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Roberts MF, Hedstrom L. High Resolution 31P Field Cycling NMR Reveals Unsuspected Features of Enzyme-Substrate-Cofactor Dynamics. Front Mol Biosci 2022; 9:865519. [PMID: 35433832 PMCID: PMC9009223 DOI: 10.3389/fmolb.2022.865519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
The dynamic interactions of enzymes and substrates underpins catalysis, yet few techniques can interrogate the dynamics of protein-bound ligands. Here we describe the use of field cycling NMR relaxometry to measure the dynamics of enzyme-bound substrates and cofactors in catalytically competent complexes of GMP reductase. These studies reveal new binding modes unanticipated by x-ray crystal structures and reaction-specific dynamic networks. Importantly, this work demonstrates that distal interactions not usually considered part of the reaction coordinate can play an active role in catalysis. The commercialization of shuttling apparatus will make field cycling relaxometry more accessible and expand its use to additional nuclei, promising more intriguing findings to come.
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Affiliation(s)
- Mary F. Roberts
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States
| | - Lizbeth Hedstrom
- Departments of Biology and Chemistry, Brandeis University, Waltham, MA, United States
- *Correspondence: Lizbeth Hedstrom,
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2
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Kaleağasıoğlu F, Zaharieva MM, Konstantinov SM, Berger MR. Alkylphospholipids are Signal Transduction Modulators with Potential for Anticancer Therapy. Anticancer Agents Med Chem 2019; 19:66-91. [PMID: 30318001 DOI: 10.2174/1871520618666181012093056] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 03/19/2018] [Accepted: 06/12/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND Alkylphospholipids (APLs) are synthetically derived from cell membrane components, which they target and thus modify cellular signalling and cause diverse effects. This study reviews the mechanism of action of anticancer, antiprotozoal, antibacterial and antiviral activities of ALPs, as well as their clinical use. METHODS A literature search was used as the basis of this review. RESULTS ALPs target lipid rafts and alter phospholipase D and C signalling cascades, which in turn will modulate the PI3K/Akt/mTOR and RAS/RAF/MEK/ERK pathways. By feedback coupling, the SAPK/JNK signalling chain is also affected. These changes lead to a G2/M phase cell cycle arrest and subsequently induce programmed cell death. The available knowledge on inhibition of AKT phosphorylation, mTOR phosphorylation and Raf down-regulation renders ALPs as attractive candidates for modern medical treatment, which is based on individualized diagnosis and therapy. Corresponding to their unusual profile of activities, their side effects result from cholinomimetic activity mainly and focus on the gastrointestinal tract. These aspects together with their bone marrow sparing features render APCs well suited for modern combination therapy. Although the clinical success has been limited in cancer diseases so far, the use of miltefosine against leishmaniosis is leading the way to better understanding their optimized use. CONCLUSION Recent synthetic programs generate congeners with the increased therapeutic ratio, liposomal formulations, as well as diapeutic (or theranostic) derivatives with optimized properties. It is anticipated that these innovative modifications will pave the way for the further successful development of ALPs.
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Affiliation(s)
- Ferda Kaleağasıoğlu
- Toxicology and Chemotherapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pharmacology, Faculty of Medicine, Near East University, Mersin 10, Turkey
| | - Maya M Zaharieva
- Toxicology and Chemotherapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Infectious Microbiology, The "Stephan Angeloff" Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Spiro M Konstantinov
- Toxicology and Chemotherapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pharmacology, Pharmacotherapy and Toxicology, Faculty of Pharmacy, Medical University Sofia, Sofia, Bulgaria
| | - Martin R Berger
- Toxicology and Chemotherapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
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3
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Hassan AHE, Park HR, Yoon YM, Kim HI, Yoo SY, Lee KW, Lee YS. Antiproliferative 3-deoxysphingomyelin analogs: Design, synthesis, biological evaluation and molecular docking of pyrrolidine-based 3-deoxysphingomyelin analogs as anticancer agents. Bioorg Chem 2018; 84:444-455. [PMID: 30576908 DOI: 10.1016/j.bioorg.2018.11.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 11/21/2018] [Accepted: 11/24/2018] [Indexed: 12/13/2022]
Abstract
Sphingomyelins and glycerophospholipids are structurally related phospholipids. Nevertheless, glycerophospholipids analogs are known as antitumor agents while sphingomyelin analogs were reported as cytoprotective agents. Herein, we have addressed the development of 3-deoxysphingomyelin analogs as cytotoxic agents possessing modified sphingobases. Thus, pyrrolidine-based 3-deoxysphingomyelin analogs were synthesized and evaluated against a panel of cell lines representing four major types of cancers. Compounds 3d, 4d and 6d elicited better GI50 values than the FDA approved drug miltefosine. Investigation of their impact on Akt phosphorylation as a possible mechanism for the antiproliferative activity of this class of compounds revealed that these compounds might elicit a concentration-dependent mechanism via inhibition of Akt phosphorylation at the lower concentration. Molecular docking predicted their binding modes to Akt to involve polar head binding to the Pleckstrin homology domain and hydrophobic tail extension into a hydrophobic pocket connecting the Pleckstrin homology domain and the kinase domain. As a whole, the described work suggests compounds 3d, 4d and 6d as promising pyrrolidine-based 3-deoxysphingomyelin analogs for development of novel cancer therapies.
