1
|
Liu Z, Rivera S, Newmister SA, Sanders JN, Nie Q, Liu S, Zhao F, Ferrara JD, Shih HW, Patil S, Xu W, Miller MD, Phillips GN, Houk KN, Sherman DH, Gao X. An NmrA-like enzyme-catalysed redox-mediated Diels-Alder cycloaddition with anti-selectivity. Nat Chem 2023; 15:526-534. [PMID: 36635598 PMCID: PMC10073347 DOI: 10.1038/s41557-022-01117-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 11/22/2022] [Indexed: 01/14/2023]
Abstract
The Diels-Alder cycloaddition is one of the most powerful approaches in organic synthesis and is often used in the synthesis of important pharmaceuticals. Yet, strictly controlling the stereoselectivity of the Diels-Alder reactions is challenging, and great efforts are needed to construct complex molecules with desired chirality via organocatalysis or transition-metal strategies. Nature has evolved different types of enzymes to exquisitely control cyclization stereochemistry; however, most of the reported Diels-Alderases have been shown to only facilitate the energetically favourable diastereoselective cycloadditions. Here we report the discovery and characterization of CtdP, a member of a new class of bifunctional oxidoreductase/Diels-Alderase, which was previously annotated as an NmrA-like transcriptional regulator. We demonstrate that CtdP catalyses the inherently disfavoured cycloaddition to form the bicyclo[2.2.2]diazaoctane scaffold with a strict α-anti-selectivity. Guided by computational studies, we reveal a NADP+/NADPH-dependent redox mechanism for the CtdP-catalysed inverse electron demand Diels-Alder cycloaddition, which serves as the first example of a bifunctional Diels-Alderase that utilizes this mechanism.
Collapse
Affiliation(s)
- Zhiwen Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Sebastian Rivera
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Qiuyue Nie
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Shuai Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Fanglong Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | | | - Hao-Wei Shih
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Siddhant Patil
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Weijun Xu
- Department of Biosciences, Rice University, Houston, TX, USA
| | | | - George N Phillips
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA.
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
- Department of Chemistry, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
| |
Collapse
|
2
|
Rebollar-Ramos D, Ovalle-Magallanes B, Palacios-Espinosa JF, Macías-Rubalcava ML, Raja HA, González-Andrade M, Mata R. α-Glucosidase and PTP-1B Inhibitors from Malbranchea dendritica. ACS OMEGA 2021; 6:22969-22981. [PMID: 34514267 PMCID: PMC8427789 DOI: 10.1021/acsomega.1c03708] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
An extract from a PDB static culture of Malbranchea dendritica exhibited α-glucosidase and PTP-1B inhibitory activities. Fractionation of the active extract led to the isolation of gymnoascolide A (1), a γ-butenolide, and xanthones sydowinin A (2), sydowinin B (3), and AGI-B4 (4), as well as orcinol (5). Compound 1 exhibited important inhibitory activity against yeast α-glucosidase (IC50 = 0.556 ± 0.009 mM) in comparison to acarbose (IC50 = 0.403 ± 0.010 mM). Kinetic analysis revealed that 1 is a mixed-type inhibitor. Furthermore, compound 1 significantly reduced the postprandial peak in mice during a sucrose tolerance test at the doses of 5.16 and 10 mg/kg. Compound 1 was reduced with Pd/C to yield a mixture of enantiomers 1a and 1b; the mixture showed similar activity against α-glucosidase (IC50 = 0.396 ± 0.003 mM) and kinetic behavior as the parent compound but might possess better drug-likeness properties according to SwissADME and Osiris Property Explorer tools. Docking analysis with yeast α-glucosidase (pdb: 3A4A) and the C-terminal subunit of human maltase-glucoamylase (pdb: 3TOP) predicted that 1, 1a, and 1b bind to an allosteric site of the enzymes. Compounds 1-5 were evaluated against PTP-1B, but only xanthone 3 moderately inhibited in a noncompetitive fashion the enzyme with an IC50 of 0.081 ± 0.004 mM. This result was consistent with that of docking analysis, which revealed that 3 might bind to an allosteric site of the enzyme. From the inactive barley-based semisolid culture of M. dendritica, the natural pigment erythroglaucin (6) and the nucleosides deoxyadenosine (7), adenosine (8), thymidine (9), and uridine (10) were also isolated and identified.
