AI is a viable alternative to high throughput screening: a 318-target study

High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.

Revealing Deformation Mechanisms in Polymer-Grafted Thermoplastic Elastomers via In Situ Small-Angle X-ray Scattering

The tunable properties of thermoplastic elastomers (TPEs), through polymer chemistry manipulations, enable these technologically critical materials to be employed in a broad range of applications. The need to "dial-in" the mechanical properties and responses of TPEs generally requires the design and synthesis of new macromolecules. In these designs, TPEs with nonlinear macromolecular architectures outperform the mechanical properties of their linear copolymer counterparts, but the differences in the deformation mechanism providing enhanced performance are unknown. Here, in situ small-angle X-ray scattering (SAXS) measurements during uniaxial extension reveal distinct deformation mechanisms between a commercially available linear poly(styrene)-poly(butadiene)-poly(styrene) (SBS) triblock copolymer and the grafted SBS version containing grafted poly(styrene) (PS) chains from the poly(butadiene) (PBD) midblock. The neat SBS (φSBS = 100%) sample deforms congruently with the macroscopic dimensions, with the domain spacing between spheres increasing and decreasing along and transverse to the stretch direction, respectively. At high extensions, end segment pullout from the PS-rich domains is detected, which is indicated by a disordering of SBS. Conversely, the PS-grafted SBS that is 30 vol % SBS and 70% styrene (φSBS = 30%) exhibits a lamellar morphology, and in situ SAXS measurements reveal an unexpected deformation mechanism. During deformation, there are two simultaneous processes: significant lamellar domain rearrangement to preferentially orient the lamellae planes parallel to the stretch direction and crazing. The samples whiten at high strains as expected for crazing, which corresponds with the emergence of features in the 2D SAXS pattern during stretching consistent with fibril-like structures that bridge the voids in crazes. The significant domain rearrangement in the grafted copolymers is attributed to the new junctions formed across multiple PS domains by the grafting of a single chain. The in situ SAXS measurements provide insights into the enhanced mechanical properties of grafted copolymers that arise through improved physical cross-linking that leads to nanostructure domain reorientation for self-reinforcement and craze formation where fibrils help to strengthen the polymer.

Small molecule targeting of transcription-replication conflict for selective chemotherapy

Targeting transcription replication conflicts, a major source of endogenous DNA double-stranded breaks and genomic instability could have important anticancer therapeutic implications. Proliferating cell nuclear antigen (PCNA) is critical to DNA replication and repair processes. Through a rational drug design approach, we identified a small molecule PCNA inhibitor, AOH1996, which selectively kills cancer cells. AOH1996 enhances the interaction between PCNA and the largest subunit of RNA polymerase II, RPB1, and dissociates PCNA from actively transcribed chromatin regions, while inducing DNA double-stranded breaks in a transcription-dependent manner. Attenuation of RPB1 interaction with PCNA, by a point mutation in RPB1's PCNA-binding region, confers resistance to AOH1996. Orally administrable and metabolically stable, AOH1996 suppresses tumor growth as a monotherapy or as a combination treatment but causes no discernable side effects. Inhibitors of transcription replication conflict resolution may provide a new and unique therapeutic avenue for exploiting this cancer-selective vulnerability.

Therapeutic Targeting of DNA Replication Stress in Cancer

This article reviews the currently used therapeutic strategies to target DNA replication stress for cancer treatment in the clinic, highlighting their effectiveness and limitations due to toxicity and drug resistance. Cancer cells experience enhanced spontaneous DNA damage due to compromised DNA replication machinery, elevated levels of reactive oxygen species, loss of tumor suppressor genes, and/or constitutive activation of oncogenes. Consequently, these cells are addicted to DNA damage response signaling pathways and repair machinery to maintain genome stability and support survival and proliferation. Chemotherapeutic drugs exploit this genetic instability by inducing additional DNA damage to overwhelm the repair system in cancer cells. However, the clinical use of DNA-damaging agents is limited by their toxicity and drug resistance often arises. To address these issues, the article discusses a potential strategy to target the cancer-associated isoform of proliferating cell nuclear antigen (caPCNA), which plays a central role in the DNA replication and damage response network. Small molecule and peptide agents that specifically target caPCNA can selectively target cancer cells without significant toxicity to normal cells or experimental animals.

Nanostructured block copolymer muscles

High-performance actuating materials are necessary for advances in robotics, prosthetics and smart clothing. Here we report a class of fibre actuators that combine solution-phase block copolymer self-assembly and strain-programmed crystallization. The actuators consist of highly aligned nanoscale structures with alternating crystalline and amorphous domains, resembling the ordered and striated pattern of mammalian skeletal muscle. The reported nanostructured block copolymer muscles excel in several aspects compared with current actuators, including efficiency (75.5%), actuation strain (80%) and mechanical properties (for example, strain-at-break of up to 900% and toughness of up to 121.2 MJ m^-3). The fibres exhibit on/off rotary actuation with a peak rotational speed of 450 r.p.m. Furthermore, the reported fibres demonstrate multi-trigger actuation (heat and hydration), offering switchable mechanical properties and various operating modes. The versatility and recyclability of the polymer fibres, combined with the facile fabrication method, opens new avenues for creating multifunctional and recyclable actuators using block copolymers.

