1
|
Smith JS, Hilibrand AS, Skiba MA, Dates AN, Calvillo-Miranda VG, Kruse AC. The M3 Muscarinic Acetylcholine Receptor Can Signal through Multiple G Protein Families. Mol Pharmacol 2024; 105:386-394. [PMID: 38641412 DOI: 10.1124/molpharm.123.000818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/01/2024] [Accepted: 04/08/2024] [Indexed: 04/21/2024] Open
Abstract
The M3 muscarinic acetylcholine receptor (M3R) is a G protein-coupled receptor (GPCR) that regulates important physiologic processes, including vascular tone, bronchoconstriction, and insulin secretion. It is expressed on a wide variety of cell types, including pancreatic beta, smooth muscle, neuronal, and immune cells. Agonist binding to the M3R is thought to initiate intracellular signaling events primarily through the heterotrimeric G protein Gq. However, reports differ on the ability of M3R to couple to other G proteins beyond Gq. Using members from the four primary G protein families (Gq, Gi, Gs, and G13) in radioligand binding, GTP turnover experiments, and cellular signaling assays, including live cell G protein dissociation and second messenger assessment of cAMP and inositol trisphosphate, we show that other G protein families, particularly Gi and Gs, can also interact with the human M3R. We further show that these interactions are productive as assessed by amplification of classic second messenger signaling events. Our findings demonstrate that the M3R is more promiscuous with respect to G protein interactions than previously appreciated. SIGNIFICANCE STATEMENT: The study reveals that the human M3 muscarinic acetylcholine receptor (M3R), known for its pivotal roles in diverse physiological processes, not only activates intracellular signaling via Gq as previously known but also functionally interacts with other G protein families such as Gi and Gs, expanding our understanding of its versatility in mediating cellular responses. These findings signify a broader and more complex regulatory network governed by M3R and have implications for therapeutic targeting.
Collapse
Affiliation(s)
- Jeffrey S Smith
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts (J.S.S., A.S.H., M.A.S., A.N.D., V.G.C.-M., A.C.K.) and Brigham and Women's Hospital, Boston, Massachusetts (J.S.S.)
| | - Ari S Hilibrand
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts (J.S.S., A.S.H., M.A.S., A.N.D., V.G.C.-M., A.C.K.) and Brigham and Women's Hospital, Boston, Massachusetts (J.S.S.)
| | - Meredith A Skiba
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts (J.S.S., A.S.H., M.A.S., A.N.D., V.G.C.-M., A.C.K.) and Brigham and Women's Hospital, Boston, Massachusetts (J.S.S.)
| | - Andrew N Dates
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts (J.S.S., A.S.H., M.A.S., A.N.D., V.G.C.-M., A.C.K.) and Brigham and Women's Hospital, Boston, Massachusetts (J.S.S.)
| | - Victor G Calvillo-Miranda
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts (J.S.S., A.S.H., M.A.S., A.N.D., V.G.C.-M., A.C.K.) and Brigham and Women's Hospital, Boston, Massachusetts (J.S.S.)
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts (J.S.S., A.S.H., M.A.S., A.N.D., V.G.C.-M., A.C.K.) and Brigham and Women's Hospital, Boston, Massachusetts (J.S.S.)
| |
Collapse
|
2
|
Skiba MA, Sterling SM, Rawson S, Zhang S, Xu H, Jiang H, Nemeth GR, Gilman MSA, Hurley JD, Shen P, Staus DP, Kim J, McMahon C, Lehtinen MK, Rockman HA, Barth P, Wingler LM, Kruse AC. Antibodies expand the scope of angiotensin receptor pharmacology. Nat Chem Biol 2024:10.1038/s41589-024-01620-6. [PMID: 38744986 DOI: 10.1038/s41589-024-01620-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 04/12/2024] [Indexed: 05/16/2024]
Abstract
G-protein-coupled receptors (GPCRs) are key regulators of human physiology and are the targets of many small-molecule research compounds and therapeutic drugs. While most of these ligands bind to their target GPCR with high affinity, selectivity is often limited at the receptor, tissue and cellular levels. Antibodies have the potential to address these limitations but their properties as GPCR ligands remain poorly characterized. Here, using protein engineering, pharmacological assays and structural studies, we develop maternally selective heavy-chain-only antibody ('nanobody') antagonists against the angiotensin II type I receptor and uncover the unusual molecular basis of their receptor antagonism. We further show that our nanobodies can simultaneously bind to angiotensin II type I receptor with specific small-molecule antagonists and demonstrate that ligand selectivity can be readily tuned. Our work illustrates that antibody fragments can exhibit rich and evolvable pharmacology, attesting to their potential as next-generation GPCR modulators.
