Modular Adapters Utilizing Binders of Different Molecular Types Expand Cell-Targeting Options for Adenovirus Gene Delivery.

Efficient and cell-specific delivery of DNA is essential for the effective and safe use of gene delivery technologies. Consequently, a large variety of technologies have been developed and applied in a wide range of ex vivo and in vivo applications, including multiple approaches based on viral vectors. However, widespread success of a technology is largely determined by the versatility of the method and the ease of use. The rationally designed adapter technology previously developed redirects widely used human adenovirus serotype 5 (HAdV-C5) to a defined cell population, by binding and blocking the adenoviral knob tropism while simultaneously allowing fusions of an N-terminal retargeting module. Here we expand modularity, and thus applicability of this adapter technology, by extending the nature of the cell-binding portion. We report successful receptor-specific transduction mediated by a retargeting module consisting of either a DARPin, a single-chain variable fragment (scFv) of an antibody, a peptide, or a small molecule ligand. Furthermore, we show that an adapter can be engineered to carry more than one specificity, allowing dual targeting. Specific HAdV-C5 retargeting was thus demonstrated to human epidermal growth factor receptor 2 (HER2), human folate receptor α, and neurotensin receptor 1, effective at vector concentrations as low as a multiplicity of infection of 2.5. Therefore, we report a modular design which allows plug-and-play combinations of different binding modules, leading to efficient and specific mono- or dual-targeting while circumventing tedious optimization procedures. This extends the technology to combinational applications of cell-specific binding, supporting research in gene therapy, synthetic biology, and biotechnology.

Thermodynamic Stability Is a Strong Predictor for the Delivery of DARPins to the Cytosol via Anthrax Toxin.

Anthrax toxin has evolved to translocate its toxic cargo proteins to the cytosol of cells carrying its cognate receptor. Cargo molecules need to unfold to penetrate the narrow pore formed by its membrane-spanning subunit, protective antigen (PA). Various alternative cargo molecules have previously been tested, with some showing only limited translocation efficiency, and it may be assumed that these were too stable to be unfolded before passing through the anthrax pore. In this study, we systematically and quantitatively analyzed the correlation between the translocation of various designed ankyrin repeat proteins (DARPins) and their different sizes and thermodynamic stabilities. To measure cytosolic uptake, we used biotinylation of the cargo by cytosolic BirA, and we measured cargo equilibrium stability via denaturant-induced unfolding, monitored by circular dichroism (CD). Most of the tested DARPin cargoes, including target-binding ones, were translocated to the cytosol. Those DARPins, which remained trapped in the endosome, were confirmed by CD to show a high equilibrium stability. We could pinpoint a stability threshold up to which cargo DARPins still get translocated to the cytosol. These experiments have outlined the requirements for translocatable binding proteins, relevant stability measurements to assess translocatable candidates, and guidelines to further engineer this property if needed.

Half-life extension of efficiently produced DARPin serum albumin fusions as a function of FcRn affinity and recycling.

Serum albumin shows slow clearance from circulation due to neonatal Fc receptor (FcRn)-mediated recycling and has been used for half-life extension. We report here fusions to a high-affinity DARPin, binding to Epithelial Cell Adhesion Molecule (EpCAM). We developed a novel, efficient expression system for such fusion proteins in Pichia pastoris with titers above 300 mg/L of lab-scale shake-flask culture. Since human serum albumin (HSA) does not bind to the murine FcRn, half-lives of therapeutic candidates are frequently measured in human FcRn transgenic mice, limiting useable tumor models. Additionally, serum albumins with extended half-life have been designed. We tested HSA7, motivated by its previously claimed extraordinarily long half-life in mice, which we could not confirm. Instead, we determined a half-life of only 29 h for HSA7, comparable to MSA. The fusion of HSA7 to a DARPin showed a similar half-life. To rationalize these findings, we measured binding kinetics and affinities to murine and human FcRn. Briefly, HSA7 showed affinity to murine FcRn only in the micromolar range, comparable to MSA to its cognate murine FcRn, and an affinity in the nanomolar range only to the human FcRn. This explains the comparable half-life of MSA and HSA7 in mice, while wild-type-HSA has a half-life of only 21 h, as it does not bind the murine FcRn and is not recycled. Thus, HSA-fusions with improved FcRn-affinity, such as HSA7, can be used for preclinical experiments in mice when FcRn transgenes cannot be used, as they reflect better the complex FcRn-mediated recycling and distribution mechanisms.

