Screening and Evaluation of Natural Product Derivative Library for Anticancer Activity in Human Prostate Cancer Cells

Abstract

Natural products have been a source for almost all major FDA approved drug categories. Presently, almost 50% of all small molecule agents in clinical use are either directly or indirectly derived from natural products. Screening of natural products and their derivatives has gained prominence due to the advances made in combinatorial chemistry and cheminformatics. Both have facilitated high throughput screening methods for lead identification and lead optimization in the drug discovery process.

For the purpose of our study we utilized Tim-Tec's Natural Product Derivative Library (NDL-3000). We screened 3000 compounds for their anti-cancer activity in the prostate cancer cell line, PC-3. First, we employed the MTS cell-viability assay for screening and those that caused a decrease in cell-viability by 50% or higher were considered “hits” and potential candidates for further evaluation. Second, we employed the cheminformatics software tools from Molinspiration to calculate important physicochemical properties such as LogP, number of hydrogen bond donors and acceptors and molecular planarity for the ten “hit” compounds obtained from the screen. Lastly, we used the SwissTragetPrediction web tool as well as Molinspiration to predict the biological activity of these ten compounds. We proceeded to conduct a preliminary evaluation of the anti-cancer activity of one of the “hit” compound, ST-985 in three prostate cancer cell lines: PC-3, DU-145 and LNCaP. As part of this evaluation, we calculated the GI50 value of ST-985 in the three prostate cancer cell lines and assessed the mechanism of cell death by examining the markers of apoptosis (caspase-7 and PARP) and autophagy (LC3-B). We have identified one lead compound, ST023985, from our screening of the NDL-3000 library on the basis of the MTS assay results followed by utilization of cheminformatics web tools. GI50 values of ST-985 in the three prostate cancer cells were found to be 8.31 +/- 0.6384 µM in PC-3, 5.492 +/- 1.124 µM in LNCaP, and 9.148+/- 0.0915 µM in DU-145 cells. Results from Molinspiration showed that ST-985 did not violate the “Lipinski five rule” for oral drugs. This compound has molecular weight (MW) 360.41 (less than 500), partition coefficient (logP) 3.75 (less than 5), the numbers of hydrogen bond donors 1 (less than 5) and acceptors 5 (less than 10). Both SwissTargetPrediction and Molinspiration web tools have predicted ST-985 to be a GPCR ligand. Finally, ST-985 induced apoptosis as evidenced by cleaved caspase-7 and PRAP as well as increased autophagy marker, LC3-B in a dose dependent manner. Future studies are aimed at further understanding the mechanism of anti-cancer activity of ST-985 and other lead compounds obtained from the screening of NDL-3000 and studying their molecular targets.

Michael Kim, Young Xiong, Shengquan Liu, Shankar Chinta, Vanishree Rajagopalan

First published: 14 May 2021

https://doi.org/10.1096/fasebj.2021.35.S1.02576

This study was funded by Touro University CA- College of Pharmacy's Internal Research Award Program in 2018 and 2019.

Virtual Screening of Natural Products Database

Abstract.

Constant research on natural products has generated, over time, a large number of compounds with the potential to be evaluated in several biological tests and subsequently have been cataloged in databases that allow other researchers to perform virtual screenings of activity in various biological systems. This considerably reduces the time for the development of new drugs. This review describes the main databases of natural products available for searching bioactive compounds. It also describes the main features of virtual screening strategies for the identification of molecules with the potential to be used as new drugs. In addition, a search was made in the Web of Science database, using the search term "Virtual screening of natural products databases" from 2003 to 2018. The search criterion resulted in 230 articles, which had their abstracts evaluated with pertinence to the criteria required for this work, which are: a) be a research article; b) performing a virtual screening on databases of natural products or containing natural products; and c) works that identified drug candidate molecules. Based on these criteria, the bibliographic review on the topic was excluded. After this analysis, 104 works were selected for this review. We selected relevant papers describing the potential drug candidates that were distributed in 15 classes, of which the anticancer, antibacterial and anti-inflammatory hits were the most abundant. The works showing efforts to search for new molecules against various other diseases in distinct biological systems were also described. In this way, this work shows an overview of several methodologies and we hope they can help and inspire the development of new research to improve people's quality of life.

Authors: de Sousa Luis, José A.; Barros, Renata P. C.; de Sousa, Natália Ferreira; Muratov, Eugene; Scotti, Luciana; Scotti, Marcus Tullius

Source: Mini Reviews in Medicinal Chemistry, Volume 21, Number 18, 2021, pp. 2657-2730(74)

Publisher: Bentham Science Publishers

DOI: https://doi.org/10.2174/1389557520666200730161549

Glutaminyl-tRNA Synthetase from Pseudomonas aeruginosa: Characterization, structure, and development as a screening platform

Abstract

Pseudomonas aeruginosa has a high potential for developing resistance to multiple antibiotics. The gene (glnS) encoding glutaminyl-tRNA synthetase (GlnRS) from P. aeruginosa was cloned and the resulting protein characterized. GlnRS was kinetically evaluated and the KM and kcatobs, governing interactions with tRNA, were 1.0 μM and 0.15 s−1, respectively. The crystal structure of the α2 form of P. aeruginosa GlnRS was solved to 1.9 Å resolution. The amino acid sequence and structure of P. aeruginosa GlnRS were analyzed and compared to that of GlnRS from Escherichia coli. Amino acids that interact with ATP, glutamine, and tRNA are well conserved and structure overlays indicate that both GlnRS proteins conform to a similar three-dimensional structure. GlnRS was developed into a screening platform using scintillation proximity assay technology and used to screen ~2,000 chemical compounds. Three inhibitory compounds were identified and analyzed for enzymatic inhibition as well as minimum inhibitory concentrations against clinically relevant bacterial strains. Two of the compounds, BM02E04 and BM04H03, were selected for further studies. These compounds displayed broad-spectrum antibacterial activity and exhibited moderate inhibitory activity against mutant efflux deficient strains of P. aeruginosa and E. coli. Growth of wild-type strains was unaffected, indicating that efflux was likely responsible for the lack of sensitivity. The global mode of action was determined using time-kill kinetics. BM04H03 did not inhibit the growth of human cell cultures at any concentration and BM02E04 only inhibit cultures at the highest concentration tested (400 μg/ml). In conclusion, GlnRS from P. aeruginosa is shown to have a structure similar to that of E. coli GlnRS and two natural product compounds were identified as inhibitors of P. aeruginosa GlnRS with the potential for utility as lead candidates in antibacterial drug development in a time of increased antibiotic resistance.

Yaritza Escamilla, Casey A. Hughes, Jan Abendroth, David M. Dranow, Samantha Balboa, Frank B. Dean, James M. Bullard

First published: 12 December 2019

https://doi.org/10.1002/pro.3800