Identification of a LNCaP-specific binding peptide using phage display

Genetically engineered bacteriophages as novel nanomaterials: applications beyond antimicrobial agents

Bacteriophages, also known as phages, are viruses that replicate in bacteria and archaea. Phages were initially discovered as antimicrobial agents, and they have been used as therapeutic agents for bacterial infection in a process known as "phage therapy." Recently, phages have been investigated as functional nanomaterials in a variety of areas, as they can function not only as therapeutic agents but also as biosensors and tissue regenerative materials. Phages are nontoxic to humans, and they possess self-assembled nanostructures and functional properties. Additionally, phages can be easily genetically modified to display specific peptides or to screen for functional peptides via phage display. Here, we demonstrated the application of phage nanomaterials in the context of tissue engineering, sensing, and probing.

Phage for drug delivery vehicles

Viruses being the natural carriers of gene have been widely used as drug delivery systems. However, the commonly used eukaryotic viruses such as adenoviruses, retroviruses, and lentiviruses, besides efficiently targeting the cells, can also stimulate immunological response or disrupt tumour suppressor genes leading to cancer. Consequently, there has been an increase interest in the scientific fraternity towards exploring other alternatives, which are safer and equally efficient for drug delivery. Bacteriophages, in this context have been at the forefront as an efficient, reliable, and safer choice. Novel phage dependent technologies led the foundation of peptide libraries and provides way to recognising abilities and targeting of specific ligands. Hybridisation of phage with inorganic complexes could be an appropriate strategy for the construction of carrying bioinorganic carriers. In this chapter, we have tried to cover major advances in the phage species that can be used as drug delivery vehicles.

Biotechnology Approach to Mineral Separation via Phage Flotation Collectors

A long-standing challenge in the mining industry is the separation of mineral particles that have similar surface characteristics for which surfactant-based flotation collectors cannot discriminate. In Florida phosphate mining, this problem occurs in the separation of dolomite [CaMg(CO₃)₂] contaminants from the desired francolite mineral {a fluorapatite [Ca₅(PO₄)₃(F,OH)]}. In this study, phage display techniques were used to select phage clones with specific binding affinity to francolite, which were then tested in a benchtop bubbler flotation apparatus for their ability to selectively float francolite particles from mixtures containing dolomite. Contact angles measured with the captive bubble technique were used to examine changes in the surface character of the mineral particles upon adsorption of the phage, which showed that the most selective phage led to an increase in the contact angle from 16 to 50°. Although this is below the level considered hydrophobic, the correlation between contact angles and increased flotation recovery suggests that the phage coat proteins are behaving as efficient bioamphiphiles for the attachment of the particles to air bubbles, demonstrating a new and environmentally friendly type of biocollector system. The chemical and physical characteristics of the phage "tail" peptides were evaluated to offer an explanation for the specificity of phage binding. We conclude with a discussion of the potential benefits of this biotechnology approach, even for commodity industries such as mining or other particle separation systems, when costs and sustainability are considered.

Phage nanofibers in nanomedicine: Biopanning for early diagnosis, targeted therapy, and proteomics analysis

Display of a peptide or protein of interest on the filamentous phage (also known as bacteriophage), a biological nanofiber, has opened a new route for disease diagnosis and therapy as well as proteomics. Earlier phage display was widely used in protein-protein or antigen-antibody studies. In recent years, its application in nanomedicine is becoming increasingly popular and encouraging. We aim to review the current status in this research direction. For better understanding, we start with a brief introduction of basic biology and structure of the filamentous phage. We present the principle of phage display and library construction method on the basis of the filamentous phage. We summarize the use of the phage displayed peptide library for selecting peptides with high affinity against cells or tissues. We then review the recent applications of the selected cell or tissue targeting peptides in developing new targeting probes and therapeutics to advance the early diagnosis and targeted therapy of different diseases in nanomedicine. We also discuss the integration of antibody phage display and modern proteomics in discovering new biomarkers or target proteins for disease diagnosis and therapy. Finally, we propose an outlook for further advancing the potential impact of phage display on future nanomedicine. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.

