Two-step fluorescence screening of CD21-binding peptides with one-bead one-compound library and investigation of binding properties of N-(2-hydroxypropyl)methacrylamide copolymer-peptide conjugates

Hydrophilic biomaterials: From crosslinked and self-assembled hydrogels to polymer-drug conjugates and drug-free macromolecular therapeutics

This "Magnum Opus" accentuates my lifelong belief that the future of science is in the interdisciplinary approach to hypotheses formulation and problem solving. Inspired by the invention of hydrogels and soft contact lenses by my mentors, my six decades of research have continuously proceeded from the synthesis of biocompatible hydrogels to the development of polymer-drug conjugates, then generation of drug-free macromolecular therapeutics (DFMT) and finally to multi-antigen T cell hybridizers (MATCH). This interdisciplinary journey was inspiring; the lifetime feeling that one is a beginner in some aspects of the research is a driving force that keeps the enthusiasm high. Also, I wanted to illustrate that systematic research in one wide area can be a life-time effort without the need to jump to areas that are temporarily en-vogue. In addition to generating general scientific knowledge, hydrogels from my laboratory have been transferred to the clinic, polymer-drug conjugates to clinical trials, and drug-free macromolecular systems have an excellent potential for personalizing patient therapies. There is a limit to life but no limit to imagination. I anticipate that systematic basic research will contribute to the expansion of our knowledge and create a foundation for the design of new paradigms based on the comprehension of mechanisms of physiological processes. The emerging novel platform technologies in biomaterial-based devices and implants as well as in personalized nanomedicines will ultimately impact clinical practice.

Polymer nanomedicines

Polymer nanomedicines (macromolecular therapeutics, polymer-drug conjugates, drug-free macromolecular therapeutics) are a group of biologically active compounds that are characterized by their large molecular weight. This review focuses on bioconjugates of water-soluble macromolecules with low molecular weight drugs and selected proteins. After analyzing the design principles, different structures of polymer carriers are discussed followed by the examination of the efficacy of the conjugates in animal models and challenges for their translation into the clinic. Two innovative directions in macromolecular therapeutics that depend on receptor crosslinking are highlighted: a) Combination chemotherapy of backbone degradable polymer-drug conjugates with immune checkpoint blockade by multivalent polymer peptide antagonists; and b) Drug-free macromolecular therapeutics, a new paradigm in drug delivery.

Efficient Screening of Combinatorial Peptide Libraries by Spatially Ordered Beads Immobilized on Conventional Glass Slides

Screening of one-bead-one-compound (OBOC) libraries is a proven procedure for the identification of protein-binding ligands. The demand for binders with high affinity and specificity towards various targets has surged in the biomedical and pharmaceutical field in recent years. The traditional peptide screening involves tedious steps such as affinity selection, bead picking, sequencing, and characterization. Herein, we present a high-throughput "all-on-one chip" system to avoid slow and technically complex bead picking steps. On a traditional glass slide provided with an electrically conductive tape, beads of a combinatorial peptide library are aligned and immobilized by application of a precision sieve. Subsequently, the chip is incubated with a fluorophore-labeled target protein. In a fluorescence scan followed by matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF) mass spectrometry, high-affinity binders are directly and unambiguously sequenced with high accuracy without picking of the positive beads. The use of an optimized ladder sequencing approach improved the accuracy of the de-novo sequencing step to nearly 100%. The new technique was validated by employing a FLAG-based model system, identifying new peptide binders for the monoclonal M2 anti-FLAG antibody, and was finally utilized to search for IgG-binding peptides. In the present format, more than 30,000 beads can be screened on one slide.

α-Synuclein-Confocal Nanoscanning (ASYN-CONA), a Bead-Based Assay for Detecting Early-Stage α-Synuclein Aggregation

