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Dvořák Z, Li H, Mani S. Microbial Metabolites as Ligands to Xenobiotic Receptors: Chemical Mimicry as Potential Drugs of the Future. Drug Metab Dispos 2023; 51:219-227. [PMID: 36184080 PMCID: PMC9900867 DOI: 10.1124/dmd.122.000860] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 08/28/2022] [Accepted: 09/19/2022] [Indexed: 01/31/2023] Open
Abstract
Xenobiotic receptors, such as the pregnane X receptor, regulate multiple host physiologic pathways including xenobiotic metabolism, certain aspects of cellular metabolism, and innate immunity. These ligand-dependent nuclear factors regulate gene expression via genomic recognition of specific promoters and transcriptional activation of the gene. Natural or endogenous ligands are not commonly associated with this class of receptors; however, since these receptors are expressed in a cell-type specific manner in the liver and intestines, there has been significant recent effort to characterize microbially derived metabolites as ligands for these receptors. In general, these metabolites are thought to be weak micromolar affinity ligands. This journal anniversary minireview focuses on recent efforts to derive potentially nontoxic microbial metabolite chemical mimics that could one day be developed as drugs combating xenobiotic receptor-modifying pathophysiology. The review will include our perspective on the field and recommend certain directions for future research. SIGNIFICANCE STATEMENT: Xenobiotic receptors (XRs) regulate host drug metabolism, cellular metabolism, and immunity. Their presence in host intestines allows them to function not only as xenosensors but also as a response to the complex metabolic environment present in the intestines. Specifically, this review focuses on describing microbial metabolite-XR interactions and the translation of these findings toward discovery of novel chemical mimics as potential drugs of the future for diseases such as inflammatory bowel disease.
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Affiliation(s)
- Zdeněk Dvořák
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Departments of Medicine (H.L., S.M.), Molecular Pharmacology (S.M.), and Genetics (S.M.), Albert Einstein College of Medicine, Bronx, New York, USA
| | - Hao Li
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Departments of Medicine (H.L., S.M.), Molecular Pharmacology (S.M.), and Genetics (S.M.), Albert Einstein College of Medicine, Bronx, New York, USA
| | - Sridhar Mani
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Departments of Medicine (H.L., S.M.), Molecular Pharmacology (S.M.), and Genetics (S.M.), Albert Einstein College of Medicine, Bronx, New York, USA
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Liang L, Liu Y, Kang B, Wang R, Sun MY, Wu Q, Meng XF, Lin JP. Large-scale comparison of machine learning algorithms for target prediction of natural products. Brief Bioinform 2022; 23:6675751. [PMID: 36007240 DOI: 10.1093/bib/bbac359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/26/2022] [Accepted: 07/31/2022] [Indexed: 11/13/2022] Open
Abstract
Natural products (NPs) and their derivatives are important resources for drug discovery. There are many in silico target prediction methods that have been reported, however, very few of them distinguish NPs from synthetic molecules. Considering the fact that NPs and synthetic molecules are very different in many characteristics, it is necessary to build specific target prediction models of NPs. Therefore, we collected the activity data of NPs and their derivatives from the public databases and constructed four datasets, including the NP dataset, the NPs and its first-class derivatives dataset, the NPs and all its derivatives and the ChEMBL26 compounds dataset. Conditions, including activity thresholds and input features, were explored to access the performance of eight machine learning methods of target prediction of NPs, including support vector machines (SVM), extreme gradient boosting, random forests, K-nearest neighbor, naive Bayes, feedforward neural networks (FNN), convolutional neural networks and recurrent neural networks. As a result, the NPs and all their derivatives datasets were selected to build the best NP-specific models. Furthermore, the consensus models, as well as the voting models, were additionally applied to improve the prediction performance. More evaluations were made on the external validation set and the results demonstrated that (1) the NP-specific model performed better on the target prediction of NPs than the traditional models training on the whole compounds of ChEMBL26. (2) The consensus model of FNN + SVM possessed the best overall performance, and the voting model can significantly improve recall and specificity.
