Synthesis and screening of positional scanning synthetic combinatorial libraries

This unit presents a combinatorial library method that consists of the synthesis and screening of mixture-based synthetic combinatorial libraries (SCL) of peptide molecules. The protocols employ peptide SCL to identify peptides recognized by mAbs and T cells. The first protocol uses a positional scanning SCL (PS-SCL) made up of hexapeptides to identify antigenic determinants recognized by mAbs. The 120 mixtures in the hexapeptide PS-SCL are tested for their inhibitory activity in a competitive ELISA. The second protocol uses a decapeptide PS-SCL to identify T cell peptide ligands. The 200 mixtures of the decapeptide PS-SCL are tested for their ability to induce proliferation. Support protocols cover optimization of the assay conditions for each mAb or T cell, to achieve the best level of sensitivity and reproducibility, and preparation of a hexapeptide PS-SCL, along with deconvolution approaches.

We describe a new method for encoded synthesis, efficient on-resin screening, and rapid unambiguous sequencing of combinatorial peptide libraries. An improved binary tag system for encoding peptide libraries during synthesis was designed to facilitate unequivocal assignment of isobaric residues by MALDI-TOF MS analysis. The improved method for encoded library synthesis was combined with a new versatile on-resin screening strategy that permitted multiple stages and types of screening to be employed successively on one library under mild conditions. The new method facilitated a combinatorial study of transglutaminase (TGase) enzyme substrate peptides, revealing new details of the effect of amino acid composition on TGase substrates. The approach was first demonstrated for an encoded library (130,321 compounds) of lysine pentapeptide substrates of TGase, synthesized using the "split-mix" method. The library was reacted on-resin with TGase enzyme and a soluble desthiobiotin labeled glutamine substrate. Initial screening was performed by adsorbing streptavidin-coated magnetic microparticles onto library beads, followed by magnetic separation. The differential binding affinities of desthiobiotin and biotin for streptavidin were exploited to release the magnetic microparticles and regenerate the desthiobiotin-labeled resin beads for further screening by flow-cytometry-based automated bead sorting, resulting in 345 beads that were sequenced by MALDI-TOF MS analysis. A second library consisted of encoded glutamine hexapeptide substrates, which was reacted on-resin with TGase enzyme and a soluble desthiobiotin-labeled cadaverine. Two-stage screening identified 267 glutamine peptides as TGase-reactive, of which 21 were further analyzed by solution-phase enzyme kinetics. Kinetic results indicated that the peptide PQQQYV from the library has a 68-fold greater substrate specificity than the best known glutamine substrate QQIV. The new encoding and screening strategies described here are expected to be broadly applicable to synthesis and screening of combinatorial peptide libraries in the future.

We report here, the design and synthesis of a positional scanning synthetic combinatorial library for the identification of novel peptide ligands targeted against the cancer-specific epidermal growth factor tyrosine kinase receptor mutation variant III (EGFRvIII). This receptor is expressed in several kinds of cancer, in particular, ovarian, glioblastomas, and breast cancer, but not in normal tissue. The library consisted of six individual positional sublibraries in the format, H-O(1-6)XXXXX-NH(2), O being one of the 19 proteinogenic amino acids (cysteine omitted) and X an equimolar mixture of these. The library consisted of 114 mixtures in total. Using a biotin-streptavidin assay, the binding of each sublibrary to NR6M, NR6W-A, and NR6 cells was tested. These cells express EGFRvIII, EGFR, and neither of the receptors, respectively. The result from each sublibrary was examined to identify the most active amino acid residue at each position. On the basis of this knowledge, eight peptides were synthesized and tested for binding to EGFRvIII. We identified one peptide, H-FALGEA-NH(2), that showed more selective binding to the mutated receptor than the EGFRvIII specific peptide PEPHC1. This study demonstrates the value of using mixture-based combinatorial positional scanning libraries for the identification of novel peptide ligands targeted against the cancer-specific EGFRvIII. Our best candidate H-FALGEA-NH(2) will be radioactively labeled and evaluated as an imaging agent for positron emission tomography investigation for diagnosis, staging, and monitoring of therapy of various types of cancer.