Discovery of low-molecular weight anti-PD-L1 peptides for cancer immunotherapy

Background

Immunotherapy using checkpoint inhibitors, especially PD-1/PD-L1 inhibitors, has now evolved into the most promising therapy for cancer patients. However, most of these inhibitors are monoclonal antibodies, and their large size may limit their tumor penetration, leading to suboptimal efficacy. As a result, there has been a growing interest in developing low-molecular-weight checkpoint inhibitors.

Methods

We developed a novel biopanning strategy to discover small peptide-based anti-PD-L1 inhibitors. The affinity and specificity of the peptides to PD-L1 were examined using various assays. Three-dimensional (3D) spheroid penetration study was performed to determine the tumor penetration capability of the peptides. Anti-tumor activity of the peptides was evaluated in mice bearing CT26 tumor cells.

Results

We discover several anti-PD-L1 peptide inhibitors to block PD-1/PD-L1 interaction. The peptides exhibit high affinity and specificity to human PD-L1 protein as well as PD-L1-overexpressing human cancer cells MDA-MB-231 and DU-145. Molecular docking studies indicate that the peptide CLP002 specifically binds to PD-L1 at the residues where PD-L1 interacts with PD-1. The peptide also blocks the CD80/PD-L1 interaction, which may further enhance the immune response of tumor-infiltrating T cells. Compared to antibody, the peptide CLP002 exhibits better tumor penetration in a 3D tumor spheroid model. The peptide CLP002 restores proliferation and prevents apoptosis of T cells that are co-cultured with cancer cells. The peptide CLP002 also inhibits tumor growth and increases survival of CT26 tumor-bearing mice.

Conclusions

This study demonstrated the feasibility of using phage display to discover small peptide-based checkpoint inhibitors. Our results also suggested that the anti-PD-L1 peptide represents a promising low-molecular-weight checkpoint inhibitor for cancer immunotherapy.

Electronic supplementary material

The online version of this article (10.1186/s40425-019-0705-y) contains supplementary material, which is available to authorized users.

Efficient Prostate Cancer Therapy with Tissue-Specific Homing Peptides Identified by Advanced Phage Display Technology

Selective targeting of drugs to tumor cells is a key goal in oncology. Here, we performed an in vivo phage display to identify peptides that specifically target xenografted prostate cancer cells. This yielded three peptide candidates, LN1 (C-TGTPARQ-C), LN2 (C-KNSMFAT-C), and LN3 (C-TNKHSPK-C); each of these peptides was synthesized and evaluated for binding and biological activity. LN1 showed the highest avidity for LNCaP prostate cancer cells in vitro and was thus administered to tumor-bearing mice to evaluate in vivo binding. Strikingly, LN1 specifically bound to the tumor tissue and exhibited very low reactivity with normal liver and kidney tissues. To demonstrate that LN1 could specifically deliver drugs to prostate cancer tissue, a therapeutic peptide, LN1-KLA (C-TGTPARQ-C-GGG-_D[KLAKLAK]₂), was prepared and used to treat LNCaP cells in vitro and was also administered to tumor-bearing mice. The therapeutic peptide significantly suppressed growth of the cells both in vitro and in vivo. Our study shows that a selective homing peptide strategy could facilitate cell-specific targeting of therapeutics while avoiding adverse reactions in normal tissues.

Discovery of peptide drug carrier candidates for targeted multi-drug delivery into prostate cancer cells

Metastatic castration-resistant prostate cancer (mCRPC) remains essentially incurable. Targeted Drug Delivery (TDD) systems may overcome the limitations of current mCRPC therapies. We describe the use of strict criteria to isolate novel prostate cancer cell targeting peptides that specifically deliver drugs into target cells. Phage from a libraries displaying 7mer peptides were exposed to PC-3 cells and only internalized phage were recovered. The ability of these phage to internalize into other prostate cancer cells (LNCaP, DU-145) was validated. The displayed peptides of selected phage clones were synthesized and their specificity for target cells was validated in vitro and in vivo. One peptide (P12) which specifically targeted PC-3 tumors in vivo was incorporated into mono-drug (Chlorambucil, Combretastatin or Camptothecin) and dual-drug (Chlorambucil/Combretastatin or Chlorambucil/Camptothecin) PDCs and the cytotoxic efficacy of these conjugates for target cells was tested. Conjugation of P12 into dual-drug PDCs allowed discovery of new drug combinations with synergistic effects. The use of strict selection criteria can lead to discovery of novel peptides for use as drug carriers for TDD. PDCs represent an effective alternative to current modes of free drug chemotherapy for prostate cancer.