Collapse
Affiliation(s)
- Meredith A Skiba
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sarah M Sterling
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Cryo-EM Facility at MIT.nano, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shuhao Zhang
- Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Huixin Xu
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Haoran Jiang
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Genevieve R Nemeth
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Morgan S A Gilman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Joseph D Hurley
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Pengxiang Shen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Dean P Staus
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC, USA
- Septerna, South San Francisco, CA, USA
| | - Jihee Kim
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC, USA
| | - Conor McMahon
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Sanofi, Large Molecule Research, Cambridge, MA, USA
| | - Maria K Lehtinen
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Howard A Rockman
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Patrick Barth
- Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research Lausanne, Epalinges, Switzerland
| | - Laura M Wingler
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
3
|
Dates AN, Jones DTD, Smith JS, Skiba MA, Rich MF, Burruss MM, Kruse AC, Blacklow SC. Heterogeneity of tethered agonist signaling in adhesion G protein-coupled receptors. Cell Chem Biol 2024:S2451-9456(24)00120-X. [PMID: 38608683 DOI: 10.1016/j.chembiol.2024.03.004] [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: 11/02/2023] [Revised: 01/25/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024]
Abstract
Adhesion G protein-coupled receptor (aGPCR) signaling influences development and homeostasis in a wide range of tissues. In the current model for aGPCR signaling, ligand binding liberates a conserved sequence that acts as an intramolecular, tethered agonist (TA), yet this model has not been evaluated systematically for all aGPCRs. Here, we assessed the TA-dependent activities of all 33 aGPCRs in a suite of transcriptional reporter, G protein activation, and β-arrestin recruitment assays using a new fusion protein platform. Strikingly, only ∼50% of aGPCRs exhibited robust TA-dependent activation, and unlike other GPCR families, aGPCRs showed a notable preference for G12/13 signaling. AlphaFold2 predictions assessing TA engagement in the predicted intramolecular binding pocket aligned with the TA dependence of the cellular responses. This dataset provides a comprehensive resource to inform the investigation of all human aGPCRs and for targeting aGPCRs therapeutically.
Collapse
Affiliation(s)
- Andrew N Dates
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel T D Jones
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey S Smith
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Dermatology, Brigham and Women's Hospital, 221 Longwood Avenue, Boston, MA 02115, USA
| | - Meredith A Skiba
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Maria F Rich
- University of Cincinnati School of Medicine, Department of Molecular Genetics, Biochemistry, and Microbiology, Cincinnati, OH 45267, USA
| | - Maggie M Burruss
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA.
| |
Collapse
|
4
|
Skiba MA, Sterling SM, Rawson S, Gilman MS, Xu H, Nemeth GR, Hurley JD, Shen P, Staus DP, Kim J, McMahon C, Lehtinen MK, Wingler LM, Kruse AC. Antibodies Expand the Scope of Angiotensin Receptor Pharmacology. bioRxiv 2023:2023.08.23.554128. [PMID: 37662341 PMCID: PMC10473732 DOI: 10.1101/2023.08.23.554128] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
G protein-coupled receptors (GPCRs) are key regulators of human physiology and are the targets of many small molecule research compounds and therapeutic drugs. While most of these ligands bind to their target GPCR with high affinity, selectivity is often limited at the receptor, tissue, and cellular level. Antibodies have the potential to address these limitations but their properties as GPCR ligands remain poorly characterized. Here, using protein engineering, pharmacological assays, and structural studies, we develop maternally selective heavy chain-only antibody ("nanobody") antagonists against the angiotensin II type I receptor (AT1R) and uncover the unusual molecular basis of their receptor antagonism. We further show that our nanobodies can simultaneously bind to AT1R with specific small-molecule antagonists and demonstrate that ligand selectivity can be readily tuned. Our work illustrates that antibody fragments can exhibit rich and evolvable pharmacology, attesting to their potential as next-generation GPCR modulators.
