Browsing by Subject "drug discovery"
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Item Computational Pharmacology Towards RGS12 Inhibitors(2021-05) Dadeboe, Ian R.; Siderovski, David; Sumien, Nathalie; Schreihofer, Derek A.Background/Introduction: "Regulator of G protein Signaling" proteins, also referred to as RGS proteins, inhibit signal transduction by accelerating the hydrolysis of guanosine triphophate (GTP) to guanosine diphosphate (GDP) on the G-alpha subunit of G protein-coupled receptors (GPCRs). Sequence variations of RGS12, which is a member of the RGS protein superfamily, have been observed in some genetic profiles of people with attention-deficit hyperactivity disorder (ADHD), bipolar disorder, and schizophrenia. Hence the purpose of this study was to perform an in silico exploration of the structure/function correlation of small molecule inhibitors of the RGS12 RGS-box domain predicted to inhibit RGS12. Using these small molecule inhibitors in the mouse or rat brain would provide information on whether inhibition of RGS12 can lead to brain changes and/or behavioral changes similar to the human mental health disorders of ADHD, bipolar disorder, or schizophrenia. Method: In silico visualization and exploration of predicted small molecule inhibitors of the RGS box of RGS proteins were evaluated using the Schrodinger software suite (version 2020-3). Ninety-six predicted inhibitors underwent ligand preparation (e.g., tautomer resolution) and Glide docking within structural models of RGS4, RGS12 and RGS14. The resulting ligand and receptor interactions were quantified using Schrodinger Maestro (2020-3). In parallel, all 96 compounds were sent to BellBrook Labs for in vitro testing of GAP inhibitory activity. Results: Three compounds Z##6112, Z##0043, and Z##6197 with shared chemical features, i.e., thioether linkages, and linked sulfur and nitrogen heteroatoms, were observed to inhibit RGS12's GAP activity at least three standard deviations away from the average assay signal. Two unique features of the Z##6197 compound, a carboxylic acid group and a halogenated, ether-coupled phenolic ring, were found to inhibit in silico Glide docking or be docked in varied poses with differing chemical-bond engagements within the RGS-box receptor grids, respectively. Conclusions: Discrepancies between the in silico Glide docking and in vitro biochemical results bring into question the validity of the Glide algorithm to correctly predict the geometry and chemical-bonding character of RGS-box / small molecule inhibitor engagement. Further testing of the three identified compounds in other in vitro assays and in establishing three-dimensional structural models of their RGS-box engagement will assist in resolving these discrepancies and reveal both shared and unique determinants of RGS12 inhibition necessary for future in vivo and clinical applications.Item GENOMICS-GUIDED DISCOVERY OF POTENT ANTICANCER NATURAL PRODUCTS FROM EXOTIC BACTERIAL SPECIES(2014-03) Liu, Xiangyang; Zhu, Hui; Thapa, Santosh; Cheng, Yi-QiangNatural products are small chemical molecules produced by bacteria, fungi or plants. Natural products have made great contributions to medicine, particularly as anticancer drugs or anti-infective drugs. Currently there is a renaissance of natural product discovery due to the development of new discovery technologies and unmet medical needs. We hypothesized that exotic Gram-negative bacterial species can be a good source of diverse natural products. We analyzed the genomes of two bacterial species originally isolated from central Thailand or north Australia, and found that each genome contains multiple natural product biosynthetic gene clusters. Those information facilitated our discovery of two groups of new natural products, named thailandepsins and thailanstatins, that were found to possess potent antiproliferative activities against an array of human cancer cell lines. Additional studies are being conducted in animal models through collaborations. We thus concluded that Gram-negative bacterial species is a good source of diverse natural products, and genomics-guided discovery approach is effective and particularly suitable for small research laboratories with limited resources. Purpose (a): We hypothesize that exotic Gram-negative bacterial species can be a good source of diverse natural products. The purpose of the research is thus to discover new bioactive natural products from exotic bacterial species. Methods (b): Burkholderia thailandensis E264, a Gram-negative beta-proteobacterium strain originally isolated from a rice paddy in central Thailand, was purchased from the American Type Culture Collection (ATCC); Burkholderia thailandensis MSMB43, another Gram-negative beta-proteobacterium strain originally isolated from a water source in north Australia, was obtained from the US Centers for Disease Control (CDC). Bacterial genome analysis and natural product discovery and identification were performed according to standard procedures. Results (c): Mining the genome of B. thailandensis E264 revealed a hybrid nonribosomal peptide synthetase-polyketide synthase (NRPS–PKS) biosynthetic gene cluster that resembles that of FK228 (romidepsin, drug name Istodax) in Chromobacterium violaceum No. 968, which led us to discover thailandepsins A–F, natural analogues of FK228, and potent histone deacetylase inhibitors and antiproliferative agents with GI50 values in the sub-nM range. Mining the genome of B. thailandensis MSMB43 revealed at least 13 biosynthetic gene clusters. Among them one hybrid NRPS–PKS gene cluster is highly homologous to that of FR901464 (a prototype spliceosome inhibitor) in Pseudomonas sp. No. 2663, which led us to discover thailanstatins A–D, natural and more stable analogues of FR901464, and potent pre-mRNA splicing inhibitors and antiproliferative agents with GI50 values in the low nM range. Selected members of those natural products are under intensive collaborative investigations as anticancer drug candidates, and preliminary results are encouraging. Metabolic engineering approach is being undertaken to increase the yield of those potent compounds that are often produced in minute amounts by the wild-type bacteria. Conclusions (d): Potent new anticancer natural products have been discovered from exotic bacterial species via a genomics-guided discovery approach, which is effective and particularly suitable for small research laboratories with limited resources. We seek additional collaborations for identifying the best possible use of our small collection of potent natural products; we also seek to establish a “Texas Network for Collaborative Natural Product Discovery and Development” for sharing the resources, risks and rewards.Item Microbial Natural Product Drug Discovery Through Systematic Sampling of Diverse Texas Soils(2021-08) Currens, Grant C.; Cheng, Yi-Qiang; Basha, Riyaz; Dong, Xiaowei; Emmitte, Kyle; Jones, Harlan P.This project aimed to explore a new approach to microbial natural product discovery through collection of soil samples from strategically determined geographic sites in the State of Texas. Morphologically distinctive bacterial and fungal isolates were obtained from the soil samples and a pilot-size, semi-fractionated natural product library was constructed and screened for cytotoxicity against human cancer cell lines. Subsequently, activity-guided purification and structural identification were performed to characterize naturally occurring bioactive small molecules. Through a pilot fungal-derived natural product study, the library construction methodology was validated and known cytotoxic compounds malformin, palmitic acid, aspergillin PZ, and trichoderone B were isolated and re-identified. Their structural data and previously unknown cytotoxicity against various cancer cell lines were studied and are reported herein.