Investigating the morphological transitions in an associative surfactant ternary system

Associative surfactants systems involving polar oils have recently been shown to stabilize immiscible liquids by forming nanostructures at the liquid interface and have been used to print soft materials. Although these associating surfactant systems show great promise for creating nanostructured soft materials, a fundamental understanding of the self-assembly process is still unknown. In this study, a ternary phase diagram for a system of cationic surfactant cetylpyridinium chloride monohydrate (CPCl), a polar oil (oleic acid), and water is established using experiment and simulation, to study the equilibrium phase behavior. A combination of visual inspection, small-angle X-ray scattering (SAXS), and rheological measurements was employed to establish the phase behavior and properties of the self-assembled materials. Dissipative particle dynamics (DPD) is used to simulate the formation of the morphologies in this system and support the experimental results. The ternary phase diagram obtained from the simulations agrees with the experimental results, indicating the robustness of the computational simulation as a supplement to the mesoscale experimental systems. We observe that morphological transitions (e.g., micelle-to-bilayer and vesicle-to-lamellar) are in agreement between experiments and simulations across the ternary diagram. DPD simulations correctly predict that associative surfactant systems form new nanoscale phases due to the co-assembly of the components. The established ternary phase diagram and the DPD model pave the way towards predicting and controlling the formation of different mesostructures like lamellar or vesicles, opening new avenues to tailor and synthesize desired morphologies for applications related to liquid-in-liquid 3D printing.

Effect of chemical substituents attached to the zwitterion cation on dielectric constant

Materials with high dielectric constant, ε_s, are desirable in a wide range of applications including energy storage and actuators. Recently, zwitterionic liquids have been reported to have the largest ε_s of any liquid and, thus, have the potential to replace inorganic fillers to modulate the material ε_s. Although the large ε_s for zwitterionic liquids is attributed to their large molecular dipole, the role of chemical substituents attached to the zwitterion cation on ε_s is not fully understood, which is necessary to enhance the performance of soft energy materials. Here, we report the impact of zwitterionic liquid cation chemical substituents on ε_s (50 < ε_s < 300 at room temperature). Dielectric relaxation spectroscopy reveals that molecular reorientation is the main contributor to the high ε_s. The low Kirkwood factor g calculated for zwitterionic liquids (e.g., 0.1-0.2) suggests the tendency for the antiparallel zwitterion dipole alignment expected from the strong electrostatic intermolecular interactions. With octyl cation substituents, the g is decreased due to the formation of hydrophobic-rich domains that restrict molecular reorientation under applied electric fields. In contrast, when zwitterion cations are functionalized with ethylene oxide (EO) segments, g increases due to the EO segments interacting with the cations, allowing more zwitterion rotation in response to the applied field. The reported results suggest that high ε_s zwitterionic liquids require a large molecular dipole, compositionally homogeneous liquids (e.g., no aggregation), a maximized zwitterion number density, and a high g, which is achievable by incorporating polar chemical substituents onto the zwitterion cations.

Current status and future directions of self-assembled block copolymer membranes for molecular separations

One of the most efficient and promising separation alternatives to thermal methods such as distillation is the use of polymeric membranes that separate mixtures based on molecular size or chemical affinity. Self-assembled block copolymer membranes have gained considerable attention within the membrane field due to precise control over nanoscale structure, pore size, and chemical versatility. Despite the rapid progress and excitement, a significant hurdle in using block copolymer membranes for nanometer and sub-nanometer separations such as nanofiltration and reverse osmosis is the lower limit on domain size features. Strategies such as polymer post-functionalization, self-assembly of oligomers, liquid crystals, and random copolymers, or incorporation of artificial/natural channels within block copolymer materials are future directions with the potential to overcome current limitations with respect to separation size.

Zwitterions Raise the Dielectric Constant of Soft Materials

Materials exhibiting high dielectric constants (ϵ_{s}) are critical for energy storage and actuators. A successful approach to increase ϵ_{s} is to incorporate polar additives (with high ϵ_{s}) but controlling the resulting dispersion state is difficult. Here, we show that significant ϵ_{s} increases are realized by adding zwitterions, which are small molecules with a cation and an anion separated by covalent bonds. The increase in ϵ_{s} with zwitterion addition is attributed to the large molecular dipole of zwitterions, ranging from 35 to 41 D, as experimentally quantified and confirmed using density functional theory. At elevated zwitterion concentration in an ethylene glycol medium, there is a nonlinear increase of ϵ_{s} that eventually saturates due to the strong Coulombic interactions between zwitterions. The presented work provides a fundamental molecular understanding of why zwitterions are effective additives in boosting ϵ_{s} in soft materials.

Lewis Adduct-Induced Phase Transitions in Polymer/Solvent Mixtures

Functionalization-induced phase transitions in polymer systems in which a postpolymerization reaction drives polymers to organize into colloidal aggregates are a versatile method to create nanoscale structures with applications related to biomedicine and nanoreactors. Current functionalization methods to stimulate polymer self-assembly are based on covalent bond formation. Therefore, there is a need to explore alternative reactions that result in noncovalent bond formation. Here, we demonstrate that when the Lewis acid, tris(pentafluorophenyl) borane (BCF), is added to a solution containing poly(4-diphenylphosphino styrene) (PDPPS), the system will either macrophase-separate or form micelles if PDPPS is a homopolymer or a block in a copolymer, respectively. The Lewis adduct-induced phase transition is hypothesized to result from the favorable interaction between the PDPPS and BCF, which results in a negative interaction parameter (χ). A modified Flory-Huggins model was used to determine the predicted phase behavior for a ternary system composed of a polymer, a solvent, and a small molecule. The model indicates that there is a demixing region (i.e., macrophase separation) when the polymer and small molecule have favorable interactions (e.g., χ < 0) and that the phase separation region coincides well with the experimentally determined two-phase region for mixtures containing PDPPS, BCF, and toluene. The work presented here highlights that Lewis adduct-induced phase separation is a new approach to functionalization-induced self-assembly (FISA) and that ternary mixtures will undergo phase separation if two of the components exhibit a sufficiently negative χ.