Optimizing the anti-tumor efficacy of protein-drug conjugates by engineering the molecular size and half-life.

Despite some approvals of antibody-drug conjugates for cancer therapy, their clinical success rate is unsatisfactory because of very small therapeutic windows, influenced by on-target and off-target toxicities of conjugate and liberated toxin. Additional formats with systematically investigated molecular parameters must therefore be explored to increase their therapeutic window. Here we focused on the effective molecular weight. To generate conjugates with exactly defined drug loads and tunable pharmacokinetics, we used Designed Ankyrin Repeat Proteins (DARPins), fused to unstructured polypeptides of different lengths, to produce proteins with any desired half-life, to identify those with the best efficacy. We generated an EpCAM-targeting DARPin-MMAF conjugate, fused to PAS or XTEN of different lengths, and a matched series of controls of a non-binding DARPin to account for the enhanced permeability and retention (EPR) effect, covering half-lives of minutes to 20.6 h in mice. All conjugates were produced at high purity, and demonstrated high specificity and cytotoxicity in human tumor cell cultures, with IC50 values in the low nM range, independent of the polypeptide type and length. Due to their more facile purification, the PASylated conjugates were tested in nude mice bearing HT29 tumor xenografts. Independent of their size, all PASylated conjugates were very well tolerated after repeated systemic administration of 300 nmol/kg. We found that the conjugates with intermediate size and half-life showed the strongest anti-tumor effects, and deduced that this effect is a compromise of serum half-life and diffusion within the tumor, as on-rates and affinities are essentially identical, with extravasation playing only a very minor role.

Near Infrared Phosphorescent Dinuclear Ir(III) Complex Exhibiting Unusually Slow Intersystem Crossing and Dual Emissive Behavior.

A dinuclear iridium(III) complex IrIr shows dual emission consisting of near infrared (NIR) phosphorescence (λmax = 714 nm, CH2Cl2, T = 300 K) and green fluorescence (λmax = 537 nm). The NIR emission stems from a triplet state (T1) localized on the ditopic bridging ligand (3LC). Because of the dinuclear molecular structure, the phosphorescence efficiency (ΦPL = 3.5%) is high compared to those of other known red/NIR-emitting iridium complexes. The weak fluorescence stems from the lowest excited singlet state (S1) of 1LC character. The occurrence of fluorescence is ascribed to relatively slow intersystem crossing (ISC) from state S1 (1LC) to the triplet manifold. The measured ISC rate corresponds to a time constant τISC of 2.1 ps, which is an order of magnitude longer than those usually found for iridium complexes. This slow ISC rate can be explained in terms of the LC character and large energy separation (0.57 eV) of the respective singlet and triplet excited states. IrIr is internalized by live HeLa cells as evidenced by confocal luminescence microscopy.

Consecutive Photoinduced Electron Transfer (conPET): The Mechanism of the Photocatalyst Rhodamine†6G.

The dye rhodamine 6G can act as a photocatalyst through photoinduced electron transfer. After electronic excitation with green light, rhodamine 6G takes an electron from an electron donor, such as N,N-diisopropylethylamine, and forms the rhodamine 6G radical. This radical has a reduction potential of around -0.90 V and can split phenyl iodide into iodine anions and phenyl radicals. Recently, it has been reported that photoexcitation of the radical at 420 nm splits aryl bromides into bromide anions and aryl radicals. This requires an increase in reduction potential, hence the electronically excited rhodamine 6G radical was proposed as the reducing agent. Here, we present a study of the mechanism of the formation and photoreactions of the rhodamine 6G radical by transient absorption spectroscopy in the time range from femtoseconds to minutes in combination with quantum chemical calculations. We conclude that one photon of 540 nm light produces two rhodamine 6G radicals. The lifetime of the photoexcited radicals of around 350 fs is too short to allow diffusion-controlled interaction with a substrate. A fraction of the excited radicals ionize spontaneously, presumably producing solvated electrons. This decay produces hot rhodamine 6G and hot rhodamine 6G radicals, which cool with a time constant of around 10 ps. In the absence of a substrate, the ejected electrons recombine with rhodamine 6G and recover the radical on a timescale of nanoseconds. Photocatalytic reactions occur only upon excitation of the rhodamine 6G radical, and due to its short excited-state lifetime, the electron transfer to the substrate probably takes place through the generation of solvated electrons as an additional step in the proposed photochemical mechanism.

