Antibodies are the paradigm for binding proteins, with their hypervariable loop region supported by a structurally rigid framework, thus providing the vast repertoire of antigen-binding sites in the ...immune system. Lipocalins are another family of proteins that exhibit a binding site with high structural plasticity, which is composed of four peptide loops mounted on a stable β-barrel scaffold. Using site-directed random mutagenesis and selection via phage display against prescribed molecular targets, it is possible to generate artificial lipocalins with novel ligand specificities, so-called anticalins. Anticalins have been successfully selected both against small hapten-like compounds and against large protein antigens and they usually possess high target affinity and specificity. Their structural analysis has yielded interesting insights into the phenomenon of molecular recognition. Compared with antibodies, they are much smaller, have a simpler molecular architecture (comprising just one polypeptide chain) and they do not require post-translational modification. In addition, anticalins exhibit robust biophysical properties and can easily be produced in microbial expression systems. As their structure-function relationships are well understood, rational engineering of additional features such as site-directed pegylation or fusion with functional effector domains, dimerization modules or even with another anticalin, can be readily achieved. Thus, anticalins offer many applications, not only as reagents for biochemical research but also as a new class of potential drugs for medical therapy.
The concept of engineering robust protein scaffolds for novel binding functions emerged 20 years ago, one decade after the advent of recombinant antibody technology. Early examples were the Affibody, ...Monobody (Adnectin), and Anticalin proteins, which were derived from fragments of streptococcal protein A, from the tenth type III domain of human fibronectin, and from natural lipocalin proteins, respectively. Since then, this concept has expanded considerably, including many other protein templates. In fact, engineered protein scaffolds with useful binding specificities, mostly directed against targets of biomedical relevance, constitute an area of active research today, which has yielded versatile reagents as laboratory tools. However, despite strong interest from basic science, only a handful of those protein scaffolds have undergone biopharmaceutical development up to the clinical stage. This includes the abovementioned pioneering examples as well as designed ankyrin repeat proteins (DARPins). Here we review the current state and clinical validation of these next-generation therapeutics.
Antibodies have been the paradigm of binding proteins with desired specificities for more than one century and during the past decade their recombinant or humanized versions have entered clinical ...application with remarkable success. Meanwhile, a new generation of receptor proteins was born, which is derived from small and robust non-immunoglobulin “scaffolds” that can be equipped with prescribed binding functions using the methods of combinatorial protein design. Their ongoing development does not only provide valuable insights into the principles of molecular recognition and protein structure–function relationships but also yields novel reagents for medical use. This technology goes hand in hand with our expanding knowledge about the molecular pathologies of cancer, immunological, and infectious diseases. Currently, questions regarding the choice of suitable medically relevant targets with regard to a certain protein scaffold, the methodology for engineering high affinity, arming with effector functions, routes of administration, plasma half-life, and immunogenicity are in the focus. While many protein scaffolds have been proposed during the past years, the technology shows a trend toward consolidation with a smaller set of systems that are being applied against multiple targets and in different settings, with emphasis on the development of drug candidates for therapy or
in vivo diagnostics: Adnectins, Affibodies, Anticalins, DARPins, and engineered Kunitz-type inhibitors, among others. Only few data from early clinical studies are available yet, but many more are likely to come in the near future, thus providing a growing basis for assessing the therapeutic potential – but possibly also some limitations – of this exciting new class of protein drugs.
While immunoglobulins are well-known for their characteristic ability to bind macromolecular antigens (i.e., as antibodies during an immune response), the lipocalins constitute a family of proteins ...whose role is the complexation of small molecules for various physiological processes. In fact, a number of low-molecular-weight substances in multicellular organisms show poor solubility, are prone to chemical decomposition, or play a pathophysiological role and thus require specific binding proteins for transport through body fluids, storage, or sequestration. In many cases, lipocalins are involved in such tasks. Lipocalins are small, usually monomeric proteins with 150–180 residues and diameters of approximately 40 Å, adopting a compact fold that is dominated by a central eight-stranded up-and-down β-barrel. At the amino-terminal end, this core is flanked by a coiled polypeptide segment, while its carboxy-terminal end is followed by an α-helix that leans against the β-barrel as well as an amino acid stretch in a more-or-less extended conformation, which finally is fixed by a disulfide bond. Within the β-barrel, the antiparallel strands (designated A to H) are arranged in a (+1)7 topology and wind around a central axis in a right-handed manner such that part of strand A is hydrogen-bonded to strand H again. Whereas the lower region of the β-barrel is closed by short loops and densely packed hydrophobic side chains, including many aromatic residues, the upper end is usually open to solvent. There, four long loops, each connecting one pair of β-strands, together form the entrance to a cup-shaped cavity. Depending on the individual structure of a lipocalin, and especially on the lengths and amino acid sequences of its four loops, this pocket can accommodate chemical ligands of various sizes and shapes, including lipids, steroids, and other chemical hormones as well as secondary metabolites such as vitamins, cofactors, or odorants. While lipocalins are ubiquitous in all higher organisms, physiologically important members of this family have long been known in the human body, for example with the plasma retinol-binding protein that serves for the transport of vitamin A. This prototypic human lipocalin was the first for which a crystal structure was solved. Notably, several other lipocalins were discovered and assigned to this protein class before the term itself became familiar, which explains their diverse names in the scientific literature. To date, up to 15 distinct members of the lipocalin family have been characterized in humans, and during the last two decades the three-dimensional structures of a dozen major subtypes have been elucidated. This Account presents a comprehensive overview of the human lipocalins, revealing common structural principles but also deviations that explain individual functional features. Taking advantage of modern methods for combinatorial protein design, lipocalins have also been employed as scaffolds for the construction of artifical binding proteins with novel ligand specificities, so-called Anticalins, hence opening perspectives as a new class of biopharmaceuticals for medical therapy.