Influence of Hydrotropes on the Solubilities and Diffusivities of Redox-Active Organic Compounds for Aqueous Flow Batteries

In this study, we explored the extent to which hydrotropes can be used to increase the aqueous solubilities of redox-active compounds previously used in flow batteries. We measured how five hydrotropes influenced the solubilities of five redox-active compounds already soluble in aqueous electrolytes (≥0.5 M). The solubilities of the compounds varied as a function of hydrotrope type and concentration, with larger solubility changes observed at higher hydrotrope concentrations. 4-OH-TEMPO underwent the largest solubility increase (1.18 ± 0.04 to 1.99 ± 0.12 M) in 20 weight percent sodium xylene sulfonate. The presence of a hydrotrope in solution decreased the diffusion coefficients of 4-OH-TEMPO and 4,5-dihydroxy-1,3-benzenedisulfonate, which was likely due to the increased solution viscosity as opposed to a specific hydrotrope-solute interaction because the hydrotropes did not alter their molecules' hydraulic radii. The standard rate constants and formal potentials of both 4-OH-TEMPO and 4,5-dihydroxy-1,3-benzenedisulfonate remained largely unchanged in the presence of a hydrotrope. The results suggest that using hydrotropes may be a feasible strategy for increasing the solubilities of redox-active compounds in aqueous flow batteries without substantially altering their electrochemical properties.

Cocrystalline Polymer Films Exhibiting Second-Order Nonlinear Optical Properties

Tailored polymer materials exhibiting high-glass transition temperatures, cross-linked matrices, and/or strong intermolecular interactions containing electric-field poled nonlinear optical (NLO) chromophores are promising materials for applications in optical telecommunication, high-performance computing, and data transmission. Although the current design parameters have led to significant advances in NLO materials, we introduce an alternative, yet highly effective, approach in which a NLO chromophore is cocrystallized with a polymer, forming a noncentrosymmetric hybrid host-guest complex. Specifically, poly(ethylene oxide) (PEO) and 2-chloro-4-nitroaniline (CNA) will cocrystallize and exhibit second harmonic generation (SHG) activity due to the formation of a noncentrosymmetric cocrystalline unit cell where the chromophore exhibits acentric alignment. Furthermore, the hybrid PEO/CNA films exhibit interesting SHG activity at elevated temperature in which SHG intensity decreases to zero when the cocrystal orientation randomizes due to sample melting. Aligning and maintaining a cocrystalline domain orientation via the formation of hybrid host-guest complexes, while imparting SHG properties, is an innovative approach for creating materials exhibiting SHG properties.

Fabricating Robust Constructs with Internal Phase Nanostructures via Liquid-in-Liquid 3D Printing

The ability to print soft materials into predefined architectures with programmable nanostructures and mechanical properties is a necessary requirement for creating synthetic biomaterials that mimic living tissues. However, the low viscosity of common materials and lack of required mechanical properties in the final product present an obstacle to the use of traditional additive manufacturing approaches. Here, a new liquid-in-liquid 3D printing approach is used to successfully fabricate constructs with internal nanostructures using in situ self-assembly during the extrusion of an aqueous solution containing surfactant and photocurable polymer into a stabilizing polar oil bath. Subsequent photopolymerization preserves the nanostructures created due to surfactant self-assembly at the immiscible liquid-liquid interface, which is confirmed by small-angle X-ray scattering. Mechanical properties of the photopolymerized prints are shown to be tunable based on constituent components of the aqueous solution. The reported 3D printing approach expands the range of low-viscosity materials that can be used in 3D printing, and enables robust constructs production with internal nanostructures and spatially defined features. The reported approach has broad applications in regenerative medicine by providing a platform to print self-assembling biomaterials into complex tissue mimics where internal supramolecular structures and their functionality control biological processes, similar to natural extracellular matrices.

Investigating Nanoparticle Organization in Polymer Matrices during Reaction-Induced Phase Transitions and Material Processing

Controlling nanoparticle organization in polymer matrices has been and is still a long-standing issue and directly impacts the performance of the materials. In the majority of instances, simply mixing nanoparticles and polymers leads to macroscale aggregation, resulting in deleterious effects. An alternative method to physically blending independent components such as nanoparticle and polymers is to conduct polymerizations in one-phase monomer/nanoparticle mixtures. Here, we report on the mechanism of nanoparticle aggregation in hybrid materials in which gold nanoparticles are initially homogeneously dispersed in a monomer mixture and then undergo a two-step aggregation process during polymerization and material processing. Specifically, oleylamine-functionalized gold nanoparticles (AuNP) are first synthesized in a methyl methacrylate (MMA) solution and then subsequently polymerized by using a free radical polymerization initiated with azobis(isobutyronitrile) (AIBN) to create hybrid AuNP and poly(methyl methacrylate) (PMMA) materials. The resulting products are easily pressed to obtain bulk films with nanoparticle organization defined as either well-dispersed or aggregated. Polymerizations are performed at various temperatures (T) and MMA volume fractions (Φ_MMA) to systematically influence the final nanoparticle dispersion state. During the polymerization of MMA and subsequent material processing, the initially homogeneous AuNP/MMA mixture undergoes macrophase separation between PMMA and oleylamine during the polymerization, yet the AuNP are dispersed in the oleylamine phase. The nanoparticles then aggregate within the oleylamine phase when the materials are processed via vacuum drying and pressing. Nanoparticle organization is tracked throughout the polymerization and processing steps by using a combination of transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS). The resulting dispersion state of AuNPs in PMMA bulk films is ultimately dictated by the thermodynamics of mixing between the PMMA and oleylamine phases, but the mechanism of nanoparticle aggregation occurs in two steps that correspond to the polymerization and processing of the materials. Flory-Huggins mixing theory is used to support the PMMA and oleylamine phase separation. The reported results highlight how the integration of nonequilibrium processing and mean-field approximations reveal nanoparticle aggregation in hybrid materials synthesized by using reaction-induced phase transitions.