Collapse
Affiliation(s)
- Meredith A. Skiba
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah M. Sterling
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Morgan S.A. Gilman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Huixin Xu
- Department of Pathology, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Genevieve R. Nemeth
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph D. Hurley
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Pengxiang Shen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Dean P. Staus
- Department of Medicine and Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Jihee Kim
- Department of Medicine and Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Conor McMahon
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Maria K. Lehtinen
- Department of Pathology, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Laura M. Wingler
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Andrew C. Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
5
|
Harvey EP, Shin JE, Skiba MA, Nemeth GR, Hurley JD, Wellner A, Shaw AY, Miranda VG, Min JK, Liu CC, Marks DS, Kruse AC. An in silico method to assess antibody fragment polyreactivity. Nat Commun 2022; 13:7554. [PMID: 36477674 PMCID: PMC9729196 DOI: 10.1038/s41467-022-35276-4] [Citation(s) in RCA: 6] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Antibodies are essential biological research tools and important therapeutic agents, but some exhibit non-specific binding to off-target proteins and other biomolecules. Such polyreactive antibodies compromise screening pipelines, lead to incorrect and irreproducible experimental results, and are generally intractable for clinical development. Here, we design a set of experiments using a diverse naïve synthetic camelid antibody fragment (nanobody) library to enable machine learning models to accurately assess polyreactivity from protein sequence (AUC > 0.8). Moreover, our models provide quantitative scoring metrics that predict the effect of amino acid substitutions on polyreactivity. We experimentally test our models' performance on three independent nanobody scaffolds, where over 90% of predicted substitutions successfully reduced polyreactivity. Importantly, the models allow us to diminish the polyreactivity of an angiotensin II type I receptor antagonist nanobody, without compromising its functional properties. We provide a companion web-server that offers a straightforward means of predicting polyreactivity and polyreactivity-reducing mutations for any given nanobody sequence.
Collapse
Affiliation(s)
- Edward P Harvey
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Jung-Eun Shin
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Meredith A Skiba
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Genevieve R Nemeth
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Joseph D Hurley
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Alon Wellner
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, CA, 92692, USA
| | - Ada Y Shaw
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Victor G Miranda
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Joseph K Min
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Chang C Liu
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, CA, 92692, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
6
|
Lao Y, Skiba MA, Chun SW, Narayan ARH, Smith JL. Structural Basis for Control of Methylation Extent in Polyketide Synthase Metal-Dependent C-Methyltransferases. ACS Chem Biol 2022; 17:2088-2098. [PMID: 35594521 PMCID: PMC9462956 DOI: 10.1021/acschembio.2c00085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Indexed: 12/24/2022]
Abstract
Installation of methyl groups can significantly improve the binding of small-molecule drugs to protein targets; however, site-selective methylation often presents a significant synthetic challenge. Metal- and S-adenosyl-methionine (SAM)-dependent methyltransferases (MTs) in natural-product biosynthetic pathways are powerful enzymatic tools for selective or chemically challenging C-methylation reactions. Each of these MTs selectively catalyzes one or two methyl transfer reactions. Crystal structures and biochemical assays of the Mn2+-dependent monomethyltransferase from the saxitoxin biosynthetic pathway (SxtA MT) revealed the structural basis for control of methylation extent. The SxtA monomethyltransferase was converted to a dimethyltransferase by modification of the metal binding site, addition of an active site base, and an amino acid substitution to provide space in the substrate pocket for two methyl substituents. A reciprocal change converted a related dimethyltransferase into a monomethyltransferase, supporting our hypothesis that steric hindrance can prevent a second methylation event. A novel understanding of MTs will accelerate the development of MT-based catalysts and MT engineering for use in small-molecule synthesis.
Collapse
Affiliation(s)
- Yongtong Lao
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Meredith A Skiba
- 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
| | - Stephanie W Chun
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alison R H Narayan
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Janet L Smith
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- 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
| |
Collapse
|
7
|
Skiba MA, Kruse AC. Autoantibodies as Endogenous Modulators of GPCR Signaling. Trends Pharmacol Sci 2020; 42:135-150. [PMID: 33358695 DOI: 10.1016/j.tips.2020.11.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 08/17/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 02/06/2023]
Abstract
Endogenous self-reactive autoantibodies (AAs) recognize a range of G-protein-coupled receptors (GPCRs). They are frequently associated with cardiovascular, neurological, and autoimmune disorders, and in some cases directly impact disease progression. Many GPCR AAs modulate receptor signaling, but molecular details of their modulatory activity are not well understood. Technological advances have provided insight into GPCR biology, which now facilitates deeper understanding of GPCR AA function at the molecular level. Most GPCR AAs are allosteric modulators and exhibit a broad range of pharmacological properties, altering both receptor signaling and trafficking. Understanding GPCR AAs is not only important for defining how these unusual GPCR modulators function in disease, but also provides insight into the potential use and limitations of using therapeutic antibodies to modulate GPCR signaling.