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Affiliation(s)
- Ahmed H E Hassan
- Medicinal Chemistry Laboratory, Department of Pharmacy, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea; Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Hye Rim Park
- Department of Life and Nanopharmaceutical Science, Kyung Hee University, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yoon Mi Yoon
- Department of Life and Nanopharmaceutical Science, Kyung Hee University, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hye In Kim
- Department of Life and Nanopharmaceutical Science, Kyung Hee University, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sung Yeun Yoo
- Department of Life and Nanopharmaceutical Science, Kyung Hee University, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Kun Won Lee
- Department of Life and Nanopharmaceutical Science, Kyung Hee University, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yong Sup Lee
- Medicinal Chemistry Laboratory, Department of Pharmacy, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea; Department of Life and Nanopharmaceutical Science, Kyung Hee University, Kyung Hee University, Seoul 02447, Republic of Korea.
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4
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Rosenberg MM, Redfield AG, Roberts MF, Hedstrom L. Dynamic Characteristics of Guanosine-5'-monophosphate Reductase Complexes Revealed by High-Resolution 31P Field-Cycling NMR Relaxometry. Biochemistry 2018; 57:3146-3154. [PMID: 29547266 DOI: 10.1021/acs.biochem.8b00142] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability of enzymes to modulate the dynamics of bound substrates and cofactors is a critical feature of catalysis, but the role of dynamics has largely been approached from the perspective of the protein. Here, we use an underappreciated NMR technique, subtesla high-resolution field-cycling 31P NMR relaxometry, to interrogate the dynamics of enzyme bound substrates and cofactors in guanosine-5'-monophosphate reductase (GMPR). These experiments reveal distinct binding modes and dynamic profiles associated with the 31P nuclei in the Michaelis complexes for the deamination and hydride transfer steps of the catalytic cycle. Importantly, the substrate is constrained and the cofactor is more dynamic in the deamination complex E·GMP·NADP+, whereas the substrate is more dynamic and the cofactor is constrained in the hydride transfer complex E·IMP·NADP+. The presence of D2O perturbed the relaxation of the 31P nuclei in E·IMP·NADP+ but not in E·GMP·NADP+, providing further evidence of distinct binding modes with different dynamic properties. dIMP and dGMP are poor substrates, and the dynamics of the cofactor complexes of dGMP/dIMP are disregulated relative to GMP/IMP. The substrate 2'-OH interacts with Asp219, and mutation of Asp219 to Ala decreases the value of Vmax by a factor of 30. Counterintuitively, loss of Asp219 makes both substrates and cofactors less dynamic. These observations suggest that the interactions between the substrate 2'-OH and Asp219 coordinate the dynamic properties of the Michaelis complexes, and these dynamics are important for progression through the catalytic cycle.