α-Synuclein fibrils are considered a hallmark of Parkinson’s disease and other synucleinopathies. However, small oligomers that formed during the early stages of α-synuclein aggregation are thought to be the main toxic species causing disease. The formation of α-synuclein oligomers has proven difficult to follow, because of the heterogeneity and transient nature of the species formed. Here, a novel bead-based aggregation assay for monitoring the earliest stages of α-synuclein oligomerization, α-Synuclein–Confocal Nanoscanning (ASYN-CONA), is presented. The α-synuclein A91C single cysteine mutant is modified with a trifunctional chemical tag, which allows simultaneous fluorescent labeling with a green dye (tetramethylrhodamine, TMR) and attachment to microbeads. Beads with bound TMR-labeled α-synuclein are then incubated with a red dye (Cy5)-labeled variant of α-synuclein A91C, and EtOH (20%) to induce aggregation. Aggregation is detected by confocal scanning imaging, below the equatorial plane of the beads, which is known as the CONA technique. On-bead TMR-labeled α-synuclein and aggregated Cy5-labeled α-synuclein from the solution are quantitatively monitored in parallel by detection of fluorescent halos or “rings”. α-Synuclein on-bead oligomerization results in a linear increase of red bead ring fluorescence intensity over a period of 5 h. Total internal reflection fluorescence microscopy was performed on oligomers cleaved from the beads, and it revealed that (i) oligomers are sufficiently stable in solution to investigate their composition, consisting of 6 ± 1 monomer units, and (ii) oligomers containing a mean of 15 monomers bind Thioflavin-T. Various known inhibitors of α-synuclein aggregation were used to validate the ASYN-CONA assay for drug screening. Baicalein, curcumin, and rifampicin showed concentration-dependent inhibition of the α-synuclein aggregation and the IC₅₀ (the concentration of the compound at which the maxiumum intensity was reduced by one-half) were calculated.

Backbone Degradable N-(2-Hydroxypropyl)methacrylamide Copolymer Conjugates with Gemcitabine and Paclitaxel: Impact of Molecular Weight on Activity toward Human Ovarian Carcinoma Xenografts

Degradable diblock and multiblock (tetrablock and hexablock) N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer-gemcitabine (GEM) and -paclitaxel (PTX) conjugates were synthesized by reversible addition-fragmentation chain-transter (RAFT) copolymerization followed by click reaction for preclinical investigation. The aim was to validate the hypothesis that long-circulating conjugates are needed to generate a sustained concentration gradient between vasculature and a solid tumor and result in significant anticancer effect. To evaluate the impact of molecular weight of the conjugates on treatment efficacy, diblock, tetrablock, and hexablock GEM and PTX conjugates were administered intravenously to nude mice bearing A2780 human ovarian xenografts. For GEM conjugates, triple doses with dosage 5 mg/kg were given on days 0, 7, and 14 (q7dx3), whereas a single dose regime with 20 mg/kg was applied on day 0 for PTX conjugates treatment. The most effective conjugates for each monotherapy were the diblock ones, 2P-GEM and 2P-PTX (Mw ≈ 100 kDa). Increasing the Mw to 200 or 300 kDa resulted in decrease of activity most probably due to changes in the conformation of the macromolecule because of interaction of hydrophobic residues at side chain termini and formation of "unimer micelles". In addition to monotherapy, a sequential combination treatment of diblock PTX conjugate followed by GEM conjugate (2P-PTX/2P-GEM) was also performed, which showed the best tumor growth inhibition due to synergistic effect: complete remission was achieved after the first treatment cycle. However, because of low dose applied, tumor recurrence was observed 2 weeks after cease of treatment. To assess optimal route of administration, intraperitoneal (i.p.) application of 2P-GEM, 2P-PTX, and their combination was examined. The fact that the highest anticancer efficiency was achieved with diblock conjugates that can be synthesized in one scalable step bodes well for the translation into clinics.

High-Throughput Approaches to the Development of Molecular Imaging Agents

Molecular imaging allows for the visualization of changes at the cellular level in diseases such as cancer. A successful molecular imaging agent must rely on disease-selective targets and ligands that specifically interact with those targets. Unfortunately, the translation of novel target-specific ligands into the clinic has been frustratingly slow with limitations including the complex design and screening approaches for ligand identification, as well as their subsequent optimization into useful imaging agents. This review focuses on combinatorial library approaches towards addressing these two challenges, with particular focus on phage display and one-bead one-compound (OBOC) libraries. Both of these peptide-based techniques have proven successful in identifying new ligands for cancer-specific targets and some of the success stories will be highlighted. New developments in screening methodology and sequencing technology have pushed the bounds of phage display and OBOC even further, allowing for even faster and more robust discovery of novel ligands. The combination of multiple high-throughput technologies will not only allow for more accurate identification, but also faster affinity maturation, while overall streamlining the process of translating novel ligands into clinical imaging agents.

Tumor-targeting peptides from combinatorial libraries

Cancer is one of the major and leading causes of death worldwide. Two of the greatest challenges in fighting cancer are early detection and effective treatments with no or minimum side effects. Widespread use of targeted therapies and molecular imaging in clinics requires high affinity, tumor-specific agents as effective targeting vehicles to deliver therapeutics and imaging probes to the primary or metastatic tumor sites. Combinatorial libraries such as phage-display and one-bead one-compound (OBOC) peptide libraries are powerful approaches in discovering tumor-targeting peptides. This review gives an overview of different combinatorial library technologies that have been used for the discovery of tumor-targeting peptides. Examples of tumor-targeting peptides identified from each combinatorial library method will be discussed. Published tumor-targeting peptide ligands and their applications will also be summarized by the combinatorial library methods and their corresponding binding receptors.