Collapse
Affiliation(s)
- Daniela Rebollar-Ramos
- Facultad
de Química, Universidad Nacional
Autónoma de México, Ciudad de México 04510, Mexico
| | | | - Juan Francisco Palacios-Espinosa
- Departamento
de Sistemas Biológicos, División de Ciencias Biológicas
y de la Salud, Universidad Autónoma
Metropolitana-Xochimilco (UAM-X), Ciudad de México 04960, Mexico
| | | | - Huzefa A. Raja
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27412, United States
| | - Martín González-Andrade
- Facultad
de Medicina, Universidad Nacional Autónoma
de México, Ciudad de México 04510, Mexico
| | - Rachel Mata
- Facultad
de Química, Universidad Nacional
Autónoma de México, Ciudad de México 04510, Mexico
| |
Collapse
|
3
|
Díaz-Rojas M, Raja H, González-Andrade M, Rivera-Chávez J, Rangel-Grimaldo M, Rivero-Cruz I, Mata R. Protein tyrosine phosphatase 1B inhibitors from the fungus Malbranchea albolutea. PHYTOCHEMISTRY 2021; 184:112664. [PMID: 33524855 DOI: 10.1016/j.phytochem.2021.112664] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
From solid rice-based cultures of Malbranchea albolutea, three undescribed ardeemins and sartoryglabrins analogs were discovered and named alboluteins A-C. 1H-Indole-3-carbaldehyde, and anthranilic acid were also isolated. 1D and 2D-NMR techniques, as well as DFT-calculated chemical shifts, allowed characterizing alboluteins A-C. Testing these compounds against PTP1B indicated their inhibitory activity with IC50's ranging from 19 to 129 μM (ursolic acid IC50 = 29.8 μM, positive control). Kinetic analysis revealed that albolutein C behaved as a non-competitive inhibitor. Docking studies of alboluteins A-C into the crystal structure of PTP1B (PDB ID: 1T49) predicted that all compounds prefer to bind at the allosteric site of the enzyme, with Ki values of 2.02 × 10-4, 1.31 × 10-4, and 2.67 × 10-4 mM, respectively. Molecular dynamic studies indicated that the active compounds remained tied to the enzyme with good binding energy.
Collapse
Affiliation(s)
- Miriam Díaz-Rojas
- Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Huzefa Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, 27412, NC, USA
| | | | - José Rivera-Chávez
- Instituto de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Manuel Rangel-Grimaldo
- Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Isabel Rivero-Cruz
- Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Rachel Mata
- Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
| |
Collapse
|
4
|
Fraley AE, Sherman DH. Enzyme evolution in fungal indole alkaloid biosynthesis. FEBS J 2020; 287:1381-1402. [PMID: 32118354 PMCID: PMC7317620 DOI: 10.1111/febs.15270] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/24/2019] [Accepted: 02/27/2020] [Indexed: 12/28/2022]
Abstract
The class of fungal indole alkaloids containing the bicyclo[2.2.2]diazaoctane ring is comprised of diverse molecules that display a range of biological activities. While much interest has been garnered due to their therapeutic potential, this class of molecules also displays unique chemical functionality, making them intriguing synthetic targets. Many elegant and intricate total syntheses have been developed to generate these alkaloids, but the selectivity required to produce them in high yield presents great barriers. Alternatively, if we can understand the molecular mechanisms behind how fungi make these complex molecules, we can leverage the power of nature to perform these chemical transformations. Here, we describe the various studies regarding the evolutionary development of enzymes involved in fungal indole alkaloid biosynthesis.
Collapse
Affiliation(s)
- Amy E. Fraley
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, United States
| |
Collapse
|
5
|
Affiliation(s)
- Jia Zeng
- Department of Molecular BioscienceUniversity of Texas at Austin Austin, Texas 89812 United States
| | - Jixun Zhan
- Department of Biological EngineeringUtah State University Logan, Utah 84321 United States
| |
Collapse
|
6
|
Fraley AE, Sherman DH. Halogenase engineering and its utility in medicinal chemistry. Bioorg Med Chem Lett 2018; 28:1992-1999. [PMID: 29731363 DOI: 10.1016/j.bmcl.2018.04.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 10/17/2022]
Abstract
Halogenation is commonly used in medicinal chemistry to improve the potency of pharmaceutical leads. While synthetic methods for halogenation present selectivity and reactivity challenges, halogenases have evolved over time to perform selective reactions under benign conditions. The optimization of halogenation biocatalysts has utilized enzyme evolution and structure-based engineering alongside biotransformation in a variety of systems to generate stable site-selective variants. The recent improvements in halogenase-catalyzed reactions has demonstrated the utility of these biocatalysts for industrial purposes, and their ability to achieve a broad substrate scope implies a synthetic tractability with increasing relevance in medicinal chemistry.