Functional peptides for siRNA delivery

siRNA is considered as a potent therapeutic agent because of its high specificity and efficiency in suppressing genes that are overexpressed during disease development. For nearly two decades, a significant amount of efforts has been dedicated to bringing the siRNA technology into clinical uses. However, only limited success has been achieved to date, largely due to the lack of a cell type-specific, safe, and efficient delivery technology to carry siRNA into the target cells' cytosol where RNA interference takes place. Among the emerging candidate nanocarriers for siRNA delivery, peptides have gained popularity because of their structural and functional diversity. A variety of peptides have been discovered for their ability to translocate siRNA into living cells via different mechanisms such as direct penetration through the cellular membrane, endocytosis-mediated cell entry followed by endosomolysis, and receptor-mediated uptake. This review is focused on the multiple roles played by peptides in siRNA delivery, such as membrane penetration, endosome disruption, targeting, as well as the combination of these functionalities.

Intracellular trafficking and exocytosis of a multi-component siRNA nanocomplex

Despite the importance of siRNA delivery systems, understanding of their intracellular fate remains elusive. We recently developed a multi-component siRNA nanocomplex to deliver siRNA to hepatic stellate cells (HSCs). The objective of this study is to study post-internalization trafficking of this siRNA nanocomplex and its multiple components like siRNA, protamine, and streptavidin, in HSCs. After internalization, the nanocomplex entrapped in early endosomes undergoes three possible routes including endosomal escape, exocytosis, and entrapment in lysosomes. Significant amount of siRNA dissociates from the nanocomplex to exert silencing activity. After escaping from endosomes, protamine dissociates from the nanocomplex and stays inside the cytoplasm. Golgi complex plays an important role in exocytosis of the nanocomplex. We also demonstrate that exocytosis is one of the major reasons accounting for the transient silencing activity of nonviral siRNA delivery. Incorporation of exocytosis inhibitors in nonviral siRNA delivery systems may extend the silencing activity of siRNA.

Discovery of Peptide ligands for hepatic stellate cells using phage display

Regardless of its cause, liver fibrosis is characterized by the excessive accumulation of extracellular matrix (ECM) in the liver. Hepatic stellate cells (HSCs) are the main producers responsible for the excessive production of ECM and profibrogenic cytokines in fibrotic liver. Therefore, development of HSC-specific delivery systems is essential for the success of antifibrotic agents. The objective of this study is to identify peptide ligands targeting the insulin-like growth factor 2 receptor (IGF2R), which is overexpressed on HSCs. We expect to use the peptide ligands for the future development of HSC-targeted drug delivery system. Protein- and whole cell-based phage display biopannings were conducted to identify phage/peptide candidates. Phage ELISA, cellular uptake, and cell viability assay were employed to evaluate the binding affinity and specificity of these peptide ligands to recombinant human IGF2R and HSCs. IGF2R siRNA was used to silence the IGF2R protein expression in human hepatic stellate cells (LX-2) to confirm the specificity of the identified peptide ligands. Among the identified peptide candidates, peptide-431 shows the highest binding affinity and specificity to recombinant human IGF2R protein and HSCs. The equilibrium dissociation constant (Kd) of peptide-431 is 6.19 μM for LX-2 cells and 12.35 μM for rat hepatic stellate cells HSC-T6. Cellular uptake of peptide-431 in LX-2 cells is significantly reduced after silencing IGF2R with siRNA. Peptide-431 also enhances the uptake of a proapoptotic peptide (KLA peptide) in LX-2 and HSC-T6 cells, indicating that peptide-431 can be used as a targeting ligand to deliver antifibrotic agents into not only rat but also human HSCs. Dimerization of peptide-431 further increase its binding affinity to LX-2 cells by approximately 9-fold.

