Affinity selection to papain yields potent peptide inhibitors of cathepsins L, B, H, and K

Antibody-peptide conjugates deliver covalent inhibitors blocking oncogenic cathepsins

Cysteine cathepsins are a family of proteases that are relevant therapeutic targets for the treatment of different cancers and other diseases. However, no clinically approved drugs for these proteins exist, as their systemic inhibition can induce deleterious side effects. To address this problem, we developed a modular antibody-based platform for targeted drug delivery by conjugating non-natural peptide inhibitors (NNPIs) to antibodies. NNPIs were functionalized with reactive warheads for covalent inhibition, optimized with deep saturation mutagenesis and conjugated to antibodies to enable cell-type-specific delivery. Our antibody-peptide inhibitor conjugates specifically blocked the activity of cathepsins in different cancer cells, as well as osteoclasts, and showed therapeutic efficacy in vitro and in vivo. Overall, our approach allows for the rapid design of selective cathepsin inhibitors and can be generalized to inhibit a broad class of proteases in cancer and other diseases.

Small and Simple, yet Sturdy: Conformationally Constrained Peptides with Remarkable Properties

The sheer size and vast chemical space (i.e., diverse repertoire and spatial distribution of functional groups) underlie peptides’ ability to engage in specific interactions with targets of various structures. However, the inherent flexibility of the peptide chain negatively affects binding affinity and metabolic stability, thereby severely limiting the use of peptides as medicines. Imposing conformational constraints to the peptide chain offers to solve these problems but typically requires laborious structure optimization. Alternatively, libraries of constrained peptides with randomized modules can be screened for specific functions. Here, we present the properties of conformationally constrained peptides and review rigidification chemistries/strategies, as well as synthetic and enzymatic methods of producing macrocyclic peptides. Furthermore, we discuss the in vitro molecular evolution methods for the development of constrained peptides with pre-defined functions. Finally, we briefly present applications of selected constrained peptides to illustrate their exceptional properties as drug candidates, molecular recognition probes, and minimalist catalysts.

Optical bioelectronic nose of outstanding sensitivity and selectivity toward volatile organic compounds implemented with genetically engineered bacteriophage: Integrated study of multi-scale computational prediction and experimental validation

Genetic engineering of a bacteriophage is a promising way to develop a highly functional biosensor. Almost countless configurational degree of freedom in the manipulation, considerable uncertainty and cost involved with the approach, however, have been huddles for the objective. In this paper, we demonstrate rapidly responding optical biosensor with high selectivity toward gaseous explosives with genetically engineered phages. The sensors are equipped with peptide sequences in phages optimally interacting with the volatile organic compounds (VOCs) in visible light regime. To overcome the conventional issues, we use extensive utilization of empirical calculations to construct a large database of 8000 tripeptides and screen the best for electronic nose sensing performance toward nine VOCs belonging to three chemical classes. First-principles density functional theory (DFT) calculations unveil underlying correlations between the chemical affinity and optical property change on an electronic band structure level. The computational outcomes are validated by in vitro experimental design and testing of multiarray sensors using genetically modified phage implemented with five selected tripeptide sequences and wild-type phages. The classification success rates estimated from hierarchical cluster analysis are shown to be very consistent with the calculations. Our optical biosensor demonstrates a 1 ppb level of sensing resolution for explosive VOCs, which is a substantial improvement over conventional biosensor. The systematic interplay of big data-based computational prediction and in situ experimental validation can provide smart design principles for unconventionally outstanding biosensors.

Asymmetric Disulfanylbenzamides as Irreversible and Selective Inhibitors of Staphylococcus aureus Sortase A

Staphylococcus aureus is one of the most frequent causes of nosocomial and community-acquired infections, with drug-resistant strains being responsible for tens of thousands of deaths per year. S. aureus sortase A inhibitors are designed to interfere with virulence determinants. We have identified disulfanylbenzamides as a new class of potent inhibitors against sortase A that act by covalent modification of the active-site cysteine. A broad series of derivatives were synthesized to derive structure-activity relationships (SAR). In vitro and in silico methods allowed the experimentally observed binding affinities and selectivities to be rationalized. The most active compounds were found to have single-digit micromolar Ki values and caused up to a 66 % reduction of S. aureus fibrinogen attachment at an effective inhibitor concentration of 10 μM. This new molecule class exhibited minimal cytotoxicity, low bacterial growth inhibition and impaired sortase-mediated adherence of S. aureus cells.

