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Orr AA, Yang J, Sule N, Chawla R, Hull KG, Zhu M, Romo D, Lele PP, Jayaraman A, Manson MD, Tamamis P. Molecular Mechanism for Attractant Signaling to DHMA by E. coli Tsr. Biophys J 2019; 118:492-504. [PMID: 31839263 DOI: 10.1016/j.bpj.2019.11.3382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/05/2019] [Accepted: 11/19/2019] [Indexed: 12/20/2022] Open
Abstract
The attractant chemotaxis response of Escherichia coli to norepinephrine requires that it be converted to 3,4-dihydroxymandelic acid (DHMA) by the monoamine oxidase TynA and the aromatic aldehyde dehydrogenase FeaB. DHMA is sensed by the serine chemoreceptor Tsr, and the attractant response requires that at least one subunit of the periplasmic domain of the Tsr homodimer (pTsr) has an intact serine-binding site. DHMA that is generated in vivo by E. coli is expected to be a racemic mixture of the (R) and (S) enantiomers, so it has been unclear whether one or both chiral forms are active. Here, we used a combination of state-of-the-art tools in molecular docking and simulations, including an in-house simulation-based docking protocol, to investigate the binding properties of (R)-DHMA and (S)-DHMA to E. coli pTsr. Our studies computationally predicted that (R)-DHMA should promote a stronger attractant response than (S)-DHMA because of a consistently greater-magnitude piston-like pushdown of the pTsr α-helix 4 toward the membrane upon binding of (R)-DHMA than upon binding of (S)-DHMA. This displacement is caused primarily by interaction of DHMA with Tsr residue Thr156, which has been shown by genetic studies to be critical for the attractant response to L-serine and DHMA. These findings led us to separate the two chiral species and test their effectiveness as chemoattractants. Both the tethered cell and motility migration coefficient assays validated the prediction that (R)-DHMA is a stronger attractant than (S)-DHMA. Our study demonstrates that refined computational docking and simulation studies combined with experiments can be used to investigate situations in which subtle differences between ligands may lead to diverse chemotactic responses.
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Affiliation(s)
- Asuka A Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Jingyun Yang
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Nitesh Sule
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Ravi Chawla
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Kenneth G Hull
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Mingzhao Zhu
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Daniel Romo
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Michael D Manson
- Department of Biology, Texas A&M University, College Station, Texas.
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas.
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Park H, Jin UH, Orr AA, Echegaray SP, Davidson LA, Allred CD, Chapkin RS, Jayaraman A, Lee K, Tamamis P, Safe S. Isoflavones as Ah Receptor Agonists in Colon-Derived Cell Lines: Structure-Activity Relationships. Chem Res Toxicol 2019; 32:2353-2364. [PMID: 31621310 DOI: 10.1021/acs.chemrestox.9b00352] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many of the protective responses observed for flavonoids in the gastrointestinal track resemble aryl hydrocarbon receptor (AhR)-mediated effects. Therefore, we examined the structure-activity relationships of isoflavones and isomeric flavone and flavanones as AhR ligands on the basis of their induction of CYP1A1, CYP1B1, and UGT1A1 gene expression in colon cancer Caco2 cells and young adult mouse colonocyte (YAMC) cells. Caco2 cells were significantly more Ah-responsive than YAMC cells, and this was due, in part, to flavonoid-induced cytotoxicity in the latter cell lines. The structure-activity relationships for the flavonoids were complex and both response and cell context specific; however, there was significant variability in the AhR activities of the isomeric substituted isoflavones and flavones. For example, 4',5,7-trihydroxyisoflavone (genistein) was AhR-inactive whereas 4',5,7-trihydroxyflavone (apigenin) induced CYP1A1, CYP1B1, and UGT1A1 in Caco2 cells. In contrast, both 5,7-dihydroxy-4-methoxy substituted isoflavone (biochanin A) and flavone (acacetin) induced all three AhR-responsive genes; 4',5,7-trimethoxyisoflavone was a potent AhR agonist, and the isomeric flavone was AhR-inactive. These results coupled with simulation studies modeling flavonoid interaction within the AhR binding pocket demonstrate that the orientation of the substituted phenyl ring at C-2 (flavones) or C-3 (isoflavones) on the common 4-H-chromen-4-one ring strongly influences the activities of isoflavones and flavones as AhR agonists.
