A disulfide intercalator toolbox for the site-directed modification of polypeptides

Peptide Bispecifics Inhibiting HIV-1 Infection by an Orthogonal Chemical and Supramolecular Strategy

Viral infections pose a significant threat to human health, and effective antiviral strategies are urgently needed. Antiviral peptides have emerged as a promising class of therapeutic agents due to their unique properties and mechanisms of action. While effective on their own, combining antiviral peptides may allow us to enhance their potency and to prevent viral resistance. Here, we developed an orthogonal chemical strategy to prepare a heterodimeric peptide conjugate assembled on a protein-based nanoplatform. Specifically, we combined the optimized version of two peptides inhibiting HIV-1 by distinct mechanisms. Virus-inhibitory peptide (VIRIP) is a 20 amino acid fragment of α1-antitrypsin that inhibits HIV-1 by targeting the gp41 fusion peptide. Endogenous peptide inhibitor of CXCR4 (EPI-X4) is a 16-residue fragment of human serum albumin that prevents HIV-1 entry by binding to the viral CXCR4 co-receptor. Optimized forms of both peptides are assembled on supramolecular nanoplatforms through the streptavidin-biotin interaction. We show that the construct consisting of the two different peptides (SAv-VIR-102C9-EPI-X4 JM#173-C) shows increased activity against CCR5- and CXCR4-tropic HIV-1 variants. Our results are a proof of concept that peptides with different modes of action can be assembled on nanoplatforms to enhance their antiviral activity.

Polymer Chemistry in Living Cells

The polymerization of biomolecules is a central operation in biology that connects molecular signals with proliferative and information-rich events in cells. As molecules arrange precisely across 3-D space, they create new functional capabilities such as catalysis and transport highways and exhibit new phase separation phenomena that fuel nonequilibrium dynamics in cells. Hence, the observed polymer chemistry manifests itself as a molecular basis leading to cellular phenotypes, expressed as a multitude of hierarchical structures found in cell biology. Although many milestone discoveries had accompanied the rise of the synthetic polymer era, fundamental studies were realized within a closed, pristine environment and that their behavior in a complex multicomponent system remains challenging and thus unexplored. From this perspective, there is a rich trove of undiscovered knowledge that awaits the polymer science community that can revolutionize understanding in the interactive nanoscale world of the living cell.In this Account, we discuss the strategies that have enabled synthetic polymer chemistry to be conducted within the cells (membrane inclusive) and to establish monomer design principles that offer spatiotemporal control of the polymerization. As reaction considerations such as monomer concentration, polymer growth dynamics, and reactivities are intertwined with the subcellular environment and transport processes, we first provide a chemical narrative of each major cellular compartment. The conditions within each compartment will therefore set the boundaries on the type of polymer chemistry that can be conducted. Both covalent and supramolecular polymerization concepts are explored separately in the context of scaffold design, polymerization mechanism, and activation. To facilitate transport into a localized subcellular space, we show that monomers can be reversibly modified by targeting groups or stimulus-responsive motifs that react within the specific compartment. Upon polymerization, we discuss the characterization of the resultant polymeric structures and how these phase-separated structures would impact biological processes such as cell cycle, metabolism, and apoptosis. As we begin to integrate cellular biochemistry with in situ polymer science, we identify landmark challenges and technological hurdles that, when overcome, would lead to invaluable discoveries in macromolecular therapeutics and biology.

A disintegrin derivative as a case study for PHIP labeling of disulfide bridged biomolecules

A specific labeling strategy for bioactive molecules is presented for eptifibatide (integrilin) an antiplatelet aggregation inhibitor, which derives from the disintegrin protein barbourin in the venom of certain rattlesnakes. By specifically labeling the disulfide bridge this molecule becomes accessible for the nuclear spin hyperpolarization method of parahydrogen induced polarization (PHIP). The PHIP-label was synthesized and inserted into the disulfide bridge of eptifibatide via reduction of the peptide and insertion by a double Michael addition under physiological conditions. This procedure is universally applicable for disulfide-containing biomolecules and preserves their tertiary structure with a minimum of change. HPLC and MS spectra prove the successful insertion of the label. ¹H-PHIP-NMR experiments yield a factor of over 1000 as lower limit for the enhancement factor. These results demonstrate the high potential of the labeling strategy for the introduction of site selective PHIP-labels into biomolecules’ disulfide bonds.