The important role of phagocytosis and interleukins for nile tilapia (Oreochromis niloticus) to defense infection of Aeromonas hydrophila based on transcriptome analysis

Tilapia is an important economic fish worldwide. It is vital to understand the mechanism of immune response for the prevention and treatment the infection of Aeromonas hydrophila. Based on high-throughput sequencing of Illumina HiSeq™, we found differentially expressed genes in the immune-related pathway were classified into phagosome, cytokine-cytokine receptor interaction and toll-like receptor signaling pathway. Gene Ontology terms were divided into three categories of transporting function, DNA replication activity and energy supply activity. The first one was related to phagocytosis and the process or transporting of antigen driven by tubulins; the second one was to differentiation and proliferation of lymphocyte activated by cytokines; and the former two both needed energy provided by the third one. According to colchicine assay, cross-immune assay, ELISA of interleukins and classical phagocytosis assay, phagocytosis and interleukins were verified to be most important to defense the infection of A. hydrophila.

Magnetotactic bacteria: nanodrivers of the future

Magnetotactic bacteria (MTB) represent a heterogeneous group of Gram-negative aquatic prokaryotes with a broad range of morphological types, including vibrioid, coccoid, rod and spirillum. MTBs possess the virtuosity to passively align and actively swim along the magnetic field. Magnetosomes are the trademark nano-ranged intracellular structures of MTB, which comprise magnetic iron-bearing inorganic crystals enveloped by an organic membrane, and are dedicated organelles for their magnetotactic lifestyle. Magnetosomes endue high and even dispersion in aqueous solutions compared with artificial magnetites, claiming them as paragon nanomaterials. MTB and magnetosomes offer high technological potential in modern science, technology and medicines. This review focuses on the applicability of MTB and magnetosomes in various areas of modern benefits.

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.

Selection of a T7 promoter mutant with enhanced in vitro activity by a novel multi-copy bead display approach for in vitro evolution

In vitro evolution of nucleic acids and proteins is a powerful strategy to optimize their biological and physical properties. To select proteins with the desired phenotype from large gene libraries, the proteins need to be linked to the gene they are encoded by. To facilitate selection of the desired phenotype and isolation of the encoding DNA, a novel bead display approach was developed, in which each member of a library of beads is first linked to multiple copies of a clonal gene variant by emulsion polymerase chain reaction. Beads are transferred to a second emulsion for an in vitro transcription-translation reaction, in which the protein encoded by each bead's amplicon covalently binds to the bead present in the same picoliter reactor. The beads then contain multiple copies of a clonal gene variant and multiple molecules of the protein encoded by the bead's gene variant and serve as the unit of selection. As a proof of concept, we screened a randomized library of the T7 promoter for high expression levels by flow cytometry and identified a T7 promoter variant with an ~10-fold higher in vitro transcriptional activity, confirming that the multi-copy bead display approach can be efficiently applied to in vitro evolution.

Identification of heptapeptides interacting with IFN-α-sensitive CML cells

BACKGROUND

Interferon-alpha (IFN-α) is the traditional therapeutic agent for chronic myeloid leukemia (CML). The molecular mechanism of IFN-α efficacy in the treatment of CML is not fully clear.

OBJECTIVES

To identify the peptides and/or proteins that bind to the proteins specifically expressed on the surface of IFN-α-sensitive CML cells by using a phage display library.

DESIGN/METHODS

IFN-α-sensitive KT-1/A3 cells were used as the target, and IFN-α-resistant subline KT-1/A3R was used as absorber for phage display biopanning. The positive phage clones were identified by enzyme-linked immunosorbent assay and flow cytometry. The peptides were deduced from their DNA sequences.

RESULTS

Multiple clones showed high binding efficiency to KT-1/A3 cells compared with that of the other leukemia cells. One of the peptides, KLWVIPQ, has a partial amino acid sequence homology with the C-terminal domain of E3 ubiquitin-protein ligase.

CONCLUSIONS

This study presents the identification of specific heptapeptides that bind to IFN-α-sensitive KT-1/A3 cells. The cancer-selective ligands provide novel strategies for early and differential diagnoses, as well as potential targeted drug delivery.

Engineered staphylococcal protein A's IgG-binding domain with cathepsin L inhibitory activity

Inhibitory peptide of papain-like cysteine proteases, affinity selected from a random disulfide constrained phage-displayed peptide library, was grafted to staphylococcal protein A's B domain. Scaffold protein was additionally modified in order to allow solvent exposed display of peptide loop. Correct folding of fusion proteins was confirmed by CD-spectroscopy and by the ability to bind the Fc-region of rabbit IgG, a characteristic of parent domain. The recombinant constructs inhibited cathepsin L with inhibitory constants in the low-micromolar range.