Disulfide-Directed Multicyclic Peptide Libraries for the Discovery of Peptide Ligands and Drugs.

Multicyclic peptides with stable 3D structures are a kind of novel and promising peptide formats for drug design and discovery as they have the potential to combine the best characteristics of small molecules and proteins. However, the development of multicyclic peptides is largely limited to naturally occurring products. It remains a big challenge to develop multicyclic peptides with new structures and functions without recourse to the existing natural scaffolds. Here, we report a general and robust method relying on the utility of new disulfide-directing motifs for designing and discovering diverse multicyclic peptides with potent protein-binding capability. These peptides, referred to as disulfide-directed multicyclic peptides (DDMPs), are tolerant to extensive sequence manipulations and variations of disulfide-pairing frameworks, enabling the development of de novo DDMP libraries useful for ligand and drug discovery. This study opens a new avenue for creating a new generation of multicyclic peptides in sequence and structure space inaccessible by natural scaffolds, thus would greatly benefit the field of peptide drug discovery.

Structure-guided design of CPPC-paired disulfide-rich peptide libraries for ligand and drug discovery.

Peptides constrained through multiple disulfides (or disulfide-rich peptides, DRPs) have been an emerging frontier for ligand and drug discovery. Such peptides have the potential to combine the binding capability of biologics with the stability and bioavailability of smaller molecules. However, DRPs with stable three-dimensional (3D) structures are usually of natural origin or engineered from natural ones. Here, we report the discovery and identification of CPPC (cysteine-proline-proline-cysteine) motif-directed DRPs with stable 3D structures (i.e., CPPC-DRPs). A range of new CPPC-DRPs were designed or selected from either random or structure-convergent peptide libraries. Thus, for the first time we revealed that the CPPC-DRPs can maintain diverse 3D structures by taking advantage of constraints from unique dimeric CPPC mini-loops, including irregular structures and regular α-helix and ß-sheet folds. New CPPC-DRPs that can specifically bind the receptors (CD28) on the cell surface were also successfully discovered and identified using our DRP-discovery platform. Overall, this study provides the basis for accessing an unconventional peptide structure space previously inaccessible by natural DRPs and computational designs, inspiring the development of new peptide ligands and therapeutics.

Role of BCAR4 in prostate cancer cell autophagy.

BACKGROUND: Increased autophagy of prostate cancer (PC) cells contributes to their resistance to chemotherapy. Recently, we reported that a long non-coding RNA (lncRNA)-breast-cancer anti-estrogen resistance 4 (BCAR4)-is highly expressed in PC and contributes to castration resistance through activation of GLI2 signaling. However, the role of BCAR4 in the regulation of PC cell autophagy is unknown and is the subject of the current study. METHODS: BCAR4 and Beclin-1 levels and the alteration in autophagy pathway genes were assessed in PC using a public database and in our own clinical specimens. The correlation between BCAR4 and Beclin-1 levels in PC and PC cell lines was determined and their regulatory relationship was assessed by overexpression and knockout assay. The final effect on autophagy was measured by microtubule-associated protein 1A/1B-light chain 3 (LC3) levels. The mechanism that underlies the control of Beclin-1 by BCAR4 was analyzed by cancer database and gain-of-function and loss-of-function approaches. RESULTS: BCAR4 and Beclin-1 were both upregulated in PC and were positively correlated. BCAR4 directly activated Beclin-1 at transcriptional level, which subsequently increased the ratio of LC3 II to LC3I to augment PC cell autophagy. Beclin-1 did not control levels of BCAR4. Mechanically, BCAR4 and Beclin-1 shared several targeting microRNAs, among which miR-15 and miR-146 appeared to be the mediators of the effects of BACR4 on Beclin-1. CONCLUSIONS: BCAR4 may enhance PC cell autophagy through altering miRNA-regulated Beclin-1 expression in PC.

Directed Disulfide Pairing and Folding of Peptides for the De Novo Development of Multicyclic Peptide Libraries.