Can Coumarins Break Kasha's Rule?

Coumarin C-2 was reported ( Signore et al., J. Am. Chem. Soc. , 2010 , 132 , 1276 and Brancato et al., J. Phys. Chem. B , 2015 , 119 , 6144 ) to break Kasha's rule. However, the two lowest excited singlet states of C-2 are separated by less than 0.5 eV. To slow down the S2 → S1 internal conversion and thus to enable the Kasha's rule-breaking S2 fluorescence, a much larger energy separation seems to be necessary. Thus, the photophysical behavior reported for C-2 raised very basic questions concerning mechanisms of nonradiative transitions in organic molecules. Herein we reinvestigated luminescence of C-2 and found that thoroughly purified C-2 does not show any dual fluorescence in steady-state experiments, contrary to the previous findings. The higher-energy emission, previously erroneously assigned as S2 → S0 fluorescence of C-2, stems from persistent impurity of the synthetic precursor (C-1).

Facile Site-Specific Multiconjugation Strategies in Recombinant Proteins Produced in Bacteria.

For biomedical applications, proteins may require conjugation to small and large molecules. Typical examples are dyes for imaging, cytotoxic effector molecules for cell killing, or half-life extension modules for optimized pharmacokinetics. Although many conjugation strategies are straightforward to apply, most of them do not enable site-specific and orthogonal conjugation, and do not yield a defined stoichiometry. Moreover, techniques offering these desirable features often rely on complex expression procedures and suffer from low production yields. A more promising manufacturing strategy for flexible, site-specific and stoichiometrically defined payloading of proteins is the combination of click chemistry and thiol-maleimide conjugation, which even enables dual labeling when used consecutively. Here, we describe as an example the production of Designed Ankyrin Repeat Proteins (DARPins), a non-IgG binding scaffold, in a specific E. coli strain to obtain high yields of protein carrying both a thiol and an azide group. We provide straightforward protocols for strain-promoted azide-alkyne cycloaddition (SPAAC) and thiol-maleimide conjugation, and furthermore compare these conjugation chemistries with existing alternatives like copper-catalyzed azide-alkyne cycloaddition (CuAAC). Finally, detailed instructions for reactivity analysis and yield estimations of the reactions are provided.

Influence of size and charge of unstructured polypeptides on pharmacokinetics and biodistribution of targeted fusion proteins.

Alternative non-IgG binding proteins developed for therapy are small in size and, thus, are rapidly cleared from the circulation by renal filtration. To avoid repeated injection or continuous infusion for the maintenance of therapeutic serum concentrations, extensions of unfolded polypeptides have been developed to prolong serum half-life, but systematic, comparative studies investigating the influence of their size and charge on serum half-life, extravasation, tumor localization and excretion mechanisms have so far been lacking. Here we used a high-affinity Designed Ankyrin Repeat Protein (DARPin) targeting the tumor marker epithelial cell adhesion molecule (EpCAM) in a preclinical tumor xenograft model in mice, and fused it with a series of defined unstructured polypeptides. We used three different sizes of two previously described polypeptides, an uncharged one consisting of only Pro, Ala and Ser (termed PAS) and a charged one consisting of Pro, Ala, Ser, Thr, Gly, Glu (termed XTEN) and performed for the first time a precise comparative localization, distribution and extravasation study. Pharmacokinetic analysis showed a clear linear relationship between hydrodynamic radius and serum half-life across both polypeptides, reaching a half-life of up to 21 h in mice. Tumor uptake was EpCAM-dependent and directly proportional to half-life and size, showing an even tumor penetration for all fusion proteins without unspecific accumulation in non-target tissue. Unexpectedly, charge had no influence on any parameter, neither tumor nor tissue accumulation nor kidney elimination kinetics. Thus, both polypeptide types have a very similar potential for precise half-life modification and tumor targeting.

Targeted delivery and endosomal cellular uptake of DARPin-siRNA bioconjugates: Influence of linker stability on gene silencing.

