AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor.

Protein-protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays or AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold-Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.

AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor.

Protein-protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays and AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.

Versatile Microfluidics Separation of Colloids by Combining External Flow with Light-Induced Chemical Activity.

Separation of particles by size, morphology, or material identity is of paramount importance in fields such as filtration or bioanalytics. Up to now separation of particles distinguished solely by surface properties or bulk/surface morphology remains a very challenging process. Here a combination of pressure-driven microfluidic flow and local self-phoresis/osmosis are proposed via the light-induced chemical activity of a photoactive azobenzene-surfactant solution. This process induces a vertical displacement of the sedimented particles, which depends on their size and surface properties . Consequently, different colloidal components experience different regions of the ambient microfluidic shear flow. Accordingly, a simple, versatile method for the separation of such can be achieved by elution times in a sense of particle chromatography. The concepts are illustrated via experimental studies, complemented by theoretical analysis, which include the separation of bulk-porous from bulk-compact colloidal particles and the separation of particles distinguished solely by slight differences in their surface physico-chemical properties.

Solid-Phase Microcontact Printing for Precise Patterning of Rough Surfaces: Using Polymer-Tethered Elastomeric Stamps for the Transfer of Reactive Silanes.

We present a microcontact printing (µCP) routine suitable to introduce defined (sub-) microscale patterns on surface substrates exhibiting a high capillary activity and receptive to a silane-based chemistry. This is achieved by transferring functional trivalent alkoxysilanes, such as (3-aminopropyl)-triethoxysilane (APTES) as a low-molecular weight ink via reversible covalent attachment to polymer brushes grafted from elastomeric polydimethylsiloxane (PDMS) stamps. The brushes consist of poly{N-[tris(hydroxymethyl)-methyl]acrylamide} (PTrisAAm) synthesized by reversible addition-fragmentation chain-transfer (RAFT)-polymerization and used for immobilization of the alkoxysilane-based ink by substituting the alkoxy moieties with polymer-bound hydroxyl groups. Upon physical contact of the silane-carrying polymers with surfaces, the conjugated silane transfers to the substrate, thus completely suppressing ink-flow and, in turn, maximizing printing accuracy even for otherwise not addressable substrate topographies. We provide a concisely conducted investigation on polymer brush formation using atomic force microscopy (AFM) and ellipsometry as well as ink immobilization utilizing two-dimensional proton nuclear Overhauser enhancement spectroscopy (1H-1H-NOESY-NMR). We analyze the µCP process by printing onto Si-wafers and show how even distinctively rough surfaces can be addressed, which otherwise represent particularly challenging substrates.

Impact of Multivalence and Self-Assembly in the Design of Polymeric Antimicrobial Peptide Mimics.

Antimicrobial resistance is an increasingly serious challenge for public health and could result in dramatic negative consequences for the health care sector during the next decades. To solve this problem, antibacterial materials that are unsusceptible toward the development of bacterial resistance are a promising branch of research. In this work, a new type of polymeric antimicrobial peptide mimic featuring a bottlebrush architecture is developed, using a combination of reversible addition-fragmentation chain transfer (RAFT) polymerization and ring-opening metathesis polymerization (ROMP). This approach enables multivalent presentation of antimicrobial subunits resulting in improved bioactivity and an increased hemocompatibility, boosting the selectivity of these materials for bacterial cells. Direct probing of membrane integrity of treated bacteria revealed highly potent membrane disruption caused by bottlebrush copolymers. Multivalent bottlebrush copolymers clearly outperformed their linear equivalents regarding bioactivity and selectivity. The effect of segmentation of cationic and hydrophobic subunits within bottle brushes was probed using heterograft copolymers. These materials were found to self-assemble under physiological conditions, which reduced their antibacterial activity, highlighting the importance of precise structural control for such applications. To the best of our knowledge, this is the first example to demonstrate the positive impact of multivalence, generated by a bottlebrush topology in polymeric antimicrobial peptide mimics, making these polymers a highly promising material platform for the design of new bactericidal systems.

Shaping Metallic Nanolattices: Design by Microcontact Printing from Wrinkled Stamps.