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Affiliation(s)
- Masha M Rosenberg
- Department of Biology , Brandeis University , MS009, 415 South Street , Waltham , Massachusetts 02453-9110 , United States
| | - Alfred G Redfield
- Department of Biochemistry , Brandeis University , MS009, 415 South Street , Waltham , Massachusetts 02453-9110 , United States
| | - Mary F Roberts
- Department of Chemistry , Boston College , 140 Commonwealth Avenue , Chestnut Hill , Massachusetts 02467-9110 , United States
| | - Lizbeth Hedstrom
- Department of Biology , Brandeis University , MS009, 415 South Street , Waltham , Massachusetts 02453-9110 , United States.,Department of Chemistry , Brandeis University , 415 South Street , Waltham , Massachusetts 02453-3808 , United States
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5
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Yoshioka Y, Suzuki T, Matsuo Y, Nakakido M, Tsurita G, Simone C, Watanabe T, Dohmae N, Nakamura Y, Hamamoto R. SMYD3-mediated lysine methylation in the PH domain is critical for activation of AKT1. Oncotarget 2018; 7:75023-75037. [PMID: 27626683 PMCID: PMC5342720 DOI: 10.18632/oncotarget.11898] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/24/2016] [Indexed: 12/21/2022] Open
Abstract
AKT1 is a cytosolic serine/threonine kinase that is overexpressed in various types of cancer and has a central role in human tumorigenesis. Although it is known that AKT1 is post-translationally modified in various ways including phosphorylation and ubiquitination, methylation has not been reported so far. Here we demonstrate that the protein lysine methyltransferase SMYD3 methylates lysine 14 in the PH domain of AKT1 both in vitro and in vivo. Lysine 14-substituted AKT1 shows significantly lower levels of phosphorylation at threonine 308 than wild-type AKT1, and knockdown of SMYD3 as well as treatment with a SMYD3 inhibitor significantly attenuates this phosphorylation in cancer cells. Furthermore, substitution of lysine 14 diminishes the plasma membrane accumulation of AKT1, and cancer cells overexpressing lysine 14-substiuted AKT1 shows lower growth rate than those overexpressing wild-type AKT1. These results imply that SMYD3-mediated methylation of AKT1 at lysine 14 is essential for AKT1 activation and that SMYD3-mediated AKT1 methylation appears to be a good target for development of anti-cancer therapy.
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Affiliation(s)
- Yuichiro Yoshioka
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, MC2115 Chicago, IL 60637, USA.,Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Yo Matsuo
- OncoTherapy Science, Inc., Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Makoto Nakakido
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, MC2115 Chicago, IL 60637, USA
| | - Giichiro Tsurita
- Department of Surgery, IMSUT Hospital, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Cristiano Simone
- Division of Medical Genetics, Department of Biomedical Science and Human Oncology (DIMO), University of Bari 'Aldo Moro', Bari 70124, Italy
| | - Toshiaki Watanabe
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Yusuke Nakamura
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, MC2115 Chicago, IL 60637, USA
| | - Ryuji Hamamoto
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, MC2115 Chicago, IL 60637, USA
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6
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Gradziel CS, Jordan PA, Jewel D, Dufort FJ, Miller SJ, Chiles TC, Roberts MF. d-3-Deoxy-dioctanoylphosphatidylinositol induces cytotoxicity in human MCF-7 breast cancer cells via a mechanism that involves downregulation of the D-type cyclin-retinoblastoma pathway. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1861:1808-1815. [PMID: 27600289 PMCID: PMC5115159 DOI: 10.1016/j.bbalip.2016.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/24/2016] [Accepted: 09/01/2016] [Indexed: 11/29/2022]
Abstract
Phosphatidylinositol analogs (PIAs) were originally designed to bind competitively to the Akt PH domain and prevent membrane translocation and activation. d-3-Deoxy-dioctanoylphosphatidylinositol (d-3-deoxy-diC8PI), but not compounds with altered inositol stereochemistry (e.g., l-3-deoxy-diC8PI and l-3,5-dideoxy-diC8PI), is cytotoxic. However, high resolution NMR field cycling relaxometry shows that both cytotoxic and non-toxic PIAs bind to the Akt1 PH domain at the site occupied by the cytotoxic alkylphospholipid perifosine. This suggests that another mechanism for cytotoxicity must account for the difference in efficacy of the synthetic short-chain PIAs. In MCF-7 breast cancer cells, with little constitutively active Akt, d-3-deoxy-diC8PI (but not l-compounds) decreases viability concomitant with increased cleavage of PARP and caspase 9, indicative of apoptosis. d-3-Deoxy-diC8PI also induces a decrease in endogenous levels of cyclins D1 and D3 and blocks downstream retinoblastoma protein phosphorylation. siRNA-mediated depletion of cyclin D1, but not cyclin D3, reduces MCF-7 cell proliferation. Thus, growth arrest and cytotoxicity induced by the soluble d-3-deoxy-diC8PI occur by a mechanism that involves downregulation of the D-type cyclin-pRb pathway independent of its interaction with Akt. This ability to downregulate D-type cyclins contributes, at least in part, to the anti-proliferative activity of d-3-deoxy-diC8PI and may be a common feature of other cytotoxic phospholipids.