Collapse
Affiliation(s)
- Meredith A Skiba
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
8
|
Greenfield DA, Schmidt HR, Skiba MA, Mandler MD, Anderson JR, Sliz P, Kruse AC. Virtual Screening for Ligand Discovery at the σ 1 Receptor. ACS Med Chem Lett 2020; 11:1555-1561. [PMID: 32832023 DOI: 10.1021/acsmedchemlett.9b00314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/27/2020] [Indexed: 01/04/2023] Open
Abstract
The σ1 receptor is a transmembrane protein implicated in several pathophysiological conditions, including neurodegenerative disease (J. Pharmacol. Sci.2015127 (1), 1729), drug addiction (Behav. Pharmacol.201627 (2-3 Spec Issue), 10015), cancer (Handb. Exp. Pharmacol.2017244237308), and pain (Neural Regener. Res.201813 (5), 775778). However, there are no high-throughput functional assays for σ1 receptor drug discovery. Here, we assessed high-throughput structure-based computational docking for discovery of novel ligands of the σ1 receptor. We screened a library of over 6 million compounds using the Schrödinger Glide package, followed by experimental characterization of top-scoring candidates. 77% of tested candidates bound σ1 with high affinity (KD < 1 μM). These include compounds with high selectivity for the σ1 receptor compared to the genetically unrelated but pharmacologically similar σ2 receptor, as well as compounds with substantial crossreactivity between the two receptors. These results establish structure-based virtual screening as a highly effective platform for σ1 receptor ligand discovery and provide compounds to prioritize in studies of σ1 biology.
Collapse
Affiliation(s)
- Daniel A. Greenfield
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, United States
| | - Hayden R. Schmidt
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, United States
| | - Meredith A. Skiba
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, United States
| | - Michael D. Mandler
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States
| | - Jacob R. Anderson
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, United States
| | - Piotr Sliz
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, United States
- Boston Children’s Hospital, Boston, Massachusetts 02115, United States
| | - Andrew C. Kruse
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, United States
| |
Collapse
|
9
|
Suomivuori CM, Latorraca NR, Wingler LM, Eismann S, King MC, Kleinhenz ALW, Skiba MA, Staus DP, Kruse AC, Lefkowitz RJ, Dror RO. Molecular mechanism of biased signaling in a prototypical G protein-coupled receptor. Science 2020; 367:881-887. [PMID: 32079767 DOI: 10.1126/science.aaz0326] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/23/2020] [Indexed: 12/19/2022]
Abstract
Biased signaling, in which different ligands that bind to the same G protein-coupled receptor preferentially trigger distinct signaling pathways, holds great promise for the design of safer and more effective drugs. Its structural mechanism remains unclear, however, hampering efforts to design drugs with desired signaling profiles. Here, we use extensive atomic-level molecular dynamics simulations to determine how arrestin bias and G protein bias arise at the angiotensin II type 1 receptor. The receptor adopts two major signaling conformations, one of which couples almost exclusively to arrestin, whereas the other also couples effectively to a G protein. A long-range allosteric network allows ligands in the extracellular binding pocket to favor either of the two intracellular conformations. Guided by this computationally determined mechanism, we designed ligands with desired signaling profiles.
Collapse
Affiliation(s)
- Carl-Mikael Suomivuori
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Naomi R Latorraca
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.,Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Laura M Wingler
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Stephan Eismann
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.,Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Matthew C King
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Alissa L W Kleinhenz
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Meredith A Skiba
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Dean P Staus
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Robert J Lefkowitz
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA. .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.,Biophysics Program, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
10
|
Wingler LM, Skiba MA, McMahon C, Staus DP, Kleinhenz ALW, Suomivuori CM, Latorraca NR, Dror RO, Lefkowitz RJ, Kruse AC. Angiotensin and biased analogs induce structurally distinct active conformations within a GPCR. Science 2020; 367:888-892. [PMID: 32079768 DOI: 10.1126/science.aay9813] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/23/2020] [Indexed: 12/13/2022]
Abstract
Biased agonists of G protein-coupled receptors (GPCRs) preferentially activate a subset of downstream signaling pathways. In this work, we present crystal structures of angiotensin II type 1 receptor (AT1R) (2.7 to 2.9 angstroms) bound to three ligands with divergent bias profiles: the balanced endogenous agonist angiotensin II (AngII) and two strongly β-arrestin-biased analogs. Compared with other ligands, AngII promotes more-substantial rearrangements not only at the bottom of the ligand-binding pocket but also in a key polar network in the receptor core, which forms a sodium-binding site in most GPCRs. Divergences from the family consensus in this region, which appears to act as a biased signaling switch, may predispose the AT1R and certain other GPCRs (such as chemokine receptors) to adopt conformations that are capable of activating β-arrestin but not heterotrimeric Gq protein signaling.