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Affiliation(s)
- Hyejin Park
- Department of Veterinary Physiology and Pharmacology , Texas A&M University , College Station , Texas 77843 , United States
| | - Un-Ho Jin
- Department of Veterinary Physiology and Pharmacology , Texas A&M University , College Station , Texas 77843 , United States
| | - Asuka A Orr
- Artie McFerrin Department of Chemical Engineering , Texas A&M University , College Station , Texas 77840 , United States
| | - Stephanie P Echegaray
- Artie McFerrin Department of Chemical Engineering , Texas A&M University , College Station , Texas 77840 , United States
| | - Laurie A Davidson
- Department of Nutrition and Food Science , Texas A&M University , College Station , Texas 77843 , United States
| | - Clinton D Allred
- Department of Nutrition and Food Science , Texas A&M University , College Station , Texas 77843 , United States
| | - Robert S Chapkin
- Department of Nutrition and Food Science , Texas A&M University , College Station , Texas 77843 , United States
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering , Texas A&M University , College Station , Texas 77840 , United States
| | - Kyongbum Lee
- Department of Chemical and Biological Engineering , Tufts University , Medford , Massachusetts 02155 , United States
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering , Texas A&M University , College Station , Texas 77840 , United States
| | - Stephen Safe
- Department of Veterinary Physiology and Pharmacology , Texas A&M University , College Station , Texas 77843 , United States
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Activation of COUP-TFI by a Novel Diindolylmethane Derivative. Cells 2019; 8:cells8030220. [PMID: 30866413 PMCID: PMC6468570 DOI: 10.3390/cells8030220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 12/11/2022] Open
Abstract
Chicken ovalbumin upstream promoter-transcription factor I (COUP-TFI) is an orphan receptor and member of the nuclear receptor superfamily. Among a series of methylene substituted diindolylmethanes (C-DIMs) containing substituted phenyl and heteroaromatic groups, we identified 1,1-bis(3'-indolyl)-1-(4-pyridyl)-methane (DIM-C-Pyr-4) as an activator of COUP-TFI. Structure activity studies with structurally diverse heteroaromatic C-DIMs showed that the pyridyl substituted compound was active and the 4-pyridyl substituent was more potent than the 2- or 3-pyridyl analogs in transactivation assays in breast cancer cells. The DIM-C-Pyr-4 activated chimeric GAL4-COUP-TFI constructs containing full length, C- or N-terminal deletions, and transactivation was inhibited by phosphatidylinositol-3-kinase and protein kinase A inhibitors. However, DIM-C-Pyr-4 also induced transactivation and interactions of COUP-TFI and steroid receptor coactivators-1 and -2 in mammalian two-hybrid assays, and ligand-induced interactions of the C-terminal region of COUP-TFI were not affected by kinase inhibitors. We also showed that DIM-C-Pyr-4 activated COUP-TFI-dependent early growth response 1 (Egr-1) expression and this response primarily involved COUP-TFI interactions with Sp3 and to a lesser extent Sp1 bound to the proximal region of the Egr-1 promoter. Modeling studies showed interactions of DIM-C-Pyr-4 within the ligand binding domain of COUP-TFI. This report is the first to identify a COUP-TFI agonist and demonstrate activation of COUP-TFI-dependent Egr-1 expression.
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Mohan R, Wilson M, Gorham RD, Harrison RES, Morikis VA, Kieslich CA, Orr AA, Coley AV, Tamamis P, Morikis D. Virtual Screening of Chemical Compounds for Discovery of Complement C3 Ligands. ACS OMEGA 2018; 3:6427-6438. [PMID: 30221234 PMCID: PMC6130793 DOI: 10.1021/acsomega.8b00606] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
The complement system is our first line of defense against foreign pathogens, but when it is not properly regulated, complement is implicated in the pathology of several autoimmune and inflammatory disorders. Compstatin is a peptidic complement inhibitor that acts by blocking the cleavage of complement protein C3 to the proinflammatory fragment C3a and opsonin fragment C3b. In this study, we aim to identify druglike small-molecule complement inhibitors with physicochemical, geometric, and binding properties similar to those of compstatin. We employed two approaches using various high-throughput virtual screening methods, which incorporate molecular dynamics (MD) simulations, pharmacophore model design, energy calculations, and molecular docking and scoring. We have generated a library of 274 chemical compounds with computationally predicted binding affinities for the compstatin binding site of C3. We have tested subsets of these chemical compounds experimentally for complement inhibitory activity, using hemolytic assays, and for binding affinity, using microscale thermophoresis. As a result, although none of the compounds showed inhibitory activity, compound 29 was identified to exhibit weak competitive binding against a potent compstatin analogue, therefore validating our computational approaches. Additional docking and MD simulation studies suggest that compound 29 interacts with C3 residues, which have been shown to be important in binding of compstatin to the C3c fragment of C3. Compound 29 is amenable to physicochemical optimization to acquire inhibitory properties. Additionally, it is possible that some of the untested compounds will demonstrate binding and inhibition in future experimental studies.
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Affiliation(s)
- Rohith
R. Mohan
- Department
of Bioengineering, University of California,
Riverside, 900 University
Avenue, Riverside, California 92521, United States
| | - Mark Wilson
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, Texas 77843, United
States
| | - Ronald D. Gorham
- Department
of Bioengineering, University of California,
Riverside, 900 University
Avenue, Riverside, California 92521, United States
| | - Reed E. S. Harrison
- Department
of Bioengineering, University of California,
Riverside, 900 University
Avenue, Riverside, California 92521, United States
| | - Vasilios A. Morikis
- Department
of Bioengineering, University of California,
Riverside, 900 University
Avenue, Riverside, California 92521, United States
| | - Chris A. Kieslich
- Department
of Bioengineering, University of California,
Riverside, 900 University
Avenue, Riverside, California 92521, United States
| | - Asuka A. Orr
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, Texas 77843, United
States
| | - Alexis V. Coley
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, Texas 77843, United
States
| | - Phanourios Tamamis
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, Texas 77843, United
States
| | - Dimitrios Morikis
- Department
of Bioengineering, University of California,
Riverside, 900 University
Avenue, Riverside, California 92521, United States
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