Disulfide-rich peptides (DRPs) have been an emerging frontier for drug discovery. There have been two DRPs approved as drugs (i.e., Ziconotide and Linaclotide), and many others are undergoing preclinical studies or in clinical trials. All of these DRPs are of nature origin or derived from natural peptides. It is still a challenge to design new DRPs without recourse to natural scaffolds due to the difficulty in handling the disulfide pairing. Here we developed a simple and robust strategy for directing the disulfide pairing and folding of peptides with up to six cysteine residues. Our strategy exploits the dimeric pairing of CPPC (cysteine-proline-proline-cysteine) motifs for directing disulfide formation, and DRPs with different multicyclic topologies were designed and synthesized by regulating the patterns of CPPC motifs and cysteine residues in peptides. As neither sequence manipulations nor unnatural amino acids are involved, the designed DRPs can be used as templates for the de novo development of biosynthetic multicyclic peptide libraries, enabling selection of DRPs with new functions directly from fully randomized sequences. We believe that this work represents as an important step toward the discovery and design of new multicyclic peptide ligands and therapeutics with structures not derived from natural scaffolds.

Fluorescent nanoprobe array based on carbon nanodots for qualitative and quantitative determination of biogenic polyamine.

A nanoprobe array based on fluorescent nitrogen-rich carbon dots (N-CDs) and Ag+ was constructed for simultaneous qualitative and quantitative determination of seven kinds of biogenic polyamines (BAs), including tryptamine (Try), histamine (His), putrescine (Put), cadaverine (Cad), spermine (Spm), spermidine (Spd), and agmatine (Agm). Ag+ can specifically bind to the N-CDs and quench the fluorescence of the N-CDs through a static mechanism. BAs further statically quench the fluorescence of the N-CD@Ag+ composite by bridging two Ag+ centers of the N-CD@Ag+. The nanoprobe array was constructed based on the differential fluorescence response arising from the differential binding affinity of various BAs. BAs can be differentiated and analyzed by the nanoprobe array within the concentration range 0.5-500 µM. The preliminary diluted and artificially spiked commercial human serum was utilized to simulate the serum environment for assessing the performance of the nanoprobe array in real samples. The N-CD@Ag+ system can recognize BAs with 100% accuracy in simulated human serum samples. The quantitative determination of BAs - no matter in a one-component system or a three-component system - was also realized by using the N-CD@Ag+ system even in the simulated serum environment. The recovery rates from spiked serum samples were higher 99%, and the relative standard deviation (RSD) was less than 3%. Based on the excellent multi-BA determination performance, a BA-related disease model about cerebral ischemia was constructed. Healthy cases as well as mild, moderate, and severe cerebral ischemia cases can be well identified from the disease model based on the N-CD@Ag+ nanoprobe array. Schematic representation of fluorescent nanoprobe array constructed by carbon nanodots (N-CDs) and Ag+ for qualitative and quantitative analyses of biogenic polyamines (BAs) and diagnosis of cerebral ischemia (CI) through linear discriminant analysis (LDA) and support vector machine (SVM).

Design and Synthesis of Disulfide-Rich Peptides with Orthogonal Disulfide Pairing Motifs.

Disulfide-rich peptides (DRPs) are a class of peptides that are constrained through two or more disulfide bonds. Though natural DRPs have been extensively exploited for developing protein binders or potential therapeutics, their synthesis and re-engineering to bind new targets are not straightforward due to difficulties in handling the disulfide pairing problem. Rationally designed DRPs with an intrinsically orthogonal disulfide pairing propensity provide an alternative to the natural scaffolds for developing functional DRPs. Herein we report the use of tandem CXPen/PenXC motifs ((C) cysteine; (Pen) penicillamine; (X) any residue) for directing the oxidative folding of peptides. Diverse tricyclic peptides were designed and synthesized by varying the pattern of C/Pen residues and incorporating a tandem CXPen/PenXC motif into peptides. The folding of these peptides was determined primarily by C/Pen patterns and tolerated to sequence manipulations. The applicability of the designed C/Pen-DRPs was demonstrated by designing protein binders using an epitope grafting strategy. This study thus demonstrates the potential of using orthogonal disulfide pairing to design DRP scaffolds with new structures and functions, which would greatly benefit the development of multicyclic peptide ligands and therapeutics.