Combining AI and traditional screening for discovery of a potent ROCK2 inhibitor against lymphoma

Researchers seeking to improve the efficiency and cost effectiveness of the bioactive small-molecule discovery process have recently embraced selection-based approaches, which in principle offer much higher throughput and simpler infrastructure requirements compared with traditional small-molecule screening methods. Since selection methods benefit greatly from an information-encoding molecule that can be readily amplified and decoded, several academic and industrial groups have turned to DNA as the basis for library encoding and, in some cases, library synthesis. The resulting DNA-encoded synthetic small-molecule libraries, integrated with the high sensitivity of PCR and the recent development of ultra high-throughput DNA sequencing technology, can be evaluated very rapidly for binding or bond formation with a target of interest while consuming minimal quantities of material and requiring only modest investments of time and equipment. In this tutorial review we describe the development of two classes of approaches for encoding chemical structures and reactivity with DNA: DNA-recorded library synthesis, in which encoding and library synthesis take place separately, and DNA-directed library synthesis, in which DNA both encodes and templates library synthesis. We also describe in vitro selection methods used to evaluate DNA-encoded libraries and summarize successful applications of these approaches to the discovery of bioactive small molecules and novel chemical reactivity.

Covalent fragment libraries in drug discovery-Design, synthesis, and screening methods.

3613 Background: Colorectal cancer (CRC) is the third most prevalent and the second deadliest cancer globally, accounting for an estimated 1,926,000 new cases and 903,800 deaths in the year 2022 alone. It's also established that chronic inflammatory conditions, such as Crohn's disease and ulcerative colitis, elevate the risk of developing CRC. Therefore, a timely CRC diagnosis for patients with colorectal disease can significantly improve their prognosis and therefore reduce cancer-related mortalities. Methods: In this study, we enrolled a total of 167 patients diagnosed with CRC (stages I: 43, II: 55, III: 56, IV: 13) and 217 patients with benign colorectal disease (BCD), from five participating hospitals. All participants underwent colonoscopy procedures, and their CRC or BCD status was pathologically confirmed. The development of the cancer detection model was based on a training cohort of 98 CRC patients and 131 BCD patients from three hospitals, and the evaluation of the model's performance was carried out on an independent test cohort comprising 69 CRC patients and 96 BCD patients from the remaining two hospitals. The predictive model leveraged cell-free fragmentomics profiling, employing low-pass whole-genome sequencing (WGS) on pre-operative plasma samples to identify CRC. Results: The early detection model exhibited remarkable efficacy in differentiating CRC patients from those with BCD, achieving an Area Under the Curve (AUC) of 0.930 in the training cohort and a nearly equivalent AUC of 0.926 in the independent test cohort. By applying the same cutoff determined in the training cohort, our model demonstrated a high sensitivity (91.8% in the training cohort and 91.3% in the test cohort) and a satisfactory specificity (78.6% in the training cohort and 82.3% in the test cohort). Notably, the model showed consistent and robust performance across various CRC characteristics, including tumor location, histology subtypes, grades, and mismatch repair deficiency status in both cohorts. Moreover, our model outperformed traditional CRC screening methods such as the fecal immunochemical test, carcinoembryonic antigen (CEA), and CA19-9, which achieved AUCs of 0.742, 0.720, and 0.543, respectively. Further validation was conducted using an additional cohort of 31 patients with advanced colorectal adenoma (advCRA), where the model achieved an AUC of 0.846 and a 66.7% sensitivity for distinguishing advCRA from BCD. Conclusions: The study introduces a non-invasive, cell-free fragmentomics assay that incorporates low-pass WGS and machine learning algorithms, demonstrating significant clinical potential in accurately distinguishing CRC and BCD patients. Our innovative approach offers a promising alternative to traditional screening methods that can improve early CRC detection, enhance CRC patient outcomes, and reduce mortality rates.

Recent discovery of tyrosinase inhibitors in traditional Chinese medicines and screening methods

Synthetic combinatorial libraries (SCLs) are collections of very large numbers of synthetic compounds, in which all possible combinations of the burlding blocks used are represented. The development and verification of the utility of combinatorial libraries represent a dramatic advance in the drug discovery process by greatly reducing the time needed to identify new drug leads. Positional scanning (PS) SCLs (,) represent a modified format of the origmal synthetic combinatorial libraries described by this laboratory (). In contrast to the original libraries, which required several iterative syntheses to identify individual active compounds, this library format provides mformation on the substituent responsible for activity at each varied position withm a structure. Therefore, only a single subsequent synthesis is required. The screening of PS-SCLs, in most instances, permits the identification of the most active substituents at each position of a compound in a single assay. Thus PS-SCLs serve to reduce further the time required to identify new drug leads. PS-SCLs are composed of individual positional SCLs, in which a single position is defined with one substituent while the remaining positions are composed of mixtures of substituents. The defined position is "walked" through the entire sequence of the PS-SCL. Therefore, the number of positional SCLs is equal to the number of residues in each compound of the PS-SCL. It should also be noted that each posrtional SCL, although addressing a single position of the sequence, represents the same collection of individual compounds For example, a hexapeptide, or a compound with six positions, can be represented as: O1XXXXX, XO2,XXXX, XXO3XXX, XXO4,XX, XXXXO5X, or XXXXXO6.