Peptides used in the delivery of small noncoding RNA

RNA interference (RNAi) is an endogenous process in which small noncoding RNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs), post-transcriptionally regulate gene expressions. In general, siRNA and miRNA/miRNA mimics are similar in nature and activity except their origin and specificity. Although both siRNAs and miRNAs have been extensively studied as novel therapeutics for a wide range of diseases, the large molecular weight, anionic surface charges, instability in blood circulation, and intracellular trafficking to the RISC after cellular uptake have hindered the translation of these RNAs from bench to clinic. As a result, a great variety of delivery systems have been investigated for safe and effective delivery of small noncoding RNAs. Among these systems, peptides, especially cationic peptides, have emerged as a promising type of carrier due to their inherent ability to condense negatively charged RNAs, ease of synthesis, controllable size, and tunable structure. In this review, we will focus on three major types of cationic peptides, including poly(l-lysine) (PLL), protamine, and cell penetrating peptides (CPP), as well as peptide targeting ligands that have been extensively used in RNA delivery. The delivery strategies, applications, and limitations of these cationic peptides in siRNA/miRNA delivery will be discussed.

Prostate cancer relevant antigens and enzymes for targeted drug delivery

Chemotherapy is one of the most widely used approaches in combating advanced prostate cancer, but its therapeutic efficacy is usually insufficient due to poor specificity and associated toxicity. Lack of targeted delivery to prostate cancer cells is also the primary obstacles in achieving feasible therapeutic effect of other promising agents including peptide, protein, and nucleic acid. Consequently, there remains a critical need for strategies to increase the selectivity of anti-prostate cancer agents. This review will focus on various prostate cancer-relevant antigens and enzymes that could be exploited for prostate cancer targeted drug delivery. Among various targeting strategies, active targeting is the most advanced approach to specifically deliver drugs to their designated cancer cells. In this approach, drug carriers are modified with targeting ligands that can specifically bind to prostate cancer-specific antigens. Moreover, there are several specific enzymes in the tumor microenvironment of prostate cancer that can be exploited for stimulus-responsive drug delivery systems. These systems can specifically release the active drug in the tumor microenvironment of prostate cancer, leading to enhanced tumor penetration efficiency.

Development of streptavidin-based nanocomplex for siRNA delivery

In our previous study, we have identified a PCBP2 siRNA that exhibits antifibrotic activity in rat hepatic stellate cells (HSCs) by inhibition of αCP2, a protein responsible for stabilization of the collagen α1 (I) mRNA in alcoholic liver fibrosis. This study aims to develop a streptavidin-based nanocomplex that can efficiently deliver the PCBP2 siRNA to HSCs. Biotin-siRNA and biotin-cholesterol were mixed with streptavidin to form the streptavidin-biotin complex, which was further condensed electrostatically with positively charged protamine to form the final multicomponent siRNA nanocomplex in the size range of 150-250 nm. The siRNA nanocomplex does not induce cytotoxicity in rat HSCs as compared to commercially available transfection agents. The cellular uptake efficiency of the siRNA nanocomplex is higher in rat HSCs than other cell lines, such as Caco-2 and PC-3, indicating that receptor-mediated endocytosis mainly contributes to the cellular uptake of the siRNA nanocomplex. The siRNA nanocomplex exhibits more than 85% silencing effect on the PCBP2 mRNA in HSCs. Stability study indicates that the nanocomplex can efficiently protect siRNA from degradation in the serum. The streptavidin-based multicomponent siRNA nanocomplex provides a promising strategy to deliver the PCBP2 siRNA to HSCs. Moreover, the nanocomplex can be used as a platform for other diseases by changing the siRNA sequence and targeting ligand.