Assembly of pH-Responsive Antibody-Drug-Inspired Conjugates

With the advent of chemical strategies that allow the design of smart bioconjugates, peptide- and protein-drug conjugates are emerging as highly efficient therapeutics to overcome limitations of conventional treatment, as exemplified by antibody-drug conjugates (ADCs). While targeting peptides serve similar roles as antibodies to recognize overexpressed receptors on diseased cell surfaces, peptide-drug conjugates suffer from poor stability and bioavailability due to their low molecular weights. Through a combination of a supramolecular protein-based assembly platform and a pH-responsive linker, the authors devise herein the convenient assembly of a trivalent protein-drug conjugate. The conjugate should ideally possess distinct features of ADCs such as 1) recognition sites that recognize cell receptor and are arranged on 2) distinct locations on a high molecular weight protein scaffold, 3) a stimuli-responsive linker, as well as 4) an attached payload such as a drug molecule. These AD-like conjugates target cancer cells that overexpress somatostatin receptors, can enable controlled release in the microenvironment of cancer cells through a new pH-responsive biotin linker, and exhibit stability in biological media.

A novel strategy for site selective spin-labeling to investigate bioactive entities by DNP and EPR spectroscopy

A novel specific spin-labeling strategy for bioactive molecules is presented for eptifibatide (integrilin) an antiplatelet aggregation inhibitor, which derives from the venom of certain rattlesnakes. By specifically labeling the disulfide bridge this molecule becomes accessible for analytical techniques such as Electron Paramagnetic Resonance (EPR) and solid state Dynamic Nuclear Polarization (DNP). The necessary spin-label was synthesized and inserted into the disulfide bridge of eptifibatide via reductive followed by insertion by a double Michael addition under physiological conditions. This procedure is universally applicable for disulfide containing biomolecules and is expected to preserve their tertiary structure with minimal change due to the small size of the label and restoring of the previous disulfide connection. HPLC and MS analysis show the successful introduction of the spin label and EPR spectroscopy confirms its activity. DNP-enhanced solid state NMR experiments show signal enhancement factors of up to 19 in ¹³C CP MAS experiments which corresponds to time saving factors of up to 361. This clearly shows the high potential of our new spin labeling strategy for the introduction of site selective radical spin labels into biomolecules and biosolids without compromising its conformational integrity for structural investigations employing solid-state DNP or advanced EPR techniques.

Site-selective protein modification via disulfide rebridging for fast tetrazine/trans-cyclooctene bioconjugation

An inverse electron demand Diels-Alder reaction between tetrazine and trans-cyclooctene (TCO) holds great promise for protein modification and manipulation. Herein, we report the design and synthesis of a tetrazine-based disulfide rebridging reagent, which allows the site-selective installation of a tetrazine group into disulfide-containing peptides and proteins such as the hormone somatostatin (SST) and the antigen binding fragment (Fab) of human immunoglobulin G (IgG). The fast and efficient conjugation of the tetrazine modified proteins with three different TCO-containing substrates to form a set of bioconjugates in a site-selective manner was successfully demonstrated for the first time. Homogeneous, well-defined bioconjugates were obtained underlining the great potential of our method for fast bioconjugation in emerging protein therapeutics. The formed bioconjugates were stable against glutathione and in serum, and they maintained their secondary structure. With this work, we broaden the scope of tetrazine chemistry for site-selective protein modification to prepare well-defined SST and Fab conjugates with preserved structures and good stability under biologically relevant conditions.

