1
|
Ancajas CMF, Oyedele AS, Butt CM, Walker AS. Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products. Nat Prod Rep 2024. [PMID: 38912779 DOI: 10.1039/d4np00009a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.
Collapse
Affiliation(s)
| | | | - Caitlin M Butt
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| |
Collapse
|
2
|
Harper CP, Day A, Tsingos M, Ding E, Zeng E, Stumpf SD, Qi Y, Robinson A, Greif J, Blodgett JAV. Critical analysis of polycyclic tetramate macrolactam biosynthetic gene cluster phylogeny and functional diversity. Appl Environ Microbiol 2024; 90:e0060024. [PMID: 38771054 PMCID: PMC11218653 DOI: 10.1128/aem.00600-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
Polycyclic tetramate macrolactams (PTMs) are bioactive natural products commonly associated with certain actinobacterial and proteobacterial lineages. These molecules have been the subject of numerous structure-activity investigations since the 1970s. New members continue to be pursued in wild and engineered bacterial strains, and advances in PTM biosynthesis suggest their outwardly simplistic biosynthetic gene clusters (BGCs) belie unexpected product complexity. To address the origins of this complexity and understand its influence on PTM discovery, we engaged in a combination of bioinformatics to systematically classify PTM BGCs and PTM-targeted metabolomics to compare the products of select BGC types. By comparing groups of producers and BGC mutants, we exposed knowledge gaps that complicate bioinformatics-driven product predictions. In sum, we provide new insights into the evolution of PTM BGCs while systematically accounting for the PTMs discovered thus far. The combined computational and metabologenomic findings presented here should prove useful for guiding future discovery.IMPORTANCEPolycyclic tetramate macrolactam (PTM) pathways are frequently found within the genomes of biotechnologically important bacteria, including Streptomyces and Lysobacter spp. Their molecular products are typically bioactive, having substantial agricultural and therapeutic interest. Leveraging bacterial genomics for the discovery of new related molecules is thus desirable, but drawing accurate structural predictions from bioinformatics alone remains challenging. This difficulty stems from a combination of previously underappreciated biosynthetic complexity and remaining knowledge gaps, compounded by a stream of yet-uncharacterized PTM biosynthetic loci gleaned from recently sequenced bacterial genomes. We engaged in the following study to create a useful framework for cataloging historic PTM clusters, identifying new cluster variations, and tracing evolutionary paths for these molecules. Our data suggest new PTM chemistry remains discoverable in nature. However, our metabolomic and mutational analyses emphasize the practical limitations of genomics-based discovery by exposing hidden complexity.
Collapse
Affiliation(s)
| | - Anna Day
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Maya Tsingos
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Edward Ding
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Elizabeth Zeng
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Spencer D. Stumpf
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Yunci Qi
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Adam Robinson
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jennifer Greif
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | | |
Collapse
|
3
|
Jiang P, Jin H, Zhang G, Zhang W, Liu W, Zhu Y, Zhang C, Zhang L. A Mechanistic Understanding of the Distinct Regio- and Chemoselectivity of Multifunctional P450s by Structural Comparison of IkaD and CftA Complexed with Common Substrates. Angew Chem Int Ed Engl 2023; 62:e202310728. [PMID: 37917570 DOI: 10.1002/anie.202310728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/04/2023]
Abstract
Regio- and chemoselective C-H activation at multi-positions of a single molecule is fascinating but chemically challenging. The homologous cytochrome P450 enzymes IkaD and CftA catalyze multiple C-H oxidations on the same polycyclic tetramate macrolactam (PoTeM) ikarugamycin, with distinct regio- and chemoselectivity. Herein we provide mechanistic understanding of their functional differences by solving crystal structures of IkaD and CftA in complex with ikarugamycin and unnatural substrates. Distinct conformations of the F/G region in IkaD and CftA are found to differentiate the orientation of PoTeM substrates, by causing different binding patterns with polar moieties to determine site selection, oxidation order, and chemoselectivity. Fine-tuning the polar subpocket altered the regioselectivity of IkaD, indicating that substrate re-orientation by mutating residues distal to the oxidation site could serve as an important method in future engineering of P450 enzymes.
