Linker optimization and activity validation of a cell surface vimentin targeted homo-dimeric peptoid antagonist for lung cancer stem cells.

Epithelial-to-mesenchymal transition (EMT) endows epithelia-derived cancer cells with properties of stem cells that govern cancer invasion and metastasis. Vimentin is one of the best studied EMT markers and recent reports indicate that vimentin interestingly translocated onto cell surface under various tumor conditions. We recently reported a cell surface vimentin (CSV) specific peptoid antagonist named JM3A.

A peptoid interleukin-15 receptor antagonist suppresses inflammation and arthritis in mice.

Objective: To discover a novel peptoid antagonist that targets the interleukin-15 (IL-15) receptor and to evaluate its therapeutic efficacy in the treatment of inflammation and arthritis.

Methods: A new compound (IFRA3, interleukin-15 receptor antagonist 3) was discovered using a unique on-bead two-colour combinatorial cell screening of a peptoid library. The interaction of IFRA3 with IL-15 receptor was assessed by pull-down and thermal shift assays.

Optimization of a cell surface vimentin binding peptoid to extract antagonist effect on lung cancer cells.

Targeting cytoskeletal proteins that are uniquely translocated to cancer cell surface may provide an alternative path for conventional drug discovery. Vimentin is such a cell surface-translocated cytoskeletal protein (CSV) found in non small cell lung cancer (NSCLC). We previously reported the identification of CSV-binding peptoid, named JM3A.

Unbiased peptoid cell screen identifies a peptoid targeting newly appeared cell surface vimentin on tumor transformed early lung cancer cells.

To identify potential new reagents and biomarkers for early lung cancer detection we combined the use of a novel preclinical isogenic model of human lung epithelial cells comparing non-malignant cells with those transformed to full malignancy using defined oncogenic changes and our on-bead two color (red and green stained cells) (OBTC) peptoid combinatorial screening methodology. The preclinical model used normal parent lung epithelial cells (HBEC3-KT, labeled with green dye) and isogenic fully malignant transformed derivatives (labeled with a red dye) via the sequential introduction of key genetic alterations of p53 knockdown, oncogenic KRAS and overexpression of cMYC (HBEC3). Using the unbiased OBTC screening approach, we tested 100,000 different peptoids and identified only one (named JM3A) that bound to the surface of the HBEC3 cells (red cells) but not HBEC3-KT cells (green cells).

A novel peptidomimetic therapeutic for selective suppression of lung cancer stem cells over non-stem cancer cells.

Cancers are highly heterogeneous and typically contain a small subset of drug-resisting cells called tumor initiating cells or cancer stem cells (CSCs). CSCs can self-renew, divide asymmetrically, and often cause tumor invasion and metastasis. Therefore, treatments specifically targeting CSCs are critical to improve patient survival.

"Molecular Masks" for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry.

Coronavirus Disease 2019 (COVID-19) remains a global health crisis, despite the development and success of vaccines in certain countries. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, uses its spike protein to bind to the human cell surface receptor angiotensin-converting enzyme 2 (ACE2), which allows the virus to enter the human body. Using our unique cell screening technology, we identified two ACE2-binding peptoid compounds and developed dimeric derivatives (ACE2P1D1 and ACE2P2D1) that effectively blocked spike protein-ACE2 interaction, resulting in the inhibition of SARS-CoV-2 pseudovirus entry into human cells.

Design of a dual ERK5 kinase activation and autophosphorylation inhibitor to block cancer stem cell activity.

The importance of ERK5 kinase signaling in tumorigenicity, metastasis, and drug resistance of cancer stem cells (CSCs) has been recognized recently, and we report a unique dual inhibitor that blocks binding of the ERK5 activator and ERK5 autophosphorylation simultaneously. The conventional ATP-binding site inhibitors have not yet yielded expected level of anti-cancer effects, due to complexities in converting ERK5 activation into CSC biological effects. We designed the first ERK5-targeted anti-CSC dual active hetero-bivalent inhibitor that blocks the regulatory peptide interaction involved in ERK5 kinase activation and that simultaneously inhibits the conventional ATP-binding pocket as well.

Unbiased peptoid combinatorial cell screen identifies plectin protein as a potential biomarker for lung cancer stem cells.