Precision Anisotropic Brush Polymers by Sequence Controlled Chemistry

The programming of nanomaterials at molecular length-scales to control architecture and function represents a pinnacle in soft materials synthesis. Although elusive in synthetic materials, Nature has evolutionarily refined macromolecular synthesis with perfect atomic resolution across three-dimensional space that serves specific functions. We show that biomolecules, specifically proteins, provide an intrinsic macromolecular backbone for the construction of anisotropic brush polymers with monodisperse lengths via grafting-from strategy. Using human serum albumin as a model, its sequence was exploited to chemically transform a single cysteine, such that the expression of said functionality is asymmetrically placed along the backbone of the eventual brush polymer. This positional monofunctionalization strategy was connected with biotin-streptavidin interactions to demonstrate the capabilities for site-specific self-assembly to create higher ordered architectures. Supported by systematic experimental and computational studies, we envisioned that this macromolecular platform provides unique avenues and perspectives in macromolecular design for both nanoscience and biomedicine.

Functional protein nanostructures: a chemical toolbox

Nature has evolved an optimal synthetic factory in the form of translational and posttranslational processes by which millions of proteins with defined primary sequences and 3D structures can be built. Nature's toolkit gives rise to protein building blocks, which dictates their spatial arrangement to form functional protein nanostructures that serve a myriad of functions in cells, ranging from biocatalysis, formation of structural networks, and regulation of biochemical processes, to sensing. With the advent of chemical tools for site-selective protein modifications and recombinant engineering, there is a rapid development to develop and apply synthetic methods for creating structurally defined, functional protein nanostructures for a broad range of applications in the fields of catalysis, materials and biomedical sciences. In this review, design principles and structural features for achieving and characterizing functional protein nanostructures by synthetic approaches are summarized. The synthetic customization of protein building blocks, the design and introduction of recognition units and linkers and subsequent assembly into structurally defined protein architectures are discussed herein. Key examples of these supramolecular protein nanostructures, their unique functions and resultant impact for biomedical applications are highlighted.

Homogeneous antibody-drug conjugates via site-selective disulfide bridging

Antibody-drug conjugates (ADCs) constructed using site-selective labelling methodologies are likely to dominate the next generation of these targeted therapeutics. To this end, disulfide bridging has emerged as a leading strategy as it allows the production of highly homogeneous ADCs without the need for antibody engineering. It consists of targeting reduced interchain disulfide bonds with reagents which reconnect the resultant pairs of cysteine residues, whilst simultaneously attaching drugs. The 3 main reagent classes which have been exemplified for the construction of ADCs by disulfide bridging will be discussed in this review; bissulfones, next generation maleimides and pyridazinediones, along with others in development.

Dynamic Core-Shell Bioconjugates for Targeted Protein Delivery and Release

Dynamic covalent chemistry is a versatile and powerful tool that integrates both stable chemical bonds and stimulus responsiveness into the construction of smart biotherapeutics. With minimalistic molecular design, a dynamic covalent protein assembly that incorporates selective targeting and intracellular release upon pH stimulus is presented. The construct comprises an active enzymatic protein core (cytochrome c) self-assembled with cancer cell targeting motifs (somatostatin) through boronic acid/salicylhydroxamate chemistry. The bioorthogonal assembly takes place rapidly under neutral aqueous conditions while the release of the protein is initiated under acidic conditions found within cellular vesicles during uptake. By demonstrating that these modular components act in synergy, we show the broad applicability of such chemical strategies to advance the frontier of modern nanomedicine.

Peptide-Dendron Hybrids that Adopt Sequence-Encoded β-Sheet Conformations

Rational design rules for programming hierarchical organization and function through mutations of monomers in sequence-defined polymers can accelerate the development of novel polymeric and supramolecular materials. Our strategy for designing peptide-dendron hybrids that adopt predictable secondary and quaternary structures in bulk is based on patterning the sites at which dendrons are conjugated to short peptides. To validate this approach, we have designed and characterized a series of β-sheet-forming peptide-dendron hybrids. Spectroscopic studies of the hybrids in films reveal that the peptide portion of the hybrids adopts the intended secondary structure.