Abstract 1269: Pharmacological targeting of transcription-replication conflict leads to anti-cancer efficacy with minimal side effects in preclinical models

Unchecked growth of cancer cells places simultaneous demands on DNA replication and transcription. Targeting the transcription-replication conflict (TRC), a major source of genome instability, could have important therapeutic implications. However, testing this hypothesis is difficult without agents directly targeting TRC. Here, we report a small molecule ligand (AOH1996) of the replisome component PCNA, which stabilizes interaction between PCNA and the large subunit (rpb1) of RNA polymerase II through the APIM motif, resulting in proteasome-dependent degradation of rpb1 and lethal DNA damages. Orally administrable, AOH1996 suppresses tumor growth without discernable toxicity at more than 10 time the compound's effective dose. In addition, AOH1996 works synergistically with known DNA damage agents to kill cancer cells. These results reveal TRC as cancer-selective vulnerability and demonstrated the therapeutic potential of AOH1996.

Citation Format: Long Gu, Caroline Li, Robert Lingeman, Robert J. Hickey, Linda H. Malkas. Pharmacological targeting of transcription-replication conflict leads to anti-cancer efficacy with minimal side effects in preclinical models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1269.

Controlling nanostructure and mechanical properties in triblock copolymer/monomer blends via reaction-induced phase transitions

Thermoplastic elastomers based on ABA triblock copolymers are typically limited in modulus and strength due to crack propagation within the brittle regions when the hard end-block composition favors morphologies that exhibit connected domains. Increasing the threshold end-block composition to achieve enhanced mechanical performance is possible by increasing the number of junctions or bridging points per chain, but these copolymer characteristics also tend to increase the complexity of the synthesis. Here, we report an in situ polymerization method to successfully increase the number of effective junctions per chain through grafting of poly(styrene) (PS) to a commercial thermoplastic elastomer, poly(styrene)-poly(butadiene)-poly(styrene) (SBS). The strategy described here transforms a linear SBS triblock copolymer-styrene mixture into a linear-comb-linear architecture in which poly(styrene) (PS) grafts from the mid-poly(butadiene) (PBD) block during the polymerization of styrene. Through systematic variation in the initial SBS/styrene content, nanostructural transitions from disordered spheres to lamellar through reaction-induced phase transitions (RIPT) were identified as the styrene content increased. Surprisingly, maximum mechanical performance (Young's modulus, tensile strength, and elongation at break) was obtained with samples exhibiting lamellar nanostructures, corresponding to overall PS contents of 61-77 wt% PS (including the original PS in SBS). The PS grafting from the PBD block increases the modulus and the strength of the thermoplastic elastomer while preventing brittle fracture due to the greater number of junctions afforded by the PS grafts. The work presented here demonstrates the use of RIPT to transform standard SBS materials into polymer systems with enhanced mechanical properties.

Nanoparticle-Induced Self-Assembly of Block Copolymers into Nanoporous Films at the Air-Water Interface

Herein, we report the cooperative self-assembly of nanoparticles and block copolymers at the air-water interface, which can generate highly uniform and readily transferable composite films with tunable nanoscale architecture and functionalities. Interestingly, the incorporation of nanoparticles significantly affects the self-assembly of block copolymers at the interface. The nanoparticle-induced morphology change occurs through distinct mechanisms depending on the volume fraction of the hydrophobic block. For block copolymers with a relatively small hydrophobic volume fraction, the morphology transition occurs through the nanoparticle-induced swelling of a selective block. When the hydrophobic volume fraction is large enough, added nanoparticles promote the breath figure assembly, which generates uniform honeycomb-like porous structures with unusual nanoscale periodicity. This approach is generally applicable to various types of nanoparticles, constituting a simple one-step method to porous thin films with various functionalities.

Molecular Targeting of Cancer-Associated PCNA Interactions in Pancreatic Ductal Adenocarcinoma Using a Cell-Penetrating Peptide

Pancreatic ductal adenocarcinoma is a particularly difficult cancer to treat due to a lack of effective screening or treatment. Pancreatic cancer cells exhibit high proliferating cell nuclear antigen (PCNA) expression, which is associated with poor prognosis. PCNA, an important nuclear DNA replication and repair protein, regulates a myriad of proteins via the interdomain connector loop. Within this region, amino acids 126–133 are critical for PCNA interactions in cancer cells. Here, we investigate the ability of a decoy cell-penetrating peptide, R9-caPeptide, that mimics the interdomain connector loop region of PCNA to disrupt PCNA-protein interactions in pancreatic cancer cells. Our data suggest that R9-caPeptide causes dose-dependent toxicity in a panel of pancreatic cancer cell lines by inhibiting DNA replication fork progression and PCNA-regulated DNA repair, ultimately causing lethal DNA damage. Overall, these studies lay the foundation for novel therapeutic strategies that target PCNA in pancreatic cancer.

Rapid fabrication of precise high-throughput filters from membrane protein nanosheets

Biological membranes are ideal for separations as they provide high permeability while maintaining high solute selectivity due to the presence of specialized membrane protein (MP) channels. However, successful integration of MPs into manufactured membranes has remained a significant challenge. Here, we demonstrate a two-hour organic solvent method to develop 2D crystals and nanosheets of highly packed pore-forming MPs in block copolymers (BCPs). We then integrate these hybrid materials into scalable MP-BCP biomimetic membranes. These MP-BCP nanosheet membranes maintain the molecular selectivity of the three types of β-barrel MP channels used, with pore sizes of 0.8 nm, 1.3 nm, and 1.5 nm. These biomimetic membranes demonstrate water permeability that is 20-1,000 times greater than that of commercial membranes and 1.5-45 times greater than that of the latest research membranes with comparable molecular exclusion ratings. This approach could provide high performance alternatives in the challenging sub-nanometre to few-nanometre size range.