Development of cholesteryl peptide micelles for siRNA delivery

Despite the rapid progress in the siRNA field, developing a safe and efficient delivery system of siRNA remains to be an obstacle in the therapeutical application of siRNA. The purpose of this study is to develop an efficient peptide-based siRNA delivery system for cancer therapy. To this end, cholesterol was conjugated to a series of peptides composed of lysine and histidine residues. The resultant cholesteryl peptides were characterized, and their potential for siRNA delivery was evaluated. Our results indicate that short peptides (11-21 mer) composed of various numbers of lysine and histidine residues alone are not sufficient to mediate efficient siRNA delivery. However, the amphiphilic cholesteryl peptides can self-assemble to form a micelle-like structure in aqueous solutions, which significantly promotes the siRNA condensation capability of the peptides. The cholesteryl peptides form stable complex with siRNA and effectively protect siRNA from degradation in rat serum up to three days. Furthermore, the cholesteryl peptides efficiently transfect siRNA into different cancer cells and trigger potent gene silencing effect, whereas peptides without cholesterol modification cannot deliver siRNA into the cells. In addition, one of the cholesteryl peptides Chol-H3K2s displays comparable cellular uptake and gene silencing effect but less cytotoxicity compared with branched polyethylenimine (bPEI) and Lipofectamine-2000. Our results reveal that the cholesteryl peptides possess great potential as an efficient siRNA delivery system.

Identification of chondrocyte-binding peptides by phage display

As an initial step toward targeting cartilage tissue for potential therapeutic applications, we sought cartilage-binding peptides using phage display, a powerful technology for selection of peptides that bind to molecules of interest. A library of phage displaying random 12-amino acid peptides was iteratively incubated with cultured chondrocytes to select phage that bind cartilage. The resulting phage clones demonstrated increased affinity to chondrocytes by ELISA, when compared to a wild-type, insertless phage. Furthermore, the selected phage showed little preferential binding to other cell types, including primary skin fibroblast, myocyte and hepatocyte cultures, suggesting a tissue-specific interaction. Immunohistochemical staining revealed that the selected phage bound chondrocytes themselves and the surrounding extracellular matrix. FITC-tagged peptides were synthesized based on the sequence of cartilage-binding phage clones. These peptides, but not a random peptide, bound cultured chondrocytes, and extracelluar matrix. In conclusion, using phage display, we identified peptide sequences that specifically target chondrocytes. We anticipate that such peptides may be coupled to therapeutic molecules to provide targeted treatment for cartilage disorders.

Expression profile and functional activity of peptide transporters in prostate cancer cells

Peptide transporters are expressed predominantly in intestinal and renal epithelial cells. The functional expression of peptide transporters is also identified in other types of tissues, such as glia cells, macrophages, and the epithelia of the bile duct, the lungs, and the mammary glands. However, their presence and role are poorly understood in carcinomas. We explored the expression profile and functional activity of peptide transporters in the prostate cancer cell lines LNCaP, PC-3, and DU145. Quantitative real time RT-PCR (qRT-PCR) and Western blot were used to evaluate the expression profile of peptide transporter 1 (PEPT1), peptide transporter 2 (PEPT2), peptide histidine transporter 1 (PHT1), and peptide histidine transporter 2 (PHT2) in these cells. LNCaP expresses high levels of PEPT2 and PHT1, while PC-3 demonstrates strong expression of PEPT1 and PHT1. DU145 shows only weak expression of PEPT1 and PHT1. Functional activities were studied in these cell lines using radiolabeled glycylsarcosine ([(3)H]Gly-Sar) and l-histidine ([(3)H]-l-histidine). The uptake of [(3)H]Gly-Sar and [(3)H]-l-histidine was time- and pH-dependent. A kinetic study showed that the uptake of Gly-Sar and l-histidine is saturable over the tested concentration range. The binding affinity (K(m)) and the maximal velocity (V(max)) exhibited in the three cell lines were consistent with the expression profiles we observed in qRT-PCR and Western blot analysis. A competitive inhibition study revealed that peptide transporters in prostate cancer cells exhibited broad substrate specificity with a preference for hydrophobic dipeptides, such as Leu-Leu. Fluorescence microscopy study revealed that the fluorescent dipeptide probe d-Ala-Lys-AMCA (a substrate of peptide transporters) specifically accumulated in the cytoplasm of LNCaP and PC-3, but not DU145 cells. Inhibiting the peptide transporter activity by Gly-Sar suppressed the growth of LNCaP and PC-3 cells. Our study indicated that PC-3 cells can be established as a new cell culture model for PEPT1 study, and LNCaP can be used as a model for PEPT2 study. Moreover, our results suggested that peptide transporters are overexpressed in prostate cancer cells and can be adopted as a promising target for tumor-specific drug delivery.