Collapse
Affiliation(s)
- Peng Jiang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing, 100049, China
| | - Hongbo Jin
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
| | - Guangtao Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing, 100049, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Wei Liu
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing, 100049, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing, 100049, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing, 100049, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| |
Collapse
|
4
|
Luo J, Li X, Wang H, Du L, Shen Y, Li Y. Identification and Characterization of the 28- N-Methyltransferase Involved in HSAF Analogue Biosynthesis. Biochemistry 2022; 61:2879-2883. [DOI: 10.1021/acs.biochem.2c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jie Luo
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, P. R. China
| | - Xue Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Haoxin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska─Lincoln, Lincoln, Nebraska 68588, USA
| | - Yuemao Shen
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, P. R. China
| | - Yaoyao Li
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, P. R. China
| |
Collapse
|
5
|
Zou H, Xia X, Xu Q, Wang H, Shen Y, Li Y. Discovery of Oxidized Polycyclic Tetramate Macrolactams Bearing One or Two Rings through Combinatorial Pathway Reassembly. Org Lett 2022; 24:6515-6519. [PMID: 36053065 DOI: 10.1021/acs.orglett.2c02396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structural diversity of polycyclic tetramate macrolactams (PoTeMs) are mainly generated by the cyclases and cytochrome P450s (CYPs). The PoTeM cluster sah in Saccharopolyspora hirsuta harboring two CYP genes was combinatorially reassembled and heterologously expressed in Streptomyces. As a result, six new cytotoxic PoTeMs, sahamides A-F (1-6), were discovered, and 1-3 are the first examples of oxidized one-ring PoTeMs. Remarkably, SahE represents the first CYP performing oxidative modification on the ornithine moiety of PoTeMs.
Collapse
Affiliation(s)
- Haochen Zou
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Xin Xia
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Qiushuang Xu
- State Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Haoxin Wang
- State Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yaoyao Li
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| |
Collapse
|
6
|
Yang J, Qi Y, Blodgett JAV, Wencewicz TA. Multifunctional P450 Monooxygenase CftA Diversifies the Clifednamide Pool through Tandem C-H Bond Activations. JOURNAL OF NATURAL PRODUCTS 2022; 85:47-55. [PMID: 35086337 DOI: 10.1021/acs.jnatprod.1c00606] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Polycyclic tetramate macrolactams (PTMs) are a class of structurally complex hybrid polyketide-nonribosomal peptide (PK-NRP) natural products produced by diverse bacteria. Several PTMs display pharmaceutically interesting bioactivities, and the early stages of PTM biosynthesis involving polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) enzymology are well studied. However, the timing and mechanisms of post PKS-NRPS oxidations by P450 monooxygenases encoded in PTM biosynthetic gene clusters (BGCs) remain poorly characterized. Here we demonstrate that CftA, encoded in clifednamide-type PTM BGCs, is a multifunctional P450 monooxygenase capable of converting the C29-C30 ethyl side chain of ikarugamycin to either a C29-C30 methyl ketone or a C29-C30 hydroxymethyl ketone through C-H bond activation, resulting in the formation of clifednamide A or clifednamide C, respectively. We also report the complete structure of clifednamide C solved via multidimensional NMR (COSY, HSQC, HMBC, NOESY, and TOCSY) using material purified from an engineered Streptomyces strain optimized for production. Finally, the in vitro reconstitution of recombinant CftA catalytic activity revealed the oxidation cascade for sequential conversion of ikarugamycin to clifednamide A and clifednamide C. Our findings confirm prior genetics-based predictions on the origins of clifednamide complexity via P450s encoded in PTM BGCs and place CftA into a growing group of multifunctional P450s that tailor PTM natural products through late-stage regioselective C-H bond activation.
Collapse
Affiliation(s)
- Jinping Yang
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Yunci Qi
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Joshua A V Blodgett
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Timothy A Wencewicz
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| |
Collapse
|
7
|
Xiao ZH, Dong J, Li A, Dai JM, Li YP, Hu QF, Shao LD, Matsuda Y, Wang WG. Biocatalytic and chemical derivatization of fungal meroditerpenoid chevalone E. Org Chem Front 2022. [DOI: 10.1039/d2qo00055e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fungal meroditerpenoids include diverse molecules with structural complexity and a broad range of biological activities. We have previously obtained meroditerpenoid chevalone E (1) and its oxidized analogues by heterologously expressing...
Collapse
|
8
|
Yan Y, Wang H, Li Y. Discovery of a New Polycyclic Tetramate Macrolactam 3-Hydroxycombamide I. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202110001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
9
|
Luo J, Yan Y, Wang H, Li Y. Discovery of a New Polycyclic Tetramate Macrolactam Clifednamide K. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202109042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|