Collapse
Affiliation(s)
- Laura M Wingler
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Meredith A Skiba
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Conor McMahon
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Dean P Staus
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Alissa L W Kleinhenz
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carl-Mikael Suomivuori
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA.,Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Naomi R Latorraca
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA.,Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.,Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA.,Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.,Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Robert J Lefkowitz
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA. .,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
11
|
Suomivuori CM, Latorraca NR, Wingler LM, Eismann S, King MC, Kleinhenz AL, Skiba MA, Staus DP, Kruse AC, Lefkowitz RJ, Dror RO. Molecular Mechanism of Biased Signaling in a Prototypical G-protein-coupled Receptor. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
|
12
|
Skiba MA, Tran CL, Dan Q, Sikkema AP, Klaver Z, Gerwick WH, Sherman DH, Smith JL. Repurposing the GNAT Fold in the Initiation of Polyketide Biosynthesis. Structure 2020; 28:63-74.e4. [PMID: 31785925 PMCID: PMC6949403 DOI: 10.1016/j.str.2019.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 07/21/2019] [Revised: 10/06/2019] [Accepted: 11/08/2019] [Indexed: 12/19/2022]
Abstract
Natural product biosynthetic pathways are replete with enzymes repurposed for new catalytic functions. In some modular polyketide synthase (PKS) pathways, a GCN5-related N-acetyltransferase (GNAT)-like enzyme with an additional decarboxylation function initiates biosynthesis. Here, we probe two PKS GNAT-like domains for the dual activities of S-acyl transfer from coenzyme A (CoA) to an acyl carrier protein (ACP) and decarboxylation. The GphF and CurA GNAT-like domains selectively decarboxylate substrates that yield the anticipated pathway starter units. The GphF enzyme lacks detectable acyl transfer activity, and a crystal structure with an isobutyryl-CoA product analog reveals a partially occluded acyltransfer acceptor site. Further analysis indicates that the CurA GNAT-like domain also catalyzes only decarboxylation, and the initial acyl transfer is catalyzed by an unidentified enzyme. Thus, PKS GNAT-like domains are re-classified as GNAT-like decarboxylases. Two other decarboxylases, malonyl-CoA decarboxylase and EryM, reside on distant nodes of the superfamily, illustrating the adaptability of the GNAT fold.
Collapse
Affiliation(s)
- Meredith A Skiba
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Collin L Tran
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Qingyun Dan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew P Sikkema
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zachary Klaver
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
13
|
Skiba MA, Bivins MM, Schultz JR, Bernard SM, Fiers WD, Dan Q, Kulkarni S, Wipf P, Gerwick WH, Sherman DH, Aldrich CC, Smitha JL. Structural Basis of Polyketide Synthase O-Methylation. ACS Chem Biol 2018; 13:3221-3228. [PMID: 30489068 PMCID: PMC6470024 DOI: 10.1021/acschembio.8b00687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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] [Indexed: 02/08/2023]
Abstract
Modular type I polyketide synthases (PKSs) produce some of the most chemically complex metabolites in nature through a series of multienzyme modules. Each module contains a variety of catalytic domains to selectively tailor the growing molecule. PKS O-methyltransferases ( O-MTs) are predicted to methylate β-hydroxyl or β-keto groups, but their activity and structure have not been reported. We determined the domain boundaries and characterized the catalytic activity and structure of the StiD and StiE O-MTs, which methylate opposite β-hydroxyl stereocenters in the myxobacterial stigmatellin biosynthetic pathway. Substrate stereospecificity was demonstrated for the StiD O-MT. Key catalytic residues were identified in the crystal structures and investigated in StiE O-MT via site-directed mutagenesis and further validated with the cyanobacterial CurL O-MT from the curacin biosynthetic pathway. Initial structural and biochemical analysis of PKS O-MTs supplies a new chemoenzymatic tool, with the unique ability to selectively modify hydroxyl groups during polyketide biosynthesis.
Collapse
Affiliation(s)
- Meredith A. Skiba
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Marissa M. Bivins
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
| | - John R. Schultz
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Steffen M. Bernard
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI, 48109, United States
| | - William D. Fiers
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Qingyun Dan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Sarang Kulkarni
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15206, United States
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15206, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, 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
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Janet L. Smitha
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
| |
Collapse
|
14
|
Skiba MA, Sikkema AP, Moss NA, Lowell AN, Su M, Sturgis RM, Gerwick L, Gerwick WH, Sherman DH, Smith JL. Biosynthesis of t-Butyl in Apratoxin A: Functional Analysis and Architecture of a PKS Loading Module. ACS Chem Biol 2018; 13:1640-1650. [PMID: 29701944 PMCID: PMC6003868 DOI: 10.1021/acschembio.8b00252] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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] [Indexed: 11/29/2022]
Abstract
The unusual feature of a t-butyl group is found in several marine-derived natural products including apratoxin A, a Sec61 inhibitor produced by the cyanobacterium Moorea bouillonii PNG 5-198. Here, we determine that the apratoxin A t-butyl group is formed as a pivaloyl acyl carrier protein (ACP) by AprA, the polyketide synthase (PKS) loading module of the apratoxin A biosynthetic pathway. AprA contains an inactive "pseudo" GCN5-related N-acetyltransferase domain (ΨGNAT) flanked by two methyltransferase domains (MT1 and MT2) that differ distinctly in sequence. Structural, biochemical, and precursor incorporation studies reveal that MT2 catalyzes unusually coupled decarboxylation and methylation reactions to transform dimethylmalonyl-ACP, the product of MT1, to pivaloyl-ACP. Further, pivaloyl-ACP synthesis is primed by the fatty acid synthase malonyl acyltransferase (FabD), which compensates for the ΨGNAT and provides the initial acyl-transfer step to form AprA malonyl-ACP. Additionally, images of AprA from negative stain electron microscopy reveal multiple conformations that may facilitate the individual catalytic steps of the multienzyme module.