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Affiliation(s)
- Lu Liang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Ye Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Bo Kang
- National Supercomputer Center in Tianjin, 10 Xinhuanxi Road, Tianjin Binhai New Area, Tianjin 300457, China
| | - Ru Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Meng-Yu Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Qi Wu
- National Supercomputer Center in Tianjin, 10 Xinhuanxi Road, Tianjin Binhai New Area, Tianjin 300457, China
| | - Xiang-Fei Meng
- National Supercomputer Center in Tianjin, 10 Xinhuanxi Road, Tianjin Binhai New Area, Tianjin 300457, China
| | - Jian-Ping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China.,Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China.,Platform of Pharmaceutical Intelligence, Tianjin International Joint Academy of Biomedicine, Tianjin 300457, China
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Grycová A, Joo H, Maier V, Illés P, Vyhlídalová B, Poulíková K, Sládeková L, Nádvorník P, Vrzal R, Zemánková L, Pečinková P, Poruba M, Zapletalová I, Večeřa R, Anzenbacher P, Ehrmann J, Ondra P, Jung JW, Mani S, Dvořák Z. Targeting the Aryl Hydrocarbon Receptor with Microbial Metabolite Mimics Alleviates Experimental Colitis in Mice. J Med Chem 2022; 65:6859-6868. [PMID: 35416668 DOI: 10.1021/acs.jmedchem.2c00208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Targeting the aryl hydrocarbon receptor (AhR) is an emerging therapeutic strategy for multiple diseases (e.g., inflammatory bowel disease). Thermosporothrix hazakensis microbial metabolite 2-(1'H-indole-3'-carbonyl)-thiazole-4-carboxylic acid methyl ester (ITE) is a putative AhR endogenous ligand. To improve the chemical stability, we synthesized a series of ITE chemical mimics. Using a series of in vitro assays, we identified 2-(1H-indole-3-carbonyl)-N-methyl thiazole-4-carboxamide (ITE-CONHCH3) as a highly potent (EC50 = 1.6 nM) AhR agonist with high affinity (Ki = 88 nM). ITE-CONHCH3 triggered AhR nuclear translocation and dimerization of AhR-ARNT, enhanced AhR binding in the CYP1A1 promoter, and induced AhR-regulated genes in an AhR-dependent manner. The metabolic stability of ITE-CONHCH3 in a cell culture was 10 times higher than that of ITE. Finally, we observed protective effects of ITE-CONHCH3 in mice with DSS-induced colitis. Overall, we demonstrate and validate a concept of microbial metabolite mimicry in the therapeutic targeting of AhR.
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Affiliation(s)
- Aneta Grycová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Hansol Joo
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Vítězslav Maier
- Department of Forensic Medicine and Medical Law, University Hospital Olomouc, and Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 779 00 Olomouc, Czech Republic
| | - Peter Illés
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Barbora Vyhlídalová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Karolína Poulíková
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Lucia Sládeková
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Petr Nádvorník
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Radim Vrzal
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Lenka Zemánková
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Petra Pečinková
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Martin Poruba
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 779 00 Olomouc, Czech Republic
| | - Iveta Zapletalová
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 779 00 Olomouc, Czech Republic
| | - Rostislav Večeřa
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 779 00 Olomouc, Czech Republic
| | - Pavel Anzenbacher
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 779 00 Olomouc, Czech Republic
| | - Jiří Ehrmann
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 779 00 Olomouc, Czech Republic
| | - Peter Ondra
- Department of Forensic Medicine and Medical Law, University Hospital Olomouc, and Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 779 00 Olomouc, Czech Republic
| | - Jong-Wha Jung
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Sridhar Mani
- Department of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Zdeněk Dvořák
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
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Li H, Illés P, Karunaratne CV, Nordstrøm LU, Luo X, Yang A, Qiu Y, Kurland IJ, Lukin DJ, Chen W, Jiskrová E, Krasulová K, Pečinková P, DesMarais VM, Liu Q, Albanese JM, Akki A, Longo M, Coffin B, Dou W, Mani S, Dvořák Z. Deciphering structural bases of intestinal and hepatic selectivity in targeting pregnane X receptor with indole-based microbial mimics. Bioorg Chem 2021; 109:104661. [PMID: 33636438 PMCID: PMC8646148 DOI: 10.1016/j.bioorg.2021.104661] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 02/07/2023]
Abstract