Tumors often contain a small subset of drug-resisting, self-renewing, and highly metastatic cells called tumor initiating cells or cancer stem cells (CSCs). To develop new approaches to detecting and targeting lung cancer CSCs, we applied an "unbiased" peptoid combinatorial cell screen to identify highly specific ligands that bind a CSC subpopulation of non-small cell lung cancer cells (defined by Aldefluor positivity), but not the remaining aldefluor negative cancer cells from the same preclinical model. One of the 'hit' peptoids bound to plectin, a structural protein, predominantly expressed intracellularly, but whose localization on the cell surface is linked to tumor invasion and metastasis.

Identification of side arm-modified DOTA scaffolds as multi-site binding ligands for cancer cells over normal cells.

The metal-chelated 1,4,7,10-tetraazacyclododecan-1,4,7,10-tetraacetic acid-tetraamide (DOTA) scaffold has been widely used as a contrast agent for diagnostic purposes in positron emission tomography (PET) and magnetic resonance imaging (MRI), but not as a biomarker targetable ligand. While the oxygen atoms at the stem of the four arms of the DOTA scaffold are needed for metal chelation, we previously introduced various physiochemical properties to extend these arms in a chemical library fashion to enhance the imaging contrast mechanism. We developed two such on-bead libraries, with 80 and 76 DOTA derivatives, where one arm was used to attach the DOTA scaffold onto resin beads and the other three arms were chemically modified.

A facile on-bead method for fully symmetric tetra-substituted DOTA derivatizations using peptoid moieties.

The metal-chelated 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) has made a significant impact on the field of diagnostic imaging. This imaging mechanism is largely dependent on the four side arm functionalities around the DOTA scaffold. We previously demonstrated the effect of peptoid residue modification on these DOTA side arms, thereby conferring diverse physiochemical properties to the imaging mechanism.

Converting a weaker ATP-binding site inhibitor into a potent hetero-bivalent ligand by tethering to a unique peptide sequence derived from the same kinase.

Attaching an additional binding site directed moiety or a ligand to an ATP-binding site inhibitor has been used as a strategy to increase kinase binding affinity and specificity. The moieties typically used here as the second binding partner are varied from simple organic groups to ligands such as peptides derived from substrate binding site sequences. So far these hetero-bivalent ligands were developed targeting additional binding sites closer to the ATP-binding pocket.

A mini-library system to investigate non-essential residues of lipid-phosphatidylserine (PS) binding peptide-peptoid hybrid PPS1.

We recently identified a peptide-peptoid hybrid, PPS1, which specifically recognized lipid-phosphatidylserine (PS). PPS1 consists of distinct positively charged and hydrophobic residue-containing regions. PPS1 monomer was inactive, but the dimeric form, PPS1D1, displayed strong cytotoxicity for lung cancer cells compared to normal cells in vitro, and reduced the tumor growth in vivo.

A unique mid-sequence linker used to multimerize the lipid-phosphatidylserine (PS) binding peptide-peptoid hybrid PPS1.

Ligand multimerizations enhance the binding affinity towards cell surface biomarkers through their avidity effects. Typical linkers connect individual monomeric ligand moieties from one end (e.g.

A comprehensive lipid binding and activity validation of a cancer-specific peptide-peptoid hybrid PPS1.

We recently identified a peptide-peptoid hybrid, PPS1, which recognizes lipids that have an overall negative charge, such as phosphatidylserine (PS), phosphatidylglycerol (PG), phosphatidic acid (PA), and phosphatidylinositol (PI), but that does not bind to neutral lipids, such as phosphatidylcholine (PC), phosphatidylethanolamine (PE), and sphingomyelin (SM). The simple dimeric version of PPS1, PPS1D1, displayed strong cytotoxicity to cancer cells over normal cells in vitro and tumor burden in vivo. In this study, we comprehensively characterized the direct binding and activity of PPS1 on PS, PG, and PA using liposome-based assays and lung cancer cell lines that express these negatively charged lipids.

On-bead combinatorial synthesis and imaging of europium(III)-based paraCEST agents aids in identification of chemical features that enhance CEST sensitivity.

The rate of water exchange between the inner sphere of a paramagnetic ion and bulk water is an important parameter in determining the magnitude of the chemical exchange saturation transfer signal from paramagnetic CEST agents (paraCEST). This is governed by various geometric, steric and ligand field factors created by macrocyclic ligands surrounding the paramagnetic metal ion. Our previous on-bead combinatorial studies of di-peptoid-europium(III)-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA)-tetraamide complexes revealed that negatively charged groups in the immediate vicinity of the metal center strongly enhances the CEST signal.

Identification of the minimum pharmacophore of lipid-phosphatidylserine (PS) binding peptide-peptoid hybrid PPS1D1.