Collapse
Affiliation(s)
- Amy E Fraley
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, United States.
| |
Collapse
|
7
|
Fraley AE, Garcia-Borràs M, Tripathi A, Khare D, Mercado-Marin EV, Tran H, Dan Q, Webb GP, Watts KR, Crews P, Sarpong R, Williams RM, Smith JL, Houk KN, Sherman DH. Function and Structure of MalA/MalA', Iterative Halogenases for Late-Stage C-H Functionalization of Indole Alkaloids. J Am Chem Soc 2017; 139:12060-12068. [PMID: 28777910 PMCID: PMC5595095 DOI: 10.1021/jacs.7b06773] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Malbrancheamide is a dichlorinated fungal indole alkaloid isolated from both Malbranchea aurantiaca and Malbranchea graminicola that belongs to a family of natural products containing a characteristic bicyclo[2.2.2]diazaoctane core. The introduction of chlorine atoms on the indole ring of malbrancheamide differentiates it from other members of this family and contributes significantly to its biological activity. In this study, we characterized the two flavin-dependent halogenases involved in the late-stage halogenation of malbrancheamide in two different fungal strains. MalA and MalA' catalyze the iterative dichlorination and monobromination of the free substrate premalbrancheamide as the final steps in the malbrancheamide biosynthetic pathway. Two unnatural bromo-chloro-malbrancheamide analogues were generated through MalA-mediated chemoenzymatic synthesis. Structural analysis and computational studies of MalA' in complex with three substrates revealed that the enzyme represents a new class of zinc-binding flavin-dependent halogenases and provides new insights into a potentially unique reaction mechanism.
Collapse
Affiliation(s)
- Amy E. Fraley
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dheeraj Khare
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Hong Tran
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Qingyun Dan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Gabrielle P. Webb
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Katharine R. Watts
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Richmond Sarpong
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Robert M. Williams
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Janet L. Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
8
|
Verastegui-Omaña B, Rebollar-Ramos D, Pérez-Vásquez A, Martínez AL, Madariaga-Mazón A, Flores-Bocanegra L, Mata R. α-Glucosidase Inhibitors from Malbranchea flavorosea. JOURNAL OF NATURAL PRODUCTS 2017; 80:190-195. [PMID: 28060505 DOI: 10.1021/acs.jnatprod.6b00977] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
From an extract prepared from the grain-based culture of Malbranchea flavorosea two new polyketides, namely, 8-chloroxylarinol A (1) and flavoroseoside (2), along with the known compounds xylarinol A (3), xylarinol B (4), massarigenins B and C (5 and 6), and clavatol (7), were isolated. The structures of 1 and 2 were elucidated using spectroscopic methods and corroborated by single-crystal X-ray diffraction analysis. In the case of compound 2 the absolute configuration at the stereogenic centers was established according to the method of Flack. In addition, the X-ray structure of compound 6 is reported for the first time. Compounds 3, 4, and 6 significantly inhibited yeast α-glucosidase. Compound 6 also inhibited the postprandial peak during an oral sucrose tolerance assay when tested in vivo, using normal and NA/STZ-induced hyperglycemic mice.
Collapse
Affiliation(s)
- Brisa Verastegui-Omaña
- Facultad de Química, Universidad Nacional Autónoma de México , México, Ciudad de México 04510, México
| | - Daniela Rebollar-Ramos
- Facultad de Química, Universidad Nacional Autónoma de México , México, Ciudad de México 04510, México
| | - Araceli Pérez-Vásquez
- Facultad de Química, Universidad Nacional Autónoma de México , México, Ciudad de México 04510, México
| | - Ana Laura Martínez
- Facultad de Química, Universidad Nacional Autónoma de México , México, Ciudad de México 04510, México
| | - Abraham Madariaga-Mazón
- Facultad de Química, Universidad Nacional Autónoma de México , México, Ciudad de México 04510, México
| | - Laura Flores-Bocanegra
- Facultad de Química, Universidad Nacional Autónoma de México , México, Ciudad de México 04510, México
| | - Rachel Mata
- Facultad de Química, Universidad Nacional Autónoma de México , México, Ciudad de México 04510, México
| |
Collapse
|