Thymosin α1 (Tα1) is an immunostimulatory peptide for the treatment of hepatitis B virus (HBV) and hepatitis C virus (HCV) infections and used as an immune enhancer, which also offers prospects in ...the context of COVID-19 infections and cancer. Manufacturing of this N-terminally acetylated 28-residue peptide is demanding, and its short plasma half-life limits in vivo efficacy and requires frequent dosing. Here, we combined the PASylation technology with enzymatic in situ N-acetylation by RimJ to produce a long-acting version of Tα1 in
at high yield. ESI-MS analysis of the purified fusion protein indicated the expected composition without any signs of proteolysis. SEC analysis revealed a 10-fold expanded hydrodynamic volume resulting from the fusion with a conformationally disordered Pro/Ala/Ser (PAS) polypeptide of 600 residues. This size effect led to a plasma half-life in rats extended by more than a factor 8 compared to the original synthetic peptide due to retarded kidney filtration. Our study provides the basis for therapeutic development of a next generation thymosin α1 with prolonged circulation. Generally, the strategy of producing an N-terminally protected PASylated peptide solves three major problems of peptide drugs: (i) instability in the expression host, (ii) rapid degradation by serum exopeptidases, and (iii) low bioactivity because of fast renal clearance.
The development of the Escherichia coli K‐12 laboratory strains JM83, JM109 and XL1‐Blue was instrumental in early gene technology. We report the comprehensive genome sequence analysis of JM83 and ...XL1‐Blue using Illumina and Oxford Nanopore technologies and a comparison with both the wild‐type sequence (MG1655) and the genome of JM109 deposited at GenBank. Our investigation provides insight into the way how the genomic background that allows blue/white colony selection—by complementing a functionally inactive ω‐fragment of β‐galactosidase (LacZ) with its α‐peptide encoded on the cloning vector—has been implemented independently in these three strains using classical bacterial genetics. In fact, their comparative analysis reveals recurrent motifs: (i) inactivation of the native enzyme via large deletions of chromosomal regions encompassing the lac locus, or a chemically induced frameshift deletion at the beginning of the lacZ cistron, and (ii) utilization of a defective prophage (ϕ80), or an F′‐plasmid, to provide the lacZ∆M15 allele encoding its ω‐fragment. While the genetic manipulations of the E. coli strains involved repeated use of mobile genetic elements as well as harsh chemical or physical mutagenesis, the individual modified traits appear remarkably stable as they can be found even in distantly related laboratory strains, beyond those investigated here. Our detailed characterization at the genome sequence level not only offers clues about the mechanisms of classical gene transduction and transposition but should also guide the future fine‐tuning of E. coli strains for gene cloning and protein expression, including phage display techniques, utilizing advanced tools for site‐specific genome engineering.
Based on their comparative genome analysis, JM83, JM109 and XL1‐Blue can be traced back to the classical research on the lac operon in the laboratory of F. Jacob. The Graphical depicts the genome map of JM83 superimposed on its colonies grown on an X‐gal agar plate transformed with a mixture of pUC19 plasmids with or without inserted heterologous DNA.