Collapse
Affiliation(s)
- Meredith A Skiba
- 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
| | - Andrew P Sikkema
- 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
| | - Nathan A Moss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States
| | - Andrew N Lowell
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Min Su
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Rebecca M Sturgis
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , 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
| | - 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
| |
Collapse
|
15
|
Abstract
The structural diversity and complexity of marine natural products have made them a rich and productive source of new bioactive molecules for drug development. The identification of these new compounds has led to extensive study of the protein constituents of the biosynthetic pathways from the producing microbes. Essential processes in the dissection of biosynthesis have been the elucidation of catalytic functions and the determination of 3D structures for enzymes of the polyketide synthases and nonribosomal peptide synthetases that carry out individual reactions. The size and complexity of these proteins present numerous difficulties in the process of going from gene to structure. Here, we review the problems that may be encountered at the various steps of this process and discuss some of the solutions devised in our and other labs for the cloning, production, purification, and structure solution of complex proteins using Escherichia coli as a heterologous host.
Collapse
Affiliation(s)
| | | | - Qingyun Dan
- University of Michigan, Ann Arbor, MI, United States
| | - Amy E Fraley
- University of Michigan, Ann Arbor, MI, United States
| | | | - Janet L Smith
- University of Michigan, Ann Arbor, MI, United States.
| | - W Clay Brown
- University of Michigan, Ann Arbor, MI, United States.
| |
Collapse
|
16
|
Abstract
Like many complex natural products, the intricate architecture of saxitoxin (STX) has hindered full exploration of this scaffold's utility as a tool for studying voltage-gated sodium ion channels and as a pharmaceutical agent. Established chemical strategies can provide access to the natural product; however, a chemoenzymatic route to saxitoxin that could provide expedited access to related compounds has not been devised. The first step toward realizing a chemoenzymatic approach toward this class of molecules is the elucidation of the saxitoxin biosynthetic pathway. To date, a biochemical link between STX and its putative biosynthetic enzymes has not been demonstrated. Herein, we report the first biochemical characterization of any enzyme involved in STX biosynthesis. Specifically, the chemical functions of a polyketide-like synthase, SxtA, from the cyanobacteria Cylindrospermopsis raciborskii T3 are elucidated. This unique megasynthase is comprised of four domains: methyltransferase (MT), GCN5-related N-acetyltransferase (GNAT), acyl carrier protein (ACP), and the first example of an 8-amino-7-oxononanoate synthase (AONS) associated with a multidomain synthase. We have established that this single polypeptide carries out the formation of two carbon-carbon bonds, two decarboxylation events and a stereospecific protonation to afford the linear biosynthetic precursor to STX (4). The synthetic utility of the SxtA AONS is demonstrated by the synthesis of a suite of α-amino ketones from the corresponding α-amino acid in a single step.