In less than one minute the catalytic activity and selectivity of a single catalyst was measured in combinatorial libraries of ternary Rh-Pd-Pt-Cu alloys. Only slightly more than two hours were needed to complete a library with 136 elements. The elements of the libraries (ca. 2-4 μg of material) are contained in a two-dimensional array synthesized by a thin-film technique. The analysis was performed by a scanning mass spectrometer (see picture).

In this paper, the integrated accelerated stress screening strength (IAS3) model has been proposed basing on the traditional screening methods and modern acceleration theory. The integrated stresses include constant high temperature, cyclic temperature and random vibration. The research in this paper shows IAS3 is much better than traditional screening methods and single accelerated stress screening methods in screen strength and test time. The IAS3 model is essential for guaranteeing the reliability of new developed military electronics.

High-Throughput Screening of Novel Peptide Inhibitors of an Integrin Receptor from the Hexapeptide Library by Using a Protein Microarray Chip

Encoding and display technologies for combinatorial libraries in drug discovery: The coming of age from biology to therapy

G-quadruplexes (G4s), secondary structures adopted by guanine-rich DNA and RNA sequences, are implicated in numerous biological processes and have been suggested as potential drug targets. Accordingly, there is an increasing interest in developing high-throughput methods that allow the generation of congeneric series of G4-targeting molecules ("ligands") and investigating their interactions with the targets. We have developed an operationally simple method of parallel synthesis to generate "ready-to-screen" libraries of cationic acylhydrazones, a motif that we have previously identified as a promising scaffold for potent, biologically active G4 ligands. Combined with well-established screening techniques, such as fluorescence melting, this method enables the rapid synthesis and screening of combinatorial libraries of potential G4 ligands. Following this protocol, we synthesized a combinatorial library of 90 bis(acylhydrazones) and screened it against five different nucleic acid structures. This way, we were able to analyze the structure-activity relationships within this series of G4 ligands, and identified three novel promising ligands whose interactions with G4-DNAs of different topologies were studied in detail by a combination of several biophysical techniques, including native mass spectrometry, and molecular modeling.

Drug development for first-line treatment of epithelial ovarian cancer (EOC) has been stagnant for almost three decades. Traditional cell culture methods for primary drug screening do not always accurately reflect clinical disease. To overcome this barrier, we grew a panel of EOC cell lines in three-dimensional (3D) cell cultures to form multicellular tumor spheroids (MCTS). We characterized these MCTS for molecular and cellular features of EOC and performed a comparative screen with cells grown using two-dimensional (2D) cell culture to identify previously unappreciated anticancer drugs. MCTS exhibited greater resistance to chemotherapeutic agents, showed signs of senescence and hypoxia, and expressed a number of stem cell-associated transcripts including ALDH1A and CD133, also known as PROM1 Using a library of clinically repurposed drugs, we identified candidates with preferential activity in MCTS over 2D cultured cells. One of the lead compounds, the dual COX/LOX inhibitor licofelone, reversed the stem-like properties of ovarian MCTS. Licofelone also synergized with paclitaxel in ovarian MCTS models and in a patient-derived tumor xenograft model. Importantly, the combination of licofelone with paclitaxel prolonged the median survival of mice (>141 days) relative to paclitaxel (115 days), licofelone (37 days), or vehicle (30 days). Increased efficacy was confirmed by Mantel-Haenszel HR compared with vehicle (HR = 0.037) and paclitaxel (HR = 0.017). These results identify for the first time an unappreciated, anti-inflammatory drug that can reverse chemotherapeutic resistance in ovarian cancer, highlighting the need to clinically evaluate licofelone in combination with first-line chemotherapy in primary and chemotherapy-refractory EOC.Significance: This study highlights the use of an in vitro spheroid 3D drug screening model to identify new therapeutic approaches to reverse chemotherapy resistance in ovarian cancer. Cancer Res; 78(15); 4370-85. ©2018 AACR.