BCAR4 activates GLI2 signaling in prostate cancer to contribute to castration resistance.

Long non-coding RNAs (lncRNAs) have been found essential for tumorigenesis of prostate cancer (PC), but its role in the regulation of castration-resistant prostate cancer (CRPC) is poorly identified. Here, we showed that a lncRNA, Breast-Cancer Anti-Estrogen Resistance 4 (BCAR4), which plays a pivotal role in the tamoxifen-resistance of breast cancer, was significantly upregulated in CRPC, but not in castration-sensitive prostate cancer (CSPC), compared to normal prostate tissue. High BCAR4 levels in CRPC were correlated with poor patients' overall survival. Androgen increased growth and migration of androgen receptor (AR)-positive PC346 cells, which was abolished by the antagonist of androgen. Overexpression of BCAR4 in PC346 cells increased cell growth and migration, but turned the cells insensitive to androgen. On the other hand, growth and migration of AR-negative DU145 cells are insensitive to androgen, while depletion of BCAR4 in DU145 cells not only decreased cell growth, but also turned the cells sensitive again to androgen. Moreover, BCAR4 activated GLI2 downstream genes, and correlated with the levels of these GLI2-target genes in CRPC. Depletion of GLI2 abolished the effects of BCAR4 on cell growth and migration. Together, our data suggest that BCAR4 may activate GLI2 signaling in PC to contribute to castration resistance.

Carbon Nanodots-Based Fluorescent Turn-On Sensor Array for Biothiols.

Biothiols play important roles in biological processes. In this study, a novel sensor array-based method was proposed to detect and differentiate biothiols. The sensor array was constructed using three kinds of Ag+-sensitive carbon nanodots (CDs). The CDs were synthesized with amino acids and urea as carbon sources via a simple microwave method. Results revealed that Ag+ can bind with CDs and depress the fluorescence of CDs, while the subsequently joined biothiols can take Ag+ away from CDs and recover the fluorescence of CDs. Due to the different binding ability between Ag+ and various CDs, as well as Ag+ and various biothiols, the CD-Ag+ array exhibits a unique pattern of fluorescence variations when interacting with six biothiol samples (cysteamine, dithiothreitol, mercaptosuccinic acid, glutathione, mercaptoacetic acid, and mercaptoethanol). Principal component analysis (PCA) was applied to analyze the pattern and generate a clustering map for a clearer identification of these biothiols. PCA can also be employed to simplify the established three-sensor array into a two-sensor array. Both the three- and two-sensor arrays can identify these biothiols in a wide biothiol concentration range (>10 µM).

miR-181 regulation of BAX controls cisplatin sensitivity of prostate cancer cells.

Prostate cancer is one of the most common male malignancies and remains the second leading cause for cancer-specific mortalities in men. Cisplatin is commonly used as a chemotherapeutic agent against advanced cancers, and is now used in metastatic prostate cancers. Cisplatin exerts its cytotoxic effects by cross-linking genomic DNA (gDNA) which induces DNA damage on rapidly dividing cancer cells. However, cisplatin leads to systemic side effects and some patients never respond. Our previous report demonstrated an oncogenic role of miR-181a in human prostate cancer. In this study, we investigate the mechanistic potential of miR-181a in regulating cisplatin sensitivity in this context. We report that cisplatin treatment significantly enhanced miR-181a expression and that exogenous overexpression of miR-181a decreased sensitivity of prostate cancer cells to cisplatin. Additionally, we observed that cisplatin-resistant prostate cancer cells harbored high levels of miR-181a expression. Mechanistically, we demonstrate the pro-apoptotic protein, BAX, is typically enhanced by cisplatin treatment but its suppression promoted resistance. Here we demonstrate miR-181a regulation of BAX was mediated through a complimentary interaction with the 3'UTR of the BAX transcript. We subsequently show that BAX expression restored cisplatin sensitivity in miR-181a overexpressing prostate cancer cells. In parallel, we demonstrate inhibition of miR-181a restored BAX expression as well as cisplatin sensitivity in resistant cells. This study suggests that miR-181a is a potential therapeutic target for prostate cancers that are resistant to cisplatin.