DC-SIGN (dendritic cell-specific ICAM-3 grabbing non-integrin) and Langerin are homologous C-type lectins expressed as cell-surface receptors on different populations of dendritic cells (DCs). ...DC-SIGN interacts with glycan structures on HIV-1, facilitating virus survival, transmission and infection, whereas Langerin, which is characteristic of Langerhans cells (LCs), promotes HIV-1 uptake and degradation. Here we describe a comprehensive comparison of the glycan specificities of both proteins by probing a synthetic carbohydrate microarray comprising 275 sugar compounds using the bacterially produced and fluorescence-labeled, monomeric carbohydrate-recognition domains (CRDs) of DC-SIGN and Langerin. In this side-by-side study DC-SIGN was found to preferentially bind internal mannose residues of high-mannose-type saccharides and the fucose-containing blood-type antigens H, A, B, Lea, Leb Lex, Ley, sialyl-Lea as well as sulfatated derivatives of Lea and Lex. In contrast, Langerin appeared to recognize a different spectrum of compounds, especially those containing terminal mannose, terminal N-acetylglucosamine and 6-sulfogalactose residues, but also the blood-type antigens H, A and B. Of the Lewis antigens, only Leb, Ley, sialyl-Lea and the sialyl-Lex derivative with 6′-sulfatation at the galactose (sialyl-6SGal Lex) were weakly bound by Langerin. Notably, Ca2+-independent glycan-binding activity of Langerin could not be detected either by probing the glycan array or by isothermal titration calorimetry of the CRD with mannose and mannobiose. The precise knowledge of carbohydrate specificity of DC-SIGN and Langerin receptors resulting from our study may aid the future design of microbicides that specifically affect the DC-SIGN/HIV-1 interaction while not compromising the protective function of Langerin.
The noncanonical alcohol dehydrogenase AlkJ is encoded on the alkane-metabolizing alk operon of the mesophilic bacterium Pseudomonas putida GPo1. To gain insight into the enzymology of AlkJ, we have ...produced the recombinant protein in Escherichia coli and purified it to homogeneity using His6 tag affinity and size exclusion chromatography (SEC). Despite synthesis in the cytoplasm, AlkJ was associated with the bacterial cell membrane, and solubilization with n-dodecyl-β-D-maltoside was necessary to liberate the enzyme. SEC and spectrophotometric analysis revealed a dimeric quaternary structure with stoichiometrically bound reduced flavin adenine dinucleotide (FADH2). The holoenzyme showed thermal denaturation at moderate temperatures around 35°C, according to both activity assay and temperature-dependent circular dichroism spectroscopy. The tightly bound coenzyme was released only upon denaturation with SDS or treatment with urea-KBr and, after air oxidation, exhibited the characteristic absorption spectrum of FAD. The enzymatic activity of purified AlkJ for 1-butanol, 1-hexanol, and 1-octanol as well as the n-alkanol derivative ω-hydroxy lauric acid methyl ester (HLAMe) was quantified in the presence of the artificial electron acceptors phenazine methosulfate (PMS) and 2,6-dichlorophenolindophenol (DCPIP), indicating broad substrate specificity with the lowest activity on the shortest alcohol, 1-butanol. Furthermore, AlkJ was able to accept as cosubstrates/oxidants the ubiquinone derivatives Q0 and Q1, also in conjunction with cytochrome c, which suggests coupling to the bacterial respiratory chain of this membrane-associated enzyme in its physiological environment. Using gas chromatographic analysis, we demonstrated specific biocatalytic conversion by AlkJ of the substrate HLAMe to the industrially relevant aldehyde, thus enabling the biotechnological production of 12-amino lauric acid methyl ester via subsequent enzymatic transamination.
Eculizumab inhibits the terminal, lytic pathway of complement by blocking the activation of the complement protein C5 and shows remarkable clinical benefits in certain complement-mediated diseases. ...However, several reports suggest that activation of C5 is not always completely suppressed in patients even under excess of eculizumab over C5, indicating that residual C5 activity may derogate the drug's therapeutic benefit under certain conditions. By using eculizumab and the tick-derived C5 inhibitor coversin, we determined conditions ex vivo in which C5 inhibition is incomplete. The degree of such residual lytic activity depended on the strength of the complement activator and the resulting surface density of the complement activation product C3b, which autoamplifies via the alternative pathway (AP) amplification loop. We show that at high C3b densities required for binding and activation of C5, both inhibitors reduce but do not abolish this interaction. The decrease of C5 binding to C3b clusters in the presence of C5 inhibitors correlated with the levels of residual hemolysis. However, by employing different C5 inhibitors simultaneously, residual hemolytic activity could be abolished. The importance of AP-produced C3b clusters for C5 activation in the presence of eculizumab was corroborated by the finding that residual hemolysis after forceful activation of the classical pathway could be reduced by blocking the AP. By providing insights into C5 activation and inhibition, our study delivers the rationale for the clinically observed phenomenon of residual terminal pathway activity under eculizumab treatment with important implications for anti-C5 therapy in general.
•Strong complement activation overrides the terminal pathway inhibition by the anti-C5 antibody eculizumab.•The more powerful complement is activated, the less effective is terminal pathway inhibition by diverse anti-C5 agents.
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