Collapse
Affiliation(s)
- Stephanie W Chun
- Department of Chemistry, ‡Life Sciences Institute, §Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Meagan E Hinze
- Department of Chemistry, ‡Life Sciences Institute, §Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Meredith A Skiba
- Department of Chemistry, ‡Life Sciences Institute, §Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Alison R H Narayan
- Department of Chemistry, ‡Life Sciences Institute, §Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| |
Collapse
|
17
|
Skiba MA, Sikkema AP, Moss NA, Tran CL, Sturgis RM, Gerwick L, Gerwick WH, Sherman DH, Smith JL. A Mononuclear Iron-Dependent Methyltransferase Catalyzes Initial Steps in Assembly of the Apratoxin A Polyketide Starter Unit. ACS Chem Biol 2017; 12:3039-3048. [PMID: 29096064 PMCID: PMC5784268 DOI: 10.1021/acschembio.7b00746] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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] [Indexed: 02/06/2023]
Abstract
Natural product biosynthetic pathways contain a plethora of enzymatic tools to carry out difficult biosynthetic transformations. Here, we discover an unusual mononuclear iron-dependent methyltransferase that acts in the initiation steps of apratoxin A biosynthesis (AprA MT1). Fe3+-replete AprA MT1 catalyzes one or two methyl transfer reactions on the substrate malonyl-ACP (acyl carrier protein), whereas Co2+, Fe2+, Mn2+, and Ni2+ support only a single methyl transfer. MT1 homologues exist within the "GNAT" (GCN5-related N-acetyltransferase) loading modules of several modular biosynthetic pathways with propionyl, isobutyryl, or pivaloyl starter units. GNAT domains are thought to catalyze decarboxylation of malonyl-CoA and acetyl transfer to a carrier protein. In AprA, the GNAT domain lacks both decarboxylation and acyl transfer activity. A crystal structure of the AprA MT1-GNAT di-domain with bound Mn2+, malonate, and the methyl donor S-adenosylmethionine (SAM) reveals that the malonyl substrate is a bidentate metal ligand, indicating that the metal acts as a Lewis acid to promote methylation of the malonyl α-carbon. The GNAT domain is truncated relative to functional homologues. These results afford an expanded understanding of MT1-GNAT structure and activity and permit the functional annotation of homologous GNAT loading modules both with and without methyltransferases, additionally revealing their rapid evolutionary adaptation in different biosynthetic contexts.
Collapse
Affiliation(s)
- Meredith A. Skiba
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor MI, 48109
| | - Andrew P. Sikkema
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor MI, 48109
| | - Nathan A. Moss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Collin L. Tran
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | | | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Janet L. Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor MI, 48109
| |
Collapse
|
18
|
Motl N, Skiba MA, Kabil O, Smith JL, Banerjee R. Structural and biochemical analyses indicate that a bacterial persulfide dioxygenase-rhodanese fusion protein functions in sulfur assimilation. J Biol Chem 2017; 292:14026-14038. [PMID: 28684420 PMCID: PMC5572905 DOI: 10.1074/jbc.m117.790170] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 04/06/2017] [Revised: 06/26/2017] [Indexed: 11/06/2022] Open
Abstract
Hydrogen sulfide (H2S) is a signaling molecule that is toxic at elevated concentrations. In eukaryotes, it is cleared via a mitochondrial sulfide oxidation pathway, which comprises sulfide quinone oxidoreductase, persulfide dioxygenase (PDO), rhodanese, and sulfite oxidase and converts H2S to thiosulfate and sulfate. Natural fusions between the non-heme iron containing PDO and rhodanese, a thiol sulfurtransferase, exist in some bacteria. However, little is known about the role of the PDO-rhodanese fusion (PRF) proteins in sulfur metabolism. Herein, we report the kinetic properties and the crystal structure of a PRF from the Gram-negative endophytic bacterium Burkholderia phytofirmans The crystal structures of wild-type PRF and a sulfurtransferase-inactivated C314S mutant with and without glutathione were determined at 1.8, 2.4, and 2.7 Å resolution, respectively. We found that the two active sites are distant and do not show evidence of direct communication. The B. phytofirmans PRF exhibited robust PDO activity and preferentially catalyzed sulfur transfer in the direction of thiosulfate to sulfite and glutathione persulfide; sulfur transfer in the reverse direction was detectable only under limited turnover conditions. Together with the kinetic data, our bioinformatics analysis reveals that B. phytofirmans PRF is poised to metabolize thiosulfate to sulfite in a sulfur assimilation pathway rather than in sulfide stress response as seen, for example, with the Staphylococcus aureus PRF or sulfide oxidation and disposal as observed with the homologous mammalian proteins.
Collapse
Affiliation(s)
- Nicole Motl
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Meredith A Skiba
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Omer Kabil
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Janet L Smith
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Ruma Banerjee
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600.
| |
Collapse
|
19
|
Skiba MA, Sikkema AP, Fiers WD, Gerwick WH, Sherman DH, Aldrich CC, Smith JL. Domain Organization and Active Site Architecture of a Polyketide Synthase C-methyltransferase. ACS Chem Biol 2016; 11:3319-3327. [PMID: 27723289 PMCID: PMC5224524 DOI: 10.1021/acschembio.6b00759] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [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] [Indexed: 11/28/2022]
Abstract
Polyketide metabolites produced by modular type I polyketide synthases (PKS) acquire their chemical diversity through the variety of catalytic domains within modules of the pathway. Methyltransferases are among the least characterized of the catalytic domains common to PKS systems. We determined the domain boundaries and characterized the activity of a PKS C-methyltransferase (C-MT) from the curacin A biosynthetic pathway. The C-MT catalyzes S-adenosylmethionine-dependent methyl transfer to the α-position of β-ketoacyl substrates linked to acyl carrier protein (ACP) or a small-molecule analog but does not act on β-hydroxyacyl substrates or malonyl-ACP. Key catalytic residues conserved in both bacterial and fungal PKS C-MTs were identified in a 2 Å crystal structure and validated biochemically. Analysis of the structure and the sequences bordering the C-MT provides insight into the positioning of this domain within complete PKS modules.
