractions at tunable valency. This knowledge can be used for the development of well-defined bioactive coatings, biosensors and biomimetic model systems.

Translocation Pathway-Dependent Assembly of Streptavidin- and Antibody-Binding Filamentous Virus-Like Particles

Compared to well-tolerated p3 fusion, the display of fast-folding proteins fused to the minor capsid p7 and the major capsid p8, as well as in vivo biotinylation of biotin acceptor peptide (AP) fused to p7, are found to be markedly inefficient using the filamentous phage. Here, to overcome such limitations, the effect of translocation pathways, amber mutation, and phage and phagemid display systems on p7 and p8 display of antibody-binding domains are examined, while comparing the level of in vivo biotinylation of AP fused to p7 or p3. Interestingly, the in vivo biotinylation of AP occurs only in p3 fusion and the fast-folding antibody-binding scaffolds fused to p7 and p8 are best displayed via a twin-arginine translocation pathway in TG1 cells. The lower the expression level of the wild-type p8 and the smaller the size of the guest protein, the better the display of Z-domain fused to the recombinant p8. The in vivo biotinylated multifunctional filamentous virus-like particles can be vertically immobilized on streptavidin (SAV)-coated microspheres to resemble cellular microvilli-like structures, which reportedly enhance protein-protein interactions due to dramatically expanded flexible surface area.

Communication: Simple approach for calculating the binding free energy of a multivalent particle

We present a simple yet accurate numerical approach to compute the free energy of binding of multivalent objects on a receptor-coated surface. The method correctly accounts for the fact that one ligand can bind to at most one receptor. The numerical approach is based on a saddle-point approximation to the computation of a complex residue. We compare our theory with the powerful Valence-Limited Interaction Theory (VLIT) [P. Varilly et al., J. Chem. Phys. 137, 094108 (2012); S. Angioletti-Uberti et al., ibid. 138, 021102 (2013)] and find excellent agreement in the regime where that theory is expected to work. However, the present approach even works for low receptor/ligand densities, where VLIT breaks down.

In Vivo Efficacy of Measles Virus Fusion Protein-Derived Peptides Is Modulated by the Properties of Self-Assembly and Membrane Residence

Measles virus (MV) infection is undergoing resurgence and remains one of the leading causes of death among young children worldwide despite the availability of an effective measles vaccine. MV infects its target cells by coordinated action of the MV hemagglutinin (H) and fusion (F) envelope glycoproteins; upon receptor engagement by H, the prefusion F undergoes a structural transition, extending and inserting into the target cell membrane and then refolding into a postfusion structure that fuses the viral and cell membranes. By interfering with this structural transition of F, peptides derived from the heptad repeat (HR) regions of F can inhibit MV infection at the entry stage. In previous work, we have generated potent MV fusion inhibitors by dimerizing the F-derived peptides and conjugating them to cholesterol. We have shown that prophylactic intranasal administration of our lead fusion inhibitor efficiently protects from MV infection in vivo We show here that peptides tagged with lipophilic moieties self-assemble into nanoparticles until they reach the target cells, where they are integrated into cell membranes. The self-assembly feature enhances biodistribution and the half-life of the peptides, while integration into the target cell membrane increases fusion inhibitor potency. These factors together modulate in vivo efficacy. The results suggest a new framework for developing effective fusion inhibitory peptides.

IMPORTANCE

Measles virus (MV) infection causes an acute illness that may be associated with infection of the central nervous system (CNS) and severe neurological disease. No specific treatment is available. We have shown that fusion-inhibitory peptides delivered intranasally provide effective prophylaxis against MV infection. We show here that specific biophysical properties regulate the in vivo efficacy of MV F-derived peptides.

Precision Synthesis of Alternating Copolymers via Ring-Opening Polymerization of 1-Substituted Cyclobutenes

Investigation of complex molecular systems depends on our ability to correlate physical measurements with molecular structure. Interpretation of studies that rely on synthetic polymers is generally limited by their heterogeneity; i.e., there is variation in the number and arrangement of the monomeric building blocks that have been incorporated. Superior physics and biology can be performed with materials and tools that exert precise control over the sequence and spacing of functional groups. An interest in functional ligands combined with a desire to control the orientation and stereochemistry of monomer incorporation led to the design of new substrates for ruthenium-catalyzed ring-opening metathesis polymerization (ROMP). We discovered that ROMP of cyclobutene-1-carboxamides provides uniform and translationally invariant polymers. In contrast, cyclobutene-1-carboxylate esters ring open upon treatment with ruthenium catalyst, but they are stable to homopolymerization. However, in the presence of cyclohexene monomers, they undergo alternating ROMP (AROMP or alt-ROMP) to give copolymers with a precisely controlled sequence. The alternating cyclobutene ester/cyclohexene pair provides access to functional group spacing larger than is possible with homopolymers. This can be desirable; for example, polymers with a regular 8-10 Å backbone spacing of cationic charge and with between four and eight cationic groups were the most effective antibacterial agents and had low cytotoxicity. Moreover, the AROMP chemistry allows alternation of two functional moieties: one associated with the cyclohexene and one attached to the cyclobutene. In the case of antibacterial copolymers, the alternating chemistry allowed variation of hydrophobicity via the cyclohexene while maintaining a constant cation spacing through the cyclobutene. In the case of copolymers that bear donor and acceptor groups, strict alternation of the groups increased intrachain charge transfer. Like cyclobutene-1-carboxylate esters, bicyclo[4.2.0]oct-7-ene-7-carboxylate esters ring open upon treatment with ruthenium catalyst and undergo ring opening cross-metathesis with cyclohexene to form alternating copolymers. The corresponding bicyclo[4.2.0]oct-7-ene-7-carboxyamides isomerize to the bicyclo[4.2.0]oct-1(8)-ene-8-carboxamides before they can ring open. However, the isomerized amides undergo ruthenium-catalyzed ring opening metathesis and rapidly AROMP with cyclohexene. Our alternating copolymer systems allow functionality to be placed along a polymer chain with larger than typical spacing. We have used both homopolymers and alternating copolymers for defining the functional group density required for targeting a cell surface and for the exploration of functional group positioning within a polymer chain. These polymer systems provide access to new materials with previously inaccessible types of nanoscale structures.

Polyacrylamide backbones for polyvalent bioconjugates using “post-click” chemistry

This paper reports the synthesis and application of acrylamide-type neoglycoconjugates interacting with practical targets.

Designing multivalent probes for tunable superselective targeting

Specific targeting is common in biology and is a key challenge in nanomedicine. It was recently demonstrated that multivalent probes can selectively target surfaces with a defined density of surface binding sites. Here we show, using a combination of experiments and simulations on multivalent polymers, that such "superselective" binding can be tuned through the design of the multivalent probe, to target a desired density of binding sites. We develop an analytical model that provides simple yet quantitative predictions to tune the polymer's superselective binding properties by its molecular characteristics such as size, valency, and affinity. This work opens up a route toward the rational design of multivalent probes with defined superselective targeting properties for practical applications, and provides mechanistic insight into the regulation of multivalent interactions in biology. To illustrate this, we show how the superselective targeting of the extracellular matrix polysaccharide hyaluronan to its main cell surface receptor CD44 is controlled by the affinity of individual CD44-hyaluronan interactions.