Natural Products Discovery and Characterization Through Network Collaborations

Division Of Basic Sciences - Nci

Investigators

Linked publications & trials

Abstract

We utilized high throughput screening technologies to help identify compounds and extracts that can specifically interact with or modulate the function of selected biochemical targets or processes. Bioassay-guided chemical fractionation of natural products extracts is employed to isolate and purify the individual bioactive compounds. Identification and structural characterization of these compounds provides new structural classes or molecular scaffolds for the development of potential drug leads or biological probes that can interact with the desired molecular target. In addition to extensive NMR and mass spectroscopic analyses, our efforts include rigorous evaluation of a new compound's potency, molecular target specificity, and mode of action. In FY 2022, we have been continuing our research campaign to identify bioactive natural products that interact with a wide variety of molecular targets including the oncogenic transcription factor PAX3-FOXO1, the ubiquitin ligase Cbl-b, the Merkel cell carcinoma, the PKA kinase fusion protein, and the topoisomerase-3b. (1) PAX3-FOXO1: Chemical investigation of the marine hydroid Dentitheca habereri led to the identification of eight new diacylated zoanthoxanthin alkaloids, named dentithecamides A-H , along with three previously reported analogues, zoamides B-D. These compounds are the first zoanthoxanthin alkaloids to be reported from a hydroid. Dentithecamides A and B along with zoamides B-D, which all share a conformationally mobile cycloheptadiene core, inhibited PAX3-FOXO1 regulated transcriptional activity with IC50 values in the range of 1167 uM. (2) Cbl-b: The E3 ubiquitin-protein ligase Cbl-b represents an attractive target for immunotherapeutic intervention in cancer. Bioassay-guided fractionation of the active fractions of a marine sponge Plakortis sp. afforded an unprecedented dimeric alkaloid plakoramine A. Chiral separation of the racemic plakoramine A led to the purified enantiomers (+)-plakoramine A and (-)-plakoramine A which inhibited the Cbl-b activities with IC50 values at 7.5 and 9.7 uM, respectively. (3) Merkel cell carcinoma: Merkel cell carcinoma (MCC) is a rare but highly aggressive neuroendocrine skin cancer. The treatment of advanced MCC often utilizes immune checkpoint inhibitors such as avelumab or pembrolizumab. Despite relatively high response rates to these agents, less than half of patients achieve durable benefit; thus, alternative treatments are urgently needed. A new 11 amino acid linear peptide named roseabol A and the known compound 13-oxo-trans-9,10-epoxy-11(E)-octadecenoic acid were isolated from the fungus Clonostachys rosea. 13-oxo-trans-9,10-epoxy-11(E)-octadecenoic acid showed inhibitory activity against Merkel cell carcinoma with an IC50 value of 16.5 uM. (4) The PKA kinase fusion protein (PKADJ): The DNAJB1-PRKACA (PKADJ) oncogenic gene fusion has been identified as an attractive antitumor target against the rare fibrolamellar hepatocellular carcinoma. A high-throughput assay was developed to identify selective modulators of the PKADJ catalytic activity by screening the prefractionated natural product library recently created by the NCI Program for Natural Product Discovery (NPNPD). In 2022, the NPCS has been engaged in the bioassay-guided fractionations of 35 PKADJ-active extracts. Totally 9 active compounds have been identified from these projects so far. Bioassay-guided fractionation of the extract of a marine tunicate, Aplidium sp., led to the discovery of two novel alkaloids, aplithianines A and B. Aplithianine A showed potent inhibition against both PKADJ and wide-type PKA with an IC50 value of 1.1 uM. (5) Topoisomerase-3b: Topoisomerase-3b (TOP3B) is an enzyme that alters DNA topology during transcription by catalyzing transient single strand DNA breaks and passage of the intact strand through this break. TOP3B was proposed as an attractive potential therapeutic target following studies showing that it is required for the efficient replication of positive-sense RNA viruses including SARS-CoV-2 in hosts. In this new high-throughput screening campaign, the NPCS has been engaged in the bioassay-guided fractionations of 18 TOP3B-active extracts. We are in the process of isolation and identification of active natural products from these projects. (6) Discorhabdins: We have undertaken a structure-activity relationship study of discorhabdin L, a natural product that showed promising preliminary prostate cancer xenograft results. In FY22, a series of new discorhabdin natural products were isolated and discorhabdin L was used as a scaffold for the generation of semi-synthetic derivatives probing the structure activity relationship of the lead compound. We will continue to improve the efficiency of our HTS-based bioassay-guided fractionation platform by optimizing the analytical-fingerprint-based dereplication and project selection pipelines. We will also incorporate new computational modeling and organic synthesis techniques/methodologies to establish our expertise in structure modification, target identification, and activity optimization. The long-term focus of this project is to exploit the vast spectrum of chemical diversity within the NPR for potential anticancer and anti-HIV applications. It relies on close integration with the MTP Assay Development and Screening Section, Chemical Diversity Development Section, and the Protein Chemistry and Molecular Biology Section for extract screening, data analysis, bioassay support, and functional analysis of isolated compounds. Our CCR collaborators who study aspects of cancer biology, genetics, and immunology provide expertise for target selection and subsequent compound evaluation. We have assembled a broad consortium of intramural and extramural partners with expertise in organic synthesis, chemical biology, molecular pharmacology, computational sciences, and spectroscopic analysis to help characterize and advance our natural product discoveries. The Natural Products Chemistry Section is uniquely positioned within the NCI to combine molecular target-based discovery with natural products chemistry. Natural products are a source of structural complexity and biological activity that can provide insight on the function of new targets, pathways, or cellular processes. They play an important role in dissecting and understanding the intricacies of cancer development and progression, so continued natural products discovery efforts can complement the goals of the CCR and NCI.