Author Correction: Artificial water channels enable fast and selective water permeation through water-wire networks

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Influence of block sequence on the colloidal self-assembly of poly(norbornene)-block-poly(ethylene oxide) amphiphilic block polymers using rapid injection processing

A facile self-assembly method, rapid injection, was used to study the self-assembly difference between AB diblock and ABA triblock copolymers.

Artificial water channels enable fast and selective water permeation through water-wire networks

Artificial water channels are synthetic molecules that aim to mimic the structural and functional features of biological water channels (aquaporins). Here we report on a cluster-forming organic nanoarchitecture, peptide-appended hybrid[4]arene (PAH[4]), as a new class of artificial water channels. Fluorescence experiments and simulations demonstrated that PAH[4]s can form, through lateral diffusion, clusters in lipid membranes that provide synergistic membrane-spanning paths for a rapid and selective water permeation through water-wire networks. Quantitative transport studies revealed that PAH[4]s can transport >109 water molecules per second per molecule, which is comparable to aquaporin water channels. The performance of these channels exceeds the upper bound limit of current desalination membranes by a factor of ~104, as illustrated by the water/NaCl permeability-selectivity trade-off curve. PAH[4]'s unique properties of a high water/solute permselectivity via cooperative water-wire formation could usher in an alternative design paradigm for permeable membrane materials in separations, energy production and barrier applications.

Abstract C067: Mechanistic study of the superior anti-cancer properties of a first-in-class small molecule targeting PCNA

Proliferating cell nuclear antigen (PCNA), through its interaction with various proteins involved in DNA synthesis, cell cycle regulation, and DNA repair, plays a central role in maintaining genome stability. We previously reported a novel cancer associated PCNA isoform (dubbed caPCNA), which was predominantly expressed in a broad range of cancer cells and tumor tissues, but not significantly in non-malignant cells. We found that the caPCNA-specific antigenic site lies between L126 and Y133, a region within the interdomain connector loop of PCNA that is known to be a major binding site for many of PCNA’s interacting proteins. A cell permeable peptide harboring the L126-Y133 sequence inhibited PCNA function in cancer cells and selectively kills cancer cells and xenograft tumors. Based on these observations, we sought small molecules targeting this peptide region of PCNA as potential broad-spectrum anti-cancer agents. Our effort led to a drug candidate, AOH1996, which selectively kills a broad range of cancer cells at high nanomolar concentrations, but is not associated with significant toxicity to non-malignant cells. It also works synergistically with DNA damaging chemotherapeutic drugs, such as cisplatin and irinotecan, to selectively kill cancer cells. This compound is orally available to animals and suppresses tumor growth in a dosage form compatible to clinical applications. Importantly, it doesn’t cause significant toxicity at 2.5 times its effective dose. Mechanistically, AOH1996 competes with T3, a known PCNA ligand, for binding to PCNA. However, the mechanism by which AOH1996 exerts its effect on cancer cells may not be identical to what have been reported for the T3 analogs. In particular, we found that AOH1996 interferes with the association of PCNA and its binding proteins, leading to DNA replication stress, blockade of homologous recombination-mediated DNA repair, and induction of apoptosis in cancer cells. These findings demonstrated the potential of this compound as a novel therapeutic agent warranting clinical investigation for cancer treatment. We have started planning a phase 1 clinical study for this compound.

Citation Format: Long Gu, Min Li, Robert Lingeman, Robert J Hickey, Yilun Liu, Linda H Malkas. Mechanistic study of the superior anti-cancer properties of a first-in-class small molecule targeting PCNA [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C067. doi:10.1158/1535-7163.TARG-19-C067

Solvent-non-solvent rapid-injection for preparing nanostructured materials from micelles to hydrogels

Due to their distinctive molecular architecture, ABA triblock copolymers will undergo specific self-assembly processes into various nanostructures upon introduction into a B-block selective solvent. Although much of the focus in ABA triblock copolymer self-assembly has been on equilibrium nanostructures, little attention has been paid to the guiding principles of nanostructure formation during non-equilibrium processing conditions. Here we report a universal and quantitative method for fabricating and controlling ABA triblock copolymer hierarchical structures using solvent-non-solvent rapid-injection processing. Plasmonic nanocomposite hydrogels containing gold nanoparticles and hierarchically-ordered hydrogels exhibiting structural color can be assembled within one minute using this rapid-injection technique. Surprisingly, the rapid-injection hydrogels display superior mechanical properties compared with those of conventional ABA hydrogels. This work will allow for translation into technologically relevant areas such as drug delivery, tissue engineering, regenerative medicine, and soft robotics, in which structure and mechanical property precision are essential.

Creating cross-linked lamellar block copolymer supporting layers for biomimetic membranes

The long-standing goal in membrane development is creating materials with superior transport properties, including both high flux and high selectivity. These properties are common in biological membranes, and thus mimicking nature is a promising strategy towards improved membrane design. In previous studies, we have shown that artificial water channels can have excellent water transport abilities that are comparable to biological water channel proteins, aquaporins. In this study, we propose a strategy for incorporation of artificial channels that mimic biological channels into stable polymeric membranes. Specifically, we synthesized an amphiphilic triblock copolymer, poly(isoprene)-block-poly(ethylene oxide)-block-poly(isoprene), which is a high molecular weight synthetic analog of naturally occurring lipids in terms of its self-assembled structure. This polymer was used to build stacked membranes composed of self-assembled lamellae. The resulting membranes resemble layers of natural lipid bilayers in living systems, but with superior mechanical properties suitable for real-world applications. The procedures used to synthesize the triblock copolymer resulted in membranes with increased stability due to the crosslinkability of the hydrophobic domains. Furthermore, the introduction of bridging hydrophilic domains leads to the preservation of the stacked membrane structure when the membrane is in contact with water, something that is challenging for diblock lamellae that tend to swell, and delaminate in aqueous solutions. This new method of membrane fabrication offers a practical model for making channel-based biomimetic membranes, which may lead to technological applications in reverse osmosis, nanofiltration, and ultrafiltration membranes.