Drug-Free Macromolecular Therapeutics--A New Paradigm in Polymeric Nanomedicines

This review highlights a unique research area in polymer-based nanomedicine designs. Drug-free macromolecular therapeutics induce apoptosis of malignant cells by the crosslinking of surface non-internalizing receptors. The receptor crosslinking is mediated by the biorecognition of high-fidelity natural binding motifs (such as antiparallel coiled-coil peptides or complementary oligonucleotides) that are grafted to the side chains of polymers or attached to targeting moieties against cell receptors. This approach features the absence of low-molecular-weight cytotoxic compounds. Here, we summarize the rationales, different designs, and advantages of drug-free macromolecular therapeutics. Recent developments of novel therapeutic systems for B-cell lymphomas are discussed, as well as relevant approaches for other diseases. We conclude by pointing out various potential future directions in this exciting new field.

Macromolecular therapeutics

This review covers water-soluble polymer-drug conjugates and macromolecules that possess biological activity without attached low molecular weight drugs. The main design principles of traditional and backbone degradable polymer-drug conjugates as well as the development of a new paradigm in nanomedicines - (low molecular weight) drug-free macromolecular therapeutics are discussed. To address the biological features of cancer, macromolecular therapeutics directed to stem/progenitor cells and the tumor microenvironment are deliberated. Finally, the future perspectives of the field are briefly debated.

Potential of phage-displayed peptide library technology to identify functional targeting peptides

Combinatorial peptide library technology is a valuable resource for drug discovery and development. Several peptide drugs developed through phage-displayed peptide library technology are presently in clinical trials and the authors envision that phage-displayed peptide library technology will assist in the discovery and development of many more. This review attempts to compile and summarize recent literature on targeting peptides developed through peptide library technology, with special emphasis on novel peptides with targeting capacity evaluated in vivo.

Polymer-drug conjugates: origins, progress to date and future directions

This overview focuses on bioconjugates of water-soluble polymers with low molecular weight drugs and proteins. After a short discussion of the origins of the field, the state-of-the-art is reviewed. Then research directions needed for the acceleration of the translation of nanomedicines into the clinic are outlined. Two most important directions, synthesis of backbone degradable polymer carriers and drug-free macromolecular therapeutics, a new paradigm in drug delivery, are discussed in detail. Finally, the future perspectives of the field are briefly discussed.

Photocleavable peptide-conjugated magnetic beads for protein kinase assays by MALDI-TOF MS

Peptides were immobilized onto superparamagnetic beads via photocleavable linkers. This enabled simple, rapid, and label-free protein kinase assays via MALDI-TOF MS detection of substrate peptide phosphorylation. Abltide, a model substrate for the Abl protein tyrosine kinase model, was coupled onto amine-terminated beads, incubated with ATP and recombinant c-Abl kinase, and released and further detected to determine phosphorylation. Abltide phosphorylation was found to depend significantly on the length and composition of linkers to the bead surface. Inserting a diblock spacer of poly(glycine) and poly(ethylene glycol) segments markedly enhanced phosphorylation. To validate the assay, the activity of two small-molecule kinase inhibitors, imatinib and dasatinib, which target the oncogenic mutant tyrosine kinase Bcr-Abl to treat chronic myeloid leukemia (CML), was tested. Examining inhibition of the purified c-Abl or Bcr-Abl in K562 CML cell extracts, IC(50) values were determined to be consistent with the literature. This simple, label-free, MALDI-based protein kinase assay can be readily adapted to allow multiplexed assays of multiple peptide substrates and/or analysis of alternative post-translational modifications as a tool for drug discovery and clinical testing.

HPMA copolymers: origins, early developments, present, and future

The overview covers the discovery of N-(2-hydroxypropyl)methacrylamide (HPMA) copolymers, initial studies on their synthesis, evaluation of biological properties, and explorations of their potential as carriers of biologically active compounds in general and anticancer drugs in particular. The focus is on the research in the authors' laboratory - the development of macromolecular therapeutics for the treatment of cancer and musculoskeletal diseases. In addition, the evaluation of HPMA (co)polymers as building blocks of modified and new biomaterials is presented: the utilization of semitelechelic poly(HPMA) and HPMA copolymers for the modification of biomaterial and protein surfaces and the design of hybrid block and graft HPMA copolymers that self-assemble into smart hydrogels. Finally, suggestions for the design of second-generation macromolecular therapeutics are portrayed.