Specific cell targeting and efficient intracellular delivery are major hurdles for the widespread therapeutic use of nucleic acid technologies, particularly siRNA mediated gene silencing. To enable receptor-mediated cell-specific targeting, we designed a synthesis scheme that can be generically used to engineer Designed Ankyrin Repeat Protein (DARPin)-siRNA bioconjugates. Different linkers, including labile disulfide-, and more stable thiol-maleimide- and triazole- (click chemistry) tethers were employed. Crosslinkers were first attached to a 3'-terminal aminohexyl chain on the siRNA sense strands. On the protein side thiols of a C-terminal cysteine were used as anchoring sites for disulfide- and thiol-maleimide conjugate formations, while strain-promoted azido-alkyne cycloadditions were carried out at a metabolically introduced N-terminal azidohomoalanine. After establishing efficient purification methods, highly pure products were obtained. Bioconjugates of EpCAM-targeted DARPins with siRNA directed at the luciferase gene were evaluated for cell-specific binding, uptake and gene silencing. As shown by flow cytometry and fluorescence microscopy, all constructs retained the highly specific and high-affinity antigen recognition properties of the native DARPin. As expected, internalization was observed only in EpCAM-positive cell lines, and predominantly endolysosomal localization was detected. Disulfide linked conjugates showed lower serum stability against cleavage at the linker and thus lower internalization into endosomes compared to thiol-maleimide- and triazole-linked conjugates, yet induced more pronounced gene silencing. This indicates that the siRNA payload needs to be liberated from the protein in the endosome. Our data confirm the promise of DARPin-siRNA bioconjugates for tumor targeting, but also identified endosomal retention and limited cytosolic escape of the siRNA as the rate-limiting step for more efficient gene silencing.

A survival selection strategy for engineering synthetic binding proteins that specifically recognize post-translationally phosphorylated proteins.

There is an urgent need for affinity reagents that target phospho-modified sites on individual proteins; however, generating such reagents remains a significant challenge. Here, we describe a genetic selection strategy for routine laboratory isolation of phospho-specific designed ankyrin repeat proteins (DARPins) by linking in vivo affinity capture of a phosphorylated target protein with antibiotic resistance of Escherichia coli cells. The assay is validated using an existing panel of DARPins that selectively bind the nonphosphorylated (inactive) form of extracellular signal-regulated kinase 2 (ERK2) or its doubly phosphorylated (active) form (pERK2). We then use the selection to affinity-mature a phospho-specific DARPin without compromising its selectivity for pERK2 over ERK2 and to reprogram the substrate specificity of the same DARPin towards non-cognate ERK2. Collectively, these results establish our genetic selection as a useful and potentially generalizable protein engineering tool for studying phospho-specific binding proteins and customizing their affinity and selectivity.

Visible-Light-Mediated Liberation and In Situ Conversion of Fluorophosgene.

The first example for the photocatalytic generation of a highly electrophilic intermediate that is not based on radical reactivity is reported. The single-electron reduction of bench-stable and commercially available 4-(trifluoromethoxy)benzonitrile by an organic photosensitizer leads to its fragmentation into fluorophosgene and benzonitrile. The in situ generated fluorophosgene was used for the preparation of carbonates, carbamates, and urea derivatives in moderate to excellent yields via an intramolecular cyclization reaction. Transient spectroscopic investigations suggest the formation of a catalyst charge-transfer complex-dimer as the catalytic active species. Fluorophosgene as a highly reactive intermediate, was indirectly detected via its next downstream carbonyl fluoride intermediate by NMR. Furthermore, detailed NMR analyses provided a comprehensive reaction mechanism including a water dependent off-cycle equilibrium.

Rigidly connected multispecific artificial binders with adjustable geometries.

Multivalent binding proteins can gain biological activities beyond what is inherent in the individual binders, by bringing together different target molecules, restricting their conformational flexibility or changing their subcellular localization. In this study, we demonstrate a method to build up rigid multivalent and multispecific scaffolds by exploiting the modular nature of a repeat protein scaffold and avoiding flexible linkers. We use DARPins (Designed Ankyrin Repeat Proteins), synthetic binding proteins based on the Ankyrin-repeat protein scaffold, as binding units. Their ease of in vitro selection, high production yield and stability make them ideal specificity-conferring building blocks for the design of more complex constructs. C- and N-terminal DARPin capping repeats were re-designed to be joined by a shared helix in such a way that rigid connector modules are formed. This allows us to join two or more DARPins in predefined geometries without compromising their binding affinities and specificities. Nine connector modules with distinct geometries were designed; for eight of these we were able to confirm the structure by X-ray crystallography, while only one did not crystallize. The bispecific constructs were all able to bind both target proteins simultaneously.