Biomimetic Separation of Transport and Matrix Functions in Lamellar Block Copolymer Channel-Based Membranes

Cell membranes control mass, energy, and information flow to and from the cell. In the cell membrane a lipid bilayer serves as the barrier layer, with highly efficient molecular machines, membrane proteins, serving as the transport elements. In this way, highly specialized transport properties are achieved by these composite materials by segregating the matrix function from the transport function using different components. For example, cell membranes containing aquaporin proteins can transport ∼4 billion water molecules per second per aquaporin while rejecting all other molecules including salts, a feat unmatched by any synthetic system, while the impermeable lipid bilayer provides the barrier and matrix properties. True separation of functions between the matrix and the transport elements has been difficult to achieve in conventional solute separation synthetic membranes. In this study, we created membranes with distinct matrix and transport elements through designed coassembly of solvent-stable artificial (peptide-appended pillar[5]arene, PAP5) or natural (gramicidin A) model channels with block copolymers into lamellar multilayered membranes. Self-assembly of a lamellar structure from cross-linkable triblock copolymers was used as a scalable replacement for lipid bilayers, offering better stability and mechanical properties. By coassembly of channel molecules with block copolymers, we were able to synthesize nanofiltration membranes with sharp selectivity profiles as well as uncharged ion exchange membranes exhibiting ion selectivity. The developed method can be used for incorporation of different artificial and biological ion and water channels into synthetic polymer membranes. The strategy reported here could promote the construction of a range of channel-based membranes and sensors with desired properties, such as ion separations, stimuli responsiveness, and high sensitivity.

Rapid Stabilization of Immiscible Fluids using Nanostructured Interfaces via Surfactant Association

Surfactant molecules have been extensively used as emulsifying agents to stabilize immiscible fluids. Droplet stability has been shown to be increased when ordered nanoscale phases form at the interface of the two fluids due to surfactant association. Here, we report on using mixtures of a cationic surfactant and long chained alkenes with polar head groups [e.g., cetylpyridinium chloride (CPCl) and oleic acid] to create an ordered nanoscale lamellar morphology at aqueous-oil interfaces. The self-assembled nanostructure at the liquid-liquid interface was characterized using small-angle x-ray scattering, and the mechanical properties were measured using interfacial rheology. We hypothesize that the resulting lamellar morphology at the liquid-liquid interface is driven by the change in critical packing parameter when the CPCl molecules are diluted by the presence of the long chain alkenes with polar head groups, which leads to a spherical micelle-to-lamellar phase transition. The work presented here has larger implications for using nanostructured interfacial material to separate different fluids in flowing conditions for biosystems and in 3D printing technology.

Unique selectivity trends of highly permeable PAP[5] water channel membranes

Artificial water channels are a practical alternative to biological water channels for achieving exceptional water permeability and selectivity in a stable and scalable architecture. However, channel-based membrane fabrication faces critical barriers such as: (1) increasing pore density to achieve measurable gains in permeability while maintaining selectivity, and (2) scale-up to practical membrane sizes for applications. Recently, we proposed a technique to prepare channel-based membranes using peptide-appended pillar[5]arene (PAP[5]) artificial water channels, addressing the above challenges. These multi-layered PAP[5] membranes (ML-PAP[5]) showed significantly improved water permeability compared to commercial membranes with similar molecular weight cut-offs. However, due to the distinctive pore structure of water channels and the layer-by-layer architecture of the membrane, the separation behavior is unique and was still not fully understood. In this paper, two unique selectivity trends of ML-PAP[5] membranes are discussed from the perspectives of channel geometry, ion exclusion, and linear molecule transport.

Polymerization-Induced Nanostructural Transitions Driven by In Situ Polymer Grafting

Polymerization-induced structural transitions have gained attention recently due to the ease of creating and modifying nanostructured materials with controlled morphologies and length scales. Here, we show that order-order and disorder-order nanostructural transitions are possible using in situ polymer grafting from the diblock polymer, poly(styrene)-block-poly(butadiene). In our approach, we are able to control the resulting nanostructure (lamellar, hexagonally packed cylinders, and disordered spheres) by changing the initial block polymer/monomer ratio. The nanostructural transition occurs by a grafting from mechanism in which poly(styrene) chains are initiated from the poly(butadiene) block via the creation of an allylic radical, which increases the overall molecular weight and the poly(styrene) volume fraction. The work presented here highlights how the chemical process of converting standard linear diblock copolymers to grafted block polymers drives interesting and controllable polymerization-induced morphology transitions.

The Anticancer Activity of a First-in-class Small-molecule Targeting PCNA

PURPOSE

Proliferating cell nuclear antigen (PCNA) plays an essential role in regulating DNA synthesis and repair and is indispensable to cancer cell growth and survival. We previously reported a novel cancer associated PCNA isoform (dubbed caPCNA), which was ubiquitously expressed in a broad range of cancer cells and tumor tissues, but not significantly in nonmalignant cells. We found the L126-Y133 region of caPCNA is structurally altered and more accessible to protein-protein interaction. A cell-permeable peptide harboring the L126-Y133 sequence blocked PCNA interaction in cancer cells and selectively kills cancer cells and xenograft tumors. On the basis of these findings, we sought small molecules targeting this peptide region as potential broad-spectrum anticancer agents.

EXPERIMENTAL DESIGN

By computer modeling and medicinal chemistry targeting a surface pocket partly delineated by the L126-Y133 region of PCNA, we identified a potent PCNA inhibitor (AOH1160) and characterized its therapeutic properties and potential toxicity.