A method for the fabrication of well-defined metallic nanostructures is presented here in a simple and straightforward fashion. As an alternative to lithographic techniques, this routine employs microcontact printing utilizing wrinkled stamps, which are prepared from polydimethylsiloxane (PDMS), and includes the formation of hydrophobic stripe patterns on a substrate via the transfer of oligomeric PDMS. Subsequent backfilling of the interspaces between these stripes with a hydroxyl-functional poly(2-vinyl pyridine) then provides the basic pattern for the deposition of citrate-stabilized gold nanoparticles promoted by electrostatic interaction. The resulting metallic nanostripes can be further customized by peeling off particles in a second microcontact printing step, which employs poly(ethylene imine) surface-decorated wrinkled stamps, to form nanolattices. Due to the independent adjustability of the period dimensions of the wrinkled stamps and stamp orientation with respect to the substrate, particle arrays on the (sub)micro-scale with various kinds of geometries are accessible in a straightforward fashion. This work provides an alternative, cost-effective, and scalable surface-patterning technique to fabricate nanolattice structures applicable to multiple types of functional nanoparticles. Being a top-down method, this process could be readily implemented into, e.g., the fabrication of optical and sensing devices on a large scale.

Tailoring patches on particles: a modified microcontact printing routine using polymer-functionalised stamps.

Herein, we report a modified microcontact printing (µCP) routine suitable to introduce particle patches of a low molecular weight ink (LMWI) on porous SiO2 microparticles. Thereby, patch precision could be significantly improved by utilising stamps which have been surface-functionalised with grafted polymers. This improvement was evaluated by a profound software-assisted statistical analysis.

Droplets, Evaporation and a Superhydrophobic Surface: Simple Tools for Guiding Colloidal Particles into Complex Materials.

The formation of complexly structured and shaped supraparticles can be achieved by evaporation-induced self-assembly (EISA) starting from colloidal dispersions deposited on a solid surface; often a superhydrophobic one. This versatile and interesting approach allows for generating rather complex particles with corresponding functionality in a simple and scalable fashion. The versatility is based on the aspect that basically one can employ an endless number of combinations of components in the colloidal starting solution. In addition, the structure and properties of the prepared supraparticles may be modified by appropriately controlling the evaporation process, e.g., by external parameters. In this review, we focus on controlling the shape and internal structure of such supraparticles, as well as imparted functionalities, which for instance could be catalytic, optical or electronic properties. The catalytic properties can also result in self-propelling (supra-)particles. Quite a number of experimental investigations have been performed in this field, which are compared in this review and systematically explained.

Understanding the Formation of Anisometric Supraparticles: A Mechanistic Look Inside Droplets Drying on a Superhydrophobic Surface.

Evaporating drops of nanoparticle suspensions on superhydrophobic surfaces can give anisotropic superaparticles. Previous studies implied the formation of a stiff shell that collapses, but the exact mechanism leading to anisotropy was unclear so far. Here we report on a new experiment using confocal laser scanning microscopy for a detailed characterization of particle formation from droplets of aqueous colloidal dispersions on superhydrophobic surfaces. In a customized setup, we investigated droplets of fumed silica suspensions using two different fluorescent dyes for independently marking silica and the water phase. Taking advantage of interfacial reflection, we locate the drop-air interface and extract normalized time-resolved intensity profiles for dyed silica throughout the drying process. Using comprehensive image analysis we observe and quantify shell-like interfacial particle accumulation arising from droplet evaporation. This leads to a buildup of a stiff fumed silica mantle of ∼20 µm thickness that causes deformation of the droplet throughout further shrinkage, consequently leading to the formation of solid anisometric fumed silica particles.

Controlling the shape of evaporating droplets by ionic strength: formation of highly anisometric silica supraparticles.

Anisometric silica supraparticles are produced by a simple process of evaporation of sessile droplets containing fumed silica deposited on a superhydrophobic substrate. The shape of the supraparticles is directly controlled by the salt (NaCl) concentration, becoming anisometric beyond a threshold concentration, as quantified by light microscopy. This process is easily extended to supraparticles containing further functional colloidal components.