Microbial metabolite mimicry is a new concept that promises to deliver compounds that have minimal liabilities and enhanced therapeutic effects in a host. In a previous publication, we have shown that microbial metabolites of L-tryptophan, indoles, when chemically altered, yielded potent anti-inflammatory pregnane X Receptor (PXR)-targeting lead compounds, FKK5 and FKK6, targeting intestinal inflammation. Our aim in this study was to further define structure-activity relationships between indole analogs and PXR, we removed the phenyl-sulfonyl group or replaced the pyridyl residue with imidazolopyridyl of FKK6. Our results showed that while removal of the phenyl-sulfonyl group from FKK6 (now called CVK003) shifts agonist activity away from PXR towards the aryl hydrocarbon receptor (AhR), the imidazolopyridyl addition preserves PXR activity in vitro. However, when these compounds are administered to mice, that unlike the parent molecule, FKK6, they exhibit poor induction of PXR target genes in the intestines and the liver. These data suggest that modifications of FKK6 specifically in the pyridyl moiety can result in compounds with weak PXR activity in vivo. These observations are a significant step forward for understanding the structure-activity relationships (SAR) between indole mimics and receptors, PXR and AhR.
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Affiliation(s)
- Hao Li
- Department of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Peter Illés
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | | | | | - Xiaoping Luo
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Annie Yang
- Department of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yunping Qiu
- Department of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Irwin J Kurland
- Department of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Dana J Lukin
- Department of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Weijie Chen
- Department of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Eva Jiskrová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Kristýna Krasulová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Petra Pečinková
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Vera M DesMarais
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Qiang Liu
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joseph M Albanese
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ashwin Akki
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Michael Longo
- Department of Medical Education, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Breyen Coffin
- Department of Medical Education, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Wei Dou
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Sridhar Mani
- Department of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Zdeněk Dvořák
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic.
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Dvořák Z, Poulíková K, Mani S. Indole scaffolds as a promising class of the aryl hydrocarbon receptor ligands. Eur J Med Chem 2021; 215:113231. [PMID: 33582577 DOI: 10.1016/j.ejmech.2021.113231] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/24/2021] [Accepted: 01/24/2021] [Indexed: 11/18/2022]
Abstract
The aryl hydrocarbon receptor (AhR), deemed initially as a xenobiotic sensor, plays multiple physiological roles and is involved in various pathophysiological processes and many diseases' etiology. Therefore, the therapeutic and chemopreventive targeting of AhR is a fundamental issue. To date, thousands of structurally diverse ligands of AhR have been identified. The bottleneck in targeting the AhR is that it is a Janus-faced player with beneficial vs. harmful effects in the ligand-specific context. A distinct structural class of the AhR ligands is those with indole-based scaffolds. The present review summarizes the knowledge on the existing indole-derived AhR ligands, comprising natural and dietary compounds, synthetic compounds including clinically used drugs, endogenous intermediary metabolites, and catabolites produced by human microbiota. The examples of novel, indole ring containing, rational design based AhR ligands are presented. The molecular, in vitro, and in vivo effects are described.
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Affiliation(s)
- Zdeněk Dvořák
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc, Czech Republic.
| | - Karolína Poulíková
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
| | - Sridhar Mani
- Department of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
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Gewirtz DA. "Emerging Concepts": New Article Category in Molecular Pharmacology. Mol Pharmacol 2020; 98:350. [PMID: 32764094 DOI: 10.1124/molpharm.120.000133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- David A Gewirtz
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Massey Cancer Center, 401 College St., Richmond, VA 23298, Phone: 8040828-9523, Fax: 804-827-1134
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