RESULTS

AOH1160 selectively kills many types of cancer cells at below micromolar concentrations without causing significant toxicity to a broad range of nonmalignant cells. Mechanistically, AOH1160 interferes with DNA replication, blocks homologous recombination-mediated DNA repair, and causes cell-cycle arrest. It induces apoptosis in cancer cells and sensitizes them to cisplatin treatment. AOH1160 is orally available to animals and suppresses tumor growth in a dosage form compatible to clinical applications. Importantly, it does not cause significant toxicity at 2.5 times of an effective dose.

CONCLUSIONS

These results demonstrated the favorable therapeutic properties and the potential of AOH1160 as a broad-spectrum therapeutic agent for cancer treatment.

Achieving high permeability and enhanced selectivity for Angstrom-scale separations using artificial water channel membranes

Synthetic polymer membranes, critical to diverse energy-efficient separations, are subject to permeability-selectivity trade-offs that decrease their overall efficacy. These trade-offs are due to structural variations (e.g., broad pore size distributions) in both nonporous membranes used for Angstrom-scale separations and porous membranes used for nano to micron-scale separations. Biological membranes utilize well-defined Angstrom-scale pores to provide exceptional transport properties and can be used as inspiration to overcome this trade-off. Here, we present a comprehensive demonstration of such a bioinspired approach based on pillar[5]arene artificial water channels, resulting in artificial water channel-based block copolymer membranes. These membranes have a sharp selectivity profile with a molecular weight cutoff of ~ 500 Da, a size range challenging to achieve with current membranes, while achieving a large improvement in permeability (~65 L m-2 h-1 bar-1 compared with 4-7 L m-2 h-1 bar-1) over similarly rated commercial membranes.

Comparison of Computational Algorithms for the Classification of Liver Cancer using SELDI Mass Spectrometry: A Case Study

Introduction

As an alternative to DNA microarrays, mass spectrometry based analysis of proteomic patterns has shown great potential in cancer diagnosis. The ultimate application of this technique in clinical settings relies on the advancement of the technology itself and the maturity of the computational tools used to analyze the data. A number of computational algorithms constructed on different principles are available for the classification of disease status based on proteomic patterns. Nevertheless, few studies have addressed the difference in the performance of these approaches. In this report, we describe a comparative case study on the classification accuracy of hepatocellular carcinoma based on the serum proteomic pattern generated from a Surface Enhanced Laser Desorption/Ionization (SELDI) mass spectrometer.

Methods

Nine supervised classification algorithms are implemented in R software and compared for the classification accuracy.

Results

We found that the support vector machine with radial function is preferable as a tool for classification of hepatocellular carcinoma using features in SELDI mass spectra. Among the rest of the methods, random forest and prediction analysis of microarrays have better performance. A permutation-based technique reveals that the support vector machine with a radial function seems intrinsically superior in learning from the training data since it has a lower prediction error than others when there is essentially no differential signal. On the other hand, the performance of the random forest and prediction analysis of microarrays rely on their capability of capturing the signals with substantial differentiation between groups.

Conclusions

Our finding is similar to a previous study, where classification methods based on the Matrix Assisted Laser Desorption/Ionization (MALDI) mass spectrometry are compared for the prediction accuracy of ovarian cancer. The support vector machine, random forest and prediction analysis of microarrays provide better prediction accuracy for hepatocellular carcinoma using SELDI proteomic data than six other approaches.

Conformational Asymmetry and Quasicrystal Approximants in Linear Diblock Copolymers

Small angle x-ray scattering experiments on three model low molar mass diblock copolymer systems containing minority polylactide and majority hydrocarbon blocks demonstrate that conformational asymmetry stabilizes the Frank-Kasper σ phase. Differences in block flexibility compete with space filling at constant density inducing the formation of polyhedral shaped particles that assemble into this low symmetry ordered state with local tetrahedral coordination. These results confirm predictions from self-consistent field theory that establish the origins of symmetry breaking in the ordering of block polymer melts subjected to compositional and conformational asymmetry.

Shape-controlled syntheses of metal oxide nanoparticles by the introduction of rare-earth metals

Here, we report the size- and shape-controlled synthesis of metal oxide nanoparticles through the introduction of rare-earth metals. The addition of gadolinium oleate in the synthesis of iron oxide nanoparticles induced sphere-to-cube shape changes of nanoparticles and generated iron oxide nanocubes coated with gadolinium. Based on experimental investigations and density functional theory (DFT) calculations, we attribute the shape change to the facet-selective binding of undecomposed gadolinium oleates. While many previous studies on the shape-controlled syntheses of nanoparticles rely on the stabilization of specific crystal facets by anionic surfactants or their decomposition products, this study shows that the interaction between growing transition metal oxide nanoparticles and rare-earth metal complexes can be used as a robust new mechanism for shape-controlled syntheses. Indeed, we demonstrated that this approach was applicable to other transition metal oxide nanoparticles (i.e., manganese oxide and manganese ferrite) and rare earth metals (i.e., gadolinium, europium, and cerium). This study also demonstrates that the nature of metal-ligand bonding can play an important role in the shape control of nanoparticles.