Site-specific chelator-antibody conjugation for PET and SPECT imaging with radiometals

Antibodies and their derivatives radiolabelled with positron- and gamma-emitting radiometals enable sensitive and quantitative molecular Positron Emission Tomography (PET) and Single Photon Emission Computed Tomography (SPECT) imaging of antibody distribution in vivo. Chelators that are covalently attached to antibodies allow radiolabelling with metallic PET and SPECT radioisotopes. Conventional strategies for chelator-protein conjugation generate heterogeneous mixtures of bioconjugates that can exhibit reduced affinity for their receptor targets, and undesirable biodistribution and pharmacokinetics. Recent advances in bioconjugation technology enable site-specific modification to generate well-defined constructs with superior properties. Herein we survey existing site-specific chelator-protein conjugation methods. These include chelator attachment to cysteines/disulfide bonds or the glycan region of the antibody, enzyme-mediated chelator conjugation, and incorporation of sequences of amino acids that chelate the radiometal. Such technology will allow better use of PET and SPECT imaging in the development of antibody-based therapies.

Encoding function into polypeptide-oligonucleotide precision biopolymers

We report a novel synthesis strategy to prepare precision polymers providing exact chain lengths, molecular weights and monomer sequences that allow post modifications by convenient DNA hybridization. Two grafted single strand DNA (ssDNA) side chains serve as a versatile platform for sequence-specific attachment of chromophores, proteins, cell-targeting peptide, and a Y-shape DNA linker. This approach resembles a LEGO®-type incorporation of functionalities to create functional biopolymers of high structure definition under mild conditions.

Boosting Antitumor Drug Efficacy with Chemically Engineered Multidomain Proteins

A facile chemical approach integrating supramolecular chemistry, site-selective protein chemistry, and molecular biology is described to engineer synthetic multidomain protein therapeutics that sensitize cancer cells selectively to significantly enhance antitumor efficacy of existing chemotherapeutics. The desired bioactive entities are assembled via supramolecular interactions at the nanoscale into structurally ordered multiprotein complexes comprising a) multiple copies of the chemically modified cyclic peptide hormone somatostatin for selective targeting and internalization into human A549 lung cancer cells expressing SST-2 receptors and b) a new cysteine mutant of the C3bot1 (C3) enzyme from Clostridium botulinum, a Rho protein inhibitor that affects and influences intracellular Rho-mediated processes like endothelial cell migration and blood vessel formation. The multidomain protein complex, SST3-Avi-C3, retargets C3 enzyme into non-small cell lung A549 cancer cells and exhibits exceptional tumor inhibition at a concentration ≈100-fold lower than the clinically approved antibody bevacizumab (Avastin) in vivo. Notably, SST3-Avi-C3 increases tumor sensitivity to a conventional chemotherapeutic (doxorubicin) in vivo. These findings show that the integrated approach holds vast promise to expand the current repertoire of multidomain protein complexes and can pave the way to important new developments in the area of targeted and combination cancer therapy.

Divinylsulfonamides as Specific Linkers for Stapling Disulfide Bonds in Peptides

A new class of N-phenyl-divinylsulfonamides which can be easily prepared have been successfully developed and utilized as efficient linkers in the field of disulfide bond modification. Functional divinylsulfonamides provide opportunities for the specific introduction of various functionalities, including affinity probes, fluorescent tags, and drugs, into peptides.

Spatially resolved photochemical coding of reversibly anchored cysteine-rich domains

We present a novel methodology to generate recodable surfaces using cysteine-rich domains (CRD) via a combination of photolithography and reversible covalently peptide-driven disulfide formation. Therefore, two 21mer CRD peptide derivatives were synthesized, one bearing an electron deficient fumarate group for immobilization via nitrile imine-ene mediated cycloaddition (NITEC) to a tetrazole-functional surface. Secondly, a bromine moiety is introduced to the CRD for analytic labelling purposes to detect surface encoding. The photolithography is conducted by selectively passivating the surface with a polyethylene glycol (PEG)-fumarate via NITEC using a photomask in a dotted pattern. Consecutively, the CRD-fumarate is immobilized via NITEC adjacent to the PEG-functional areas to the unaffected tetrazole covered surface layer. Subsequently, the CRD-bromide is covalently linked to the CRD-fumarate by forming disulfide bonds under mild reoxidative conditions in a buffer solution. The CRD-bromide is released from the surface upon reduction to recover the prior state of the surface without the bromine marker. The analysis of the CRD precursors is based on electrospray ionization mass spectrometry (ESI-MS). The surface analytics were carried out via time-of-flight secondary ion mass spectrometry (ToF-SIMS), unambiguously verifying the successful immobilization as well as coding and decoding of the CRD-bromide on the surface based on dynamically reversible disulfide bond formation.