Modulation of Intersystem Crossing Rate by Minor Ligand Modifications in Cyclometalated Platinum(II) Complexes.

Photophysical properties of four new platinum(II) complexes comprising extended ppy (Hppy = 2-phenylpyridine) and thpy (Hthpy = 2-(2'-thienyl)pyridine) cyclometalated ligands and acetylacetonate (acac) are reported. Substitution of the benzene ring of Pt-ppy complexes 1 and 2 with a more electron-rich thiophene of Pt-thpy complexes 3 and 4 leads to narrowing of the HOMO-LUMO gap and thus to a red shift of the lowest energy absorption band and phosphorescence band, as expected for low-energy excited states of the intraligand/metal-to-ligand charge transfer character. However, in addition to these conventional spectral shifts, another, at first unexpected, substitution effect occurs. Pt-thpy complexes 3 and 4 are dual emissive showing fluorescence about 6000 cm(-1) (∼0.75 eV) higher in energy relative to the phosphorescence band, while for Pt-ppy complexes 1 and 2 only phosphorescence is observed. For dual-emissive complexes 3 and 4, ISC rates kISC are estimated to be in order of 10(9)-10(10) s(-1), while kISC of Pt-ppy complexes 1 and 2 is much faster amounting to 10(12) s(-1) or more. The relative intensities of the fluorescence and phosphorescence signals of Pt-thpy complexes 3 and 4 depend on the excitation wavelength, showing that hyper-intersystem crossing (HISC) in these complexes is observably significant.

DNA-Based Oligochromophores as Light-Harvesting Systems.

The chromophores ethynyl pyrene as blue, ethynyl perylene as green and ethynyl Nile red as red emitter were conjugated to the 5-position of 2'-deoxyuridine via an acetylene bridge. Using phosphoramidite chemistry on solid phase labelled DNA duplexes were prepared that bear single chromophore modifications, and binary and ternary combinations of these chromophore modifications. The steady-state and time-resolved fluorescence spectra of all three chromophores were studied in these modified DNA duplexes. An energy-transfer cascade occurs from ethynyl pyrene over ethynyl perylene to ethynyl Nile red and subsequently an electron-transfer cascade in the opposite direction (from ethynyl Nile red to ethynyl perylene or ethynyl pyrene, but not from ethynyl perylene to ethynyl pyrene). The electron-transfer processes finally provide charge separation. The efficiencies by these energy and electron-transfer processes can be tuned by the distances between the chromophores and the sequences. Most importantly, excitation at any wavelength between 350 and 700 nm finally leads to charge separated states which make these DNA samples promising candidates for light-harvesting systems.

Antibody-Drug Conjugates for Tumor Targeting-Novel Conjugation Chemistries and the Promise of non-IgG Binding Proteins.

Antibody-drug conjugates (ADCs) have emerged as a promising class of anticancer agents, combining the specificity of antibodies for tumor targeting and the destructive potential of highly potent drugs as payload. An essential component of these immunoconjugates is a bifunctional linker capable of reacting with the antibody and the payload to assemble a functional entity. Linker design is fundamental, as it must provide high stability in the circulation to prevent premature drug release, but be capable of releasing the active drug inside the target cell upon receptor-mediated endocytosis. Although ADCs have demonstrated an increased therapeutic window, compared to conventional chemotherapy in recent clinical trials, therapeutic success rates are still far from optimal. To explore other regimes of half-life variation and drug conjugation stoichiometries, it is necessary to investigate additional binding proteins which offer access to a wide range of formats, all with molecularly defined drug conjugation. Here, we delineate recent progress with site-specific and biorthogonal conjugation chemistries, and discuss alternative, biophysically more stable protein scaffolds like Designed Ankyrin Repeat Proteins (DARPins), which may provide such additional engineering opportunities for drug conjugates with improved pharmacological performance.

Surface plasmon resonance sensor for dissolved and gaseous carbon dioxide.

We describe a novel kind of sensor for carbon dioxide. It is based on surface plasmon resonance (SPR) and a polymer blend that is capable of fully reversibly binding carbon dioxide. The interaction results in a change in the polarity and refractive index that can be detected via SPR. The sensor responds with high specificity. The method is simple and, unlike previous ones, enables continuous sensing over extended periods of time. It can be applied to sense both dissolved and gaseous carbon dioxide. The limits if detection of gaseous CO(2) is as low as 10 ppm.