We previously reported a unique peptide-peptoid hybrid, PPS1 that specifically recognizes lipid-phosphatidylserine (PS) and a few other negatively charged phospholipids, but not neutral phospholipids, on the cell membrane. The dimeric version of PPS1, i.e.

Development of a large peptoid-DOTA combinatorial library.

Conventional one-bead one-compound (OBOC) library synthesis is typically used to identify molecules with therapeutic value. The design and synthesis of OBOC libraries that contain molecules with imaging or even potentially therapeutic and diagnostic capacities (e.g.

Unbiased Selection of Peptide-Peptoid Hybrids Specific for Lung Cancer Compared to Normal Lung Epithelial Cells.

To develop widely applicable diagnostic and potentially therapeutic approaches overcoming protein heterogeneity in human cancer, we have developed a technology to unbiasedly select high specificity compound(s) that bind any biomolecule (e.g., proteins, lipids, carbohydrates) presented on the cancer cell surface but not on normal cells.

On-Bead Two-Color (OBTC) Cell Screen for Direct Identification of Highly Selective Cell Surface Receptor Ligands.

Combinatorial library screens can identify a suitable ligand for a biological target of interest out of thousands or even millions of compounds, and can play a key role in the modern drug development process. While conventional high-throughput cell screens based on functional assays require expensive robotics, simple on-bead combinatorial assays for ligand binding to the target protein can be done far more cheaply. This article describes one such assay, developed using combinatorial peptoid libraries for targeting integral membrane receptors or other cell surface-exposed molecules.

Development of homomultimers and heteromultimers of lung cancer-specific peptoids.

Multimeric interactions that occur in biology provide impetus for chemists to explore new types of synthetic multivalent ligands that alter cellular functions by mechanisms inaccessible to natural substances. While many different molecules such as peptides, antibody fragments, carbohydrates and organic moieties have been used in developing multimeric ligands, it is worth exploring other important molecular types that have hardly been tested in developing multimeric compounds. Peptoids are one such class of compounds with highly facile synthesis as well as much better biologically amenable qualities.

On-bead combinatorial synthesis and imaging of chemical exchange saturation transfer magnetic resonance imaging agents to identify factors that influence water exchange.

The sensitivity of magnetic resonance imaging (MRI) contrast agents is highly dependent on the rate of water exchange between the inner sphere of a paramagnetic ion and bulk water. Normally, identifying a paramagnetic complex that has optimal water exchange kinetics is done by synthesizing and testing one compound at a time. We report here a rapid, economical on-bead combinatorial synthesis of a library of imaging agents.

MRI detection of VEGFR2 in vivo using a low molecular weight peptoid-(Gd)8-dendron for targeting.

The synthesis of a polylysine dendron containing eight GdDOTA units conjugated to a peptoid dimer known to have a high affinity for the vascular endothelial growth factor receptor 2 (VEGFR2) is described. This simple low molecular weight system with a molecular r(1) relaxivity of ∼48 mM(-1) s(-1) is shown to enhance MR images of tumors grown in mice in vivo.

GU81, a VEGFR2 antagonist peptoid, enhances the anti-tumor activity of doxorubicin in the murine MMTV-PyMT transgenic model of breast cancer.

Background: Vascular endothelial growth factor (VEGF) is a primary stimulant of angiogenesis under physiological and pathological conditions. Anti-VEGF therapy is a clinically proven strategy for the treatment of a variety of cancers including colon, breast, lung, and renal cell carcinoma. Since VEGFR2 is the dominant angiogenic signaling receptor, it has become an important target in the development of novel anti-angiogenic therapies.

Potent and selective photo-inactivation of proteins with peptoid-ruthenium conjugates.

Advances in high-throughput screening now enable the rapid discovery of bioactive small molecules, but these primary hits almost always exhibit modest potency. We report a strategy for the transformation of these hits into much more potent inhibitors without compound optimization. Appending a derivative of Ru(II)(tris-bipyridyl)(2+), an efficient photosensitizer of singlet oxygen production, to synthetic protein-binding compounds results in highly potent and specific target protein inactivation upon irradiation with visible light.

Isolation of antagonists of antigen-specific autoimmune T cell proliferation.

Antigen-specific T cells play a major role in mediating the pathogenesis of a variety of autoimmune conditions as well as other diseases. In the context of experimental autoimmune encephalomyelitis, a murine model of multiple sclerosis, we present here a general approach to the discovery of highly specific ligands for autoreactive cells. These ligands are obtained from a combinatorial library of hundreds of thousands of synthetic peptoids that is screened simultaneously against two populations of CD4+ T cells.