Removal of heavy metal ions from wastewaters using dendrimer-functionalized multi-walled carbon nanotubes

Dendrimer-functionalized multi-walled carbon nanotubes (MWCNT) for heavy metal ion removal from wastewaters were developed. Triazole dendrimers (TD) were built directly onto the carbon nanotube surface by successive click chemistry reactions affording the zero- and first-generation dendrimer-functionalized MWCNT (MWCNT-TD1 and MWCNT-TD2). The Moedritzer-Irani reaction carried out on the amino groups present on the MWCNT-TD2 sample gave the corresponding α-aminophosphonate nanosystem MWCNT-TD2P. Both MWCNT-TD2 and MWCNT-TD2P nanosystems have been characterized by physical, chemical, and morphological analyses. Their chelating abilities towards the toxic metal ions Pb²⁺, Hg²⁺, and Ni²⁺ and the harmless Ca²⁺ ion have been experimentally evaluated in the two different sets of experiments and at the salt concentrations of 1 mg/mL or 1 μg/mL by inductively coupled plasma mass spectrometry (ICP-MS). The results of these studies pointed out the interesting chelating behavior for the phosphonated nanosystem towards the Hg²⁺ ion. The complexation mode of the best chelating system MWCNT-TD2P with mercury was investigated through density functional theory (DFT) calculations, suggesting a chelation mechanism involving the two oxygen atoms of the phosphate group. The synthesized dendrimers, supported on the multi-walled carbon nanotubes, have shown the potential to be used for the selective toxic metal ion removal and recovery.

Synthesis of Peptide-Functionalized Poly(bis-sulfone) Copolymers Regulating HIV-1 Entry and Cancer Stem Cell Migration

Peptide-polymer conjugates have been regarded as primary stronghold in biohybrid nanomedicine, which has seen extensive development due to its intrinsic property to provide complementary functions of both the peptide material and the synthetic polymer platform. Here we present an advanced macromolecular therapeutic that targets two exclusive classes of important diseases (namely, the HIV and cancer) that are implicated by extremely different causative agents. Using a facile thiol-reactive monomer, the eventual polymer facilitates multivalent conjugation of an endogenous peptide WSC02 that targets the CXCR4 chemokine receptor. The biohybrid material demonstrated both potent antiviral effects against HIV-1 as well as inhibiting cancer stem cell migration thus establishing the foundation for multimodal nanotherapeutics that simultaneously target more than one class of disease implications.

Site-Selective Disulfide Modification of Proteins: Expanding Diversity beyond the Proteome

The synthetic transformation of polypeptides with molecular accuracy holds great promise for providing functional and structural diversity beyond the proteome. Consequently, the last decade has seen an exponential growth of site-directed chemistry to install additional features into peptides and proteins even inside living cells. The disulfide rebridging strategy has emerged as a powerful tool for site-selective modifications since most proteins contain disulfide bonds. In this Review, we present the chemical design, advantages and limitations of the disulfide rebridging reagents, while summarizing their relevance for synthetic customization of functional protein bioconjugates, as well as the resultant impact and advancement for biomedical applications.

Receptor selective ruthenium-somatostatin photosensitizer for cancer targeted photodynamic applications

The efficient conjugation of a ruthenium complex and the peptide hormone somatostatin is presented. The resultant biohybrid offers valuable features for photodynamic therapy such as remarkable cellular selectivity, rapid cell uptake by receptor-mediated endocytosis, efficient generation of (1)O2 upon irradiation, potent phototoxicity as well as low cytotoxicity in the "off"-state.