Partial Purification of a Megadalton DNA Replication Complex by Free Flow Electrophoresis

We describe a gentle and rapid method to purify the intact multiprotein DNA replication complex using free flow electrophoresis (FFE). In particular, we applied FFE to purify the human cell DNA synthesome, which is a multiprotein complex that is fully competent to carry-out all phases of the DNA replication process in vitro using a plasmid containing the simian virus 40 (SV40) origin of DNA replication and the viral large tumor antigen (T-antigen) protein. The isolated native DNA synthesome can be of use in studying the mechanism by which mammalian DNA replication is carried-out and how anti-cancer drugs disrupt the DNA replication or repair process. Partially purified extracts from HeLa cells were fractionated in a native, liquid based separation by FFE. Dot blot analysis showed co-elution of many proteins identified as part of the DNA synthesome, including proliferating cell nuclear antigen (PCNA), DNA topoisomerase I (topo I), DNA polymerase δ (Pol δ), DNA polymerase ɛ (Pol ɛ), replication protein A (RPA) and replication factor C (RFC). Previously identified DNA synthesome proteins co-eluted with T-antigen dependent and SV40 origin-specific DNA polymerase activity at the same FFE fractions. Native gels show a multiprotein PCNA containing complex migrating with an apparent relative mobility in the megadalton range. When PCNA containing bands were excised from the native gel, mass spectrometric sequencing analysis identified 23 known DNA synthesome associated proteins or protein subunits.

Abstract 2160: Targeting SMC1 in combination therapy for triple negative breast cancer

Triple negative breast cancer (TNBC) defined primarily by lack of expression of estrogen and progesterone hormone receptors (HR) and lacking HER2 overexpression and/or gene amplification (HER2) is an aggressive subtype with poor prognosis. Presentation is frequently at an advanced stage, and TNBC is particularly prevalent in younger women, African Americans, and/or in women with BRCA1 and less frequently with BRCA2 gene mutations. Over the last several years, although great progress has been made in the treatment of early HR positive and HER2+ (as well as advanced stage) breast cancer, relapse/progression-free and overall survival of patients with TNBC remains a serious problem. Molecular subtyping identified subsets of TNBC, several of which are thought to be DNA-repair deficient (either due to germ-line mutations such as BRCA1 or 2, or somatic mutations affecting DNA-repair), may be amenable to treatment with DNA-damaging agents such as platinum compounds and PARP (poly(ADP-ribose) polymerase-1) inhibitors. This could be particularly useful in BRCA-mutated cancers. As for the other TNBC subtypes, development of novel therapeutic agents, represents a high priority.

In response to this clinical need, we tested the efficacy of a novel combinatorial strategy which targets differentiated cells and TNBC cancer stem cell like population (CSCs). Structural maintenance of chromosome-1 (SMC1) was selected as a tumor antigen based on our published studies showing its surface localization and the role in cell proliferation, survival and metastasis in TNBC cells. Bioinformatics analyses using public available patient cohorts with clinicopathological information such as TCGA, NCBI and BRAVO showed statistically higher mRNA overexpression of SMC1 in TNBC compared to HR+ and HER2+ breast cancer. To target SMC1, we developed several monoclonal antibodies against the epitope of SMC1 which showed similarity to cell-adhesion peptides in order to facilitate biochemical and cellular assays. The impact of SMC1 inhibition in combination with veliparib, an inhibitor of PARP-1 was tested in BRCA1-wild-type (MDA-MB-231) vs. mutant (MDA-MB-436) TNBC cells and in CSCs (CD44+/CD24low-) sorted from these cells by MTT and colony forming assays. TUNEL and Annexin-V flipping assays were used to determine cell apoptosis. The role of intrinsic vs. extrinsic pathways of apoptosis was examined by measuring activation of Caspase 8 and 9 as well as measurements of cytochrome-c release from mitochondria.

Our results showed that Mab-S15 recognizes SMC1 which is selectively expressed on the surface of cancer cells (including CSC’s) and differentiated TNBC’s, but has a minimal distribution in normal cells. The antibody distinctly inhibits the survival of TNBC in culture, including CSC’s, sorted from TNBC’s. The Mab-S15 and veliparib combination was more effective than the individual agents in inhibiting the growth and survival of TNBC cells including those with a functional BRCA1.

Citation Format: Sushma Yadav, David Berz, George Somlo, Kimlin Ashing, Yate-Ching Yuan, Robert J. Hickey, Sailee Yadav, Arthur D. Riggs. Targeting SMC1 in combination therapy for triple negative breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2160.

Selective cell adhesion on femtosecond laser-microstructured polydimethylsiloxane

We show that femtosecond laser irradiation of polydimethylsiloxane (PDMS) enables selective and patterned cell growth by altering the wetting properties of the surface associated with chemical and/or topographical changes. In the low pulse energy regime, the surface becomes less hydrophobic and exhibits a low water contact angle compared to the pristine material. X-ray photoelectron spectroscopy (XPS) also reveals an increased oxygen content in the irradiated regions, to which the C2C12 cells and rabbit anti-mouse protein were found to attach preferentially. In the high pulse energy regime, the laser-modified regions exhibit superhydrophobicity and were found to inhibit cell adhesion, whereas cells were found to attach to the surrounding regions due to the presence of nanoscale debris generated by the ablation process.

Validating the disruption of proliferating cell nuclear antigen interactions in the development of targeted cancer therapeutics

Human DNA replication and repair is a highly coordinated process involving the specifically timed actions of numerous proteins and enzymes. Many of these proteins require interaction with proliferating cell nuclear antigen (PCNA) for activation within the process. The interdomain connector loop (IDCL) of PCNA provides a docking site for many of those proteins, suggesting that this region is critically important in the regulation of cellular function. Previous work in this laboratory has demonstrated that a peptide mimicking a specific region of the IDCL (caPeptide) has the ability to disrupt key protein-protein interactions between PCNA and its binding partners, thereby inhibiting DNA replication within the cells. In this study, we confirm the ability of the caPeptide to disrupt DNA replication function using both intact cell and in vitro DNA replication assays. Further, we were able to demonstrate that treatment with caPeptide results in a decrease of polymerase δ activity that correlates with the observed decrease in DNA replication. We have also successfully developed a surface plasmon resonance (SPR) assay to validate the disruption of the PCNA-pol δ interaction with caPeptide.