Collapse
Affiliation(s)
- Meredith A. Skiba
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI
| | - Andrew P. Sikkema
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI
| | - William D. Fiers
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI
- Department of Chemistry, University of Michigan, Ann Arbor, MI
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI
| | | | - Janet L. Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI
| |
Collapse
|
20
|
Horowitz S, Koepnick B, Martin R, Tymieniecki A, Winburn AA, Cooper S, Flatten J, Rogawski DS, Koropatkin NM, Hailu TT, Jain N, Koldewey P, Ahlstrom LS, Chapman MR, Sikkema AP, Skiba MA, Maloney FP, Beinlich FRM, Popović Z, Baker D, Khatib F, Bardwell JCA. Corrigendum: Determining crystal structures through crowdsourcing and coursework. Nat Commun 2016; 7:13392. [PMID: 27779204 PMCID: PMC5093333 DOI: 10.1038/ncomms13392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
|
21
|
O'Callaghan CJ, Krum H, Conway EL, Lam W, Skiba MA, Howes LG, Louis WJ. Efficacy of pravastatin in combination with captopril in hypertensive patients. Med J Aust 1995; 162:206-8. [PMID: 7877544 DOI: 10.5694/j.1326-5377.1995.tb126026.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
OBJECTIVE To determine the efficacy of pravastatin in the treatment of primary hypercholesterolaemia in patients being treated with captopril for hypertension. DESIGN A double-blind parallel group study comparing 12 weeks of pravastatin therapy (20-40 mg/day) with placebo. PARTICIPANTS 25 patients (age, 37-73 years) with mild-to-moderate hypertension and hypercholesterolaemia (total cholesterol level, 5.5-8.8 mmol/L). RESULTS Pravastatin reduced total cholesterol levels by 22% (from 7.1 +/- 0.29 [SEM] to 5.5 +/- 0.25 mmol/L; P < 0.001) and low-density-lipoprotein cholesterol levels by 32% (from 5.0 +/- 0.32 to 3.4 +/- 0.28 mmol/L; P < 0.001) in four weeks and these levels were maintained for the 12 weeks of therapy. Pre-pravastatin values returned three weeks after stopping therapy. Levels of total cholesterol, cholesterol fractions and triglycerides remained constant or deteriorated in the placebo group. Pravastatin therapy was well tolerated. An integrated coronary risk score showed a 40% reduction in risk. CONCLUSION This study indicates that pravastatin (combined with captopril) is an effective cholesterol-lowering drug, but that treatment needs to be maintained.
Collapse
|
22
|
O'Callaghan CJ, Krum H, Conway EL, Lam W, Skiba MA, Howes LG, Louis WJ. Short term effects of pravastatin on blood pressure in hypercholesterolaemic hypertensive patients. Blood Press 1994; 3:404-6. [PMID: 7704289 DOI: 10.3109/08037059409102294] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In this study, which was primarily designed to determine the lipid-lowering efficacy of pravastatin in the setting of background antihypertensive therapy with ACE inhibitors and calcium antagonists, we took the opportunity to examine whether pravastatin interacts with antihypertensive therapy to produce additional falls in blood pressure. This may help clarify the mechanism of action of pravastatin's rapid beneficial effects on cardiovascular morbidity. We treated 25 hypertensive hypercholesterolaemic patients with 12 weeks of either pravastatin or placebo in this double blind, placebo controlled parallel group study. Placebo treatment did not alter plasma lipids, whereas 12 weeks' treatment with pravastatin reduced total cholesterol by 27% (from 7.1 +/- 0.27 to 5.2 +/- 0.18, p < 0.001 compared with placebo) and low density lipoprotein cholesterol by 35% (from 4.9 +/- 0.36 to 3.2 +/- 0.17, p < 0.001). There were no changes in systolic or diastolic blood pressure either following 12 weeks' treatment or 3 weeks' withdrawal of pravastatin. Thus, pravastatin remains efficacious as a lipid lowering agent in the presence of antihypertensive therapy but does not enhance the blood pressure lowering action of these drugs. Therefore it is unlikely that blood pressure reduction is the mechanism by which pravastatin mediates its reported short term effects on cardiovascular morbidity.
Collapse
Affiliation(s)
- C J O'Callaghan
- Hypertension Services, Austin Hospital, Heidelberg, Australia
| | | | | | | | | | | | | |
Collapse
|