Water-soluble allyl sulfones for dual site-specific labelling of proteins and cyclic peptides

Allyl sulfones as efficient disulfide rebridging agents for site-specific protein modifications with up to two additional functionalities in water.

Water-soluble allyl sulfones provide convenient site-specific disulfide rebridging of native proteins and cyclic peptides. The site-selective functionalization of (a) the peptide hormone somatostatin, (b) the interchain disulfide of bovine insulin and (c) functionalization of the proteins GFP and lysozyme with allyl sulfones proceeds in aqueous solution. Allyl sulfones offer three functionalizable sites that react with thiol containing molecules in a step-wise fashion. Dual labeling of proteins and cyclic peptides is achieved i.e. the attachment of a chromophore and an affinity tag in a single reaction step, which is of great significance for the construction of precise multifunctional peptide and protein conjugates.

CuAAC click reactions for the design of multifunctional luminescent ruthenium complexes

CuAAC (Cu(i) catalyzed azide–alkyne cycloaddition) click chemistry has emerged as a versatile tool in the development of photoactive ruthenium complexes with multilateral potential applicability. Three general concepts for their synthesis and selected applications are discussed.

Programming Bioactive Architectures with Cyclic Peptide Amphiphiles

We present a versatile approach for the synthesis of cyclic peptide amphiphiles of the hormone somatostatin (SST) with tunable lipophilic tails to program bioactive nanoarchitectures. A novel bis-alkylation reagent is synthesized that facilitates the functionalization of SST with a thiol anchor. Different hydrophobic moieties are introduced inspired by a biomimetic palmitoylation approach which opens access to cyclic peptide amphiphiles that display rich self-organization and cell membrane interactions.

Cycloadditions in modern polymer chemistry

Synthetic polymer chemistry has undergone two major developments in the last two decades. About 20 years ago, reversible-deactivation radical polymerization processes started to give access to a wide range of polymeric architectures made from an almost infinite reservoir of functional building blocks. A few years later, the concept of click chemistry revolutionized the way polymer chemists approached synthetic routes. Among the few reactions that could qualify as click, the copper-catalyzed azide-alkyne cycloaddition (CuAAC) initially stood out. Soon, many old and new reactions, including cycloadditions, would further enrich the synthetic macromolecular chemistry toolbox. Whether click or not, cycloadditions are in any case powerful tools for designing polymeric materials in a modular fashion, with a high level of functionality and, sometimes, responsiveness. Here, we wish to describe cycloaddition methodologies that have been reported in the last 10 years in the context of macromolecular engineering, with a focus on those developed in our laboratories. The overarching structure of this Account is based on the three most commonly encountered cycloaddition subclasses in organic and macromolecular chemistry: 1,3-dipolar cycloadditions, (hetero-)Diels-Alder cycloadditions ((H)DAC), and [2+2] cycloadditions. Our goal is to briefly describe the relevant reaction conditions, the advantages and disadvantages, and the realized polymer applications. Furthermore, the orthogonality of most of these reactions is highlighted because it has proven highly beneficial for generating unique, multifunctional polymers in a one-pot reaction. The overview on 1,3-dipolar cycloadditions is mostly centered on the application of CuAAC as the most travelled route, by far. Besides illustrating the capacity of CuAAC to generate complex polymeric architectures, alternative 1,3-dipolar cycloadditions operating without the need for a catalyst are described. In the area of (H)DA cycloadditions, beyond the popular maleimide/furan couple, we present chemistries based on more reactive species, such as cyclopentadienyl or thiocarbonylthio moieties, particularly stressing the reversibility of these systems. In these two greater families, as well as in the last section on [2+2] cycloadditions, we highlight phototriggered chemistries as a powerful tool for spatially and temporally controlled materials synthesis. Clearly, cycloaddition chemistry already has and will continue to transform the field of polymer chemistry in the years to come. Applying this chemistry enables better control over polymer composition, the development of more complicated polymer architectures, the simplification of polymer library production, and the discovery of novel applications for all of these new polymers.