Drug-free macromolecular therapeutics: induction of apoptosis by coiled-coil-mediated cross-linking of antigens on the cell surface

A new paradigm was designed for apoptosis induction mediated by the biorecognition of coiled-coil motifs at the Raji B cell surface. The heterodimerization of complementary peptides, one bound to Fab’ antibody fragment, the other as grafts to HPMA copolymer, results in crosslinking of CD20 target antigens, and consequently, initiation of apoptosis.

Single bead labeling method for combining confocal fluorescence on-bead screening and solution validation of tagged one-bead one-compound libraries

Screening of one-bead one-compound libraries by incubating beads with fluorescently labeled target protein requires isolation and structure elucidation of a large number of primary hit beads. However, the potency of the identified ligands is only revealed after time consuming and expensive larger scale resynthesis and testing in solution. Often, many of the resynthesized compounds turn out to be weak target binders in solution due to large differences between surface and solution binding affinities. For an industry style high-throughput screening (HTS) process a high false positive rate is detrimental. We have therefore combined single bead and single molecule/single cell techniques into an integrated HTS process in which the picomole amount of substance contained on one isolated hit bead is sufficient for quality control, structure determination, and precise affinity determination to the target protein in solution.

Screening of a one bead-one compound combinatorial library for beta-actin identifies molecules active toward Ramos B-lymphoma cells

The search for small molecules that specifically recognize protein targets is a laborious process if conducted in a one protein-one compound manner. A high-throughput antibody-based screening of one bead-one compound (OBOC) combinatorial small molecule libraries is described here, whereby libraries containing thousands of different small molecule ligands are synthesized on individual TentaGel beads and simultaneously screened for protein binding to individual beads, each with a different compound. The use of OBOC libraries greatly facilitates this simultaneous screening of thousands of compounds. Now, through the use of monoclonal or affinity-purified antibodies, small molecules that bind a particular protein contained in a complex mixture of biological molecules have been identified. This method identified small molecule ligands that bound beta-actin present in cytoplasmic cell extracts of Ramos B-lymphoma cells. These small molecule ligands were resynthesized in immobilized and soluble forms and tested for binding of beta-actin present in Ramos B-cell extracts and for activity against Ramos lymphoma cells. This high-throughput screening immunoassay method has great promise for improving our ability to find relevant, bioactive small molecules that target a specific native protein in a complex protein mixture without purification of the protein.

Self-association properties of HPMA copolymers containing an amphipathic heptapeptide

Receptor-binding peptides are suitable targeting moieties for macromolecular therapeutics. Binding several targeting peptides to one macromolecule may improve biorecognition due to the multivalency effect. On the other hand, the resulting amphipathic structure of such conjugates may result in the association of side-chains with a concomitant decrease in the accessibility of the side-chain-bound ligands. Using the one-bead one-compound combinatorial method, we have recently identified a heptapeptide (YILIHRN; HP) ligand for the CD21 receptor (Biomacromolecules 7, 3037, 2006). Here, we evaluated the relationship between structure and self-association of N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer-HP conjugates using fluorescence resonance energy transfer (FRET) to evaluate their conformation in solution. In addition to HP, HPMA copolymers containing side-chains terminating in tryptophan (energy donor) and dansyl (energy acceptor) were synthesized, and solutions were evaluated using an excitation wavelength of 295 nm (ratio of emission intensity 510 nm/370 nm indicated energy transfer efficiency). It was found that higher HP content correlated with higher FRET efficiency, indicating the formation of compact coils. Modification of the HPMA copolymer backbone by the incorporation of acrylic acid (AA) comonomer units resulted in decreased FRET efficiency, presumably due to the expansion of the polymer coils as a result of electrostatic repulsion. The dependence of FRET efficiency on pH was in agreement with the ionization profile of the AA residues. To determine the effect of HP content on enzymatic drug release kinetics, HPMA copolymer-HP conjugates containing GFLG side-chains terminating with doxorubicin (DOX) were incubated with papain and the release of free DOX monitored. When HP content increased above a particular threshold, the rate of DOX release decreased as a result of self-association of HPMA copolymer-GFLG-DOX-HP conjugates. The FRET data correlated well with hydrodynamic volumes determined by size exclusion chromatography (SEC), with molecular weights determined by light scattering, and with the kinetics of drug release.