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Affiliation(s)
- Cheryl S Gradziel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
| | - Peter A Jordan
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA.
| | - Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
| | - Fay J Dufort
- Department of Biology, Higgins Hall, 140 Commonwealth Avenue, Boston College, Chestnut Hill, MA, USA.
| | - Scott J Miller
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA.
| | - Thomas C Chiles
- Department of Biology, Higgins Hall, 140 Commonwealth Avenue, Boston College, Chestnut Hill, MA, USA.
| | - Mary F Roberts
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
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7
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Rosenberg MM, Redfield AG, Roberts MF, Hedstrom L. Substrate and Cofactor Dynamics on Guanosine Monophosphate Reductase Probed by High Resolution Field Cycling 31P NMR Relaxometry. J Biol Chem 2016; 291:22988-22998. [PMID: 27613871 PMCID: PMC5087720 DOI: 10.1074/jbc.m116.739516] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 08/31/2016] [Indexed: 12/31/2022] Open
Abstract
Guanosine-5'-monophosphate reductase (GMPR) catalyzes the reduction of GMP to IMP and ammonia with concomitant oxidation of NADPH. Here we investigated the structure and dynamics of enzyme-bound substrates and cofactors by measuring 31P relaxation rates over a large magnetic field range using high resolution field cycling NMR relaxometry. Surprisingly, these experiments reveal differences in the low field relaxation profiles for the monophosphate of GMP compared with IMP in their respective NADP+ complexes. These complexes undergo partial reactions that mimic different steps in the overall catalytic cycle. The relaxation profiles indicate that the substrate monophosphates have distinct interactions in E·IMP·NADP+ and E·GMP·NADP+ complexes. These findings were not anticipated by x-ray crystal structures, which show identical interactions for the monophosphates of GMP and IMP in several inert complexes. In addition, the motion of the cofactor is enhanced in the E·GMP·NADP+ complex. Last, the motions of the substrate and cofactor are coordinately regulated; the cofactor has faster local motions than GMP in the deamination complex but is more constrained than IMP in that complex, leading to hydride transfer. These results show that field cycling can be used to investigate the dynamics of protein-bound ligands and provide new insights into how portions of the substrate remote from the site of chemical transformation promote catalysis.
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Affiliation(s)
| | | | - Mary F Roberts
- the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467-3860
| | - Lizbeth Hedstrom
- From the Departments of Biology,
- Chemistry, Brandeis University, Waltham, Massachusetts 02453 and
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8
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Huang Q, Gershenson A, Roberts MF. Recombinant broad-range phospholipase C from Listeria monocytogenes exhibits optimal activity at acidic pH. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:697-705. [PMID: 26976751 DOI: 10.1016/j.bbapap.2016.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
The broad-range phospholipase C (PLC) from Listeria monocytogenes has been expressed using an intein expression system and characterized. This zinc metalloenzyme, similar to the homologous enzyme from Bacillus cereus, targets a wide range of lipid substrates. With monomeric substrates, the length of the hydrophobic acyl chain has significant impact on enzyme efficiency by affecting substrate affinity (Km). Based on a homology model of the enzyme to the B. cereus protein, several active site residue mutations were generated. While this PLC shares many of the mechanistic characteristics of the B. cereus PLC, a major difference is that the L. monocytogenes enzyme displays an acidic pH optimum regardless of substrate status (monomer, micelle, or vesicle). This unusual behavior might be advantageous for its role in the pathogenicity of L. monocytogenes.
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Affiliation(s)
- Qiongying Huang
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States.
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, United States
| | - Mary F Roberts
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States
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9
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Wei Y, Stec B, Redfield AG, Weerapana E, Roberts MF. Phospholipid-binding sites of phosphatase and tensin homolog (PTEN): exploring the mechanism of phosphatidylinositol 4,5-bisphosphate activation. J Biol Chem 2014; 290:1592-606. [PMID: 25429968 DOI: 10.1074/jbc.m114.588590] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The lipid phosphatase activity of the tumor suppressor phosphatase and tensin homolog (PTEN) is enhanced by the presence of its biological product, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). This enhancement is suggested to occur via the product binding to the N-terminal region of the protein. PTEN effects on short-chain phosphoinositide (31)P linewidths and on the full field dependence of the spin-lattice relaxation rate (measured by high resolution field cycling (31)P NMR using spin-labeled protein) are combined with enzyme kinetics with the same short-chain phospholipids to characterize where PI(4,5)P2 binds on the protein. The results are used to model a discrete site for a PI(4,5)P2 molecule close to, but distinct from, the active site of PTEN. This PI(4,5)P2 site uses Arg-47 and Lys-13 as phosphate ligands, explaining why PTEN R47G and K13E can no longer be activated by that phosphoinositide. Placing a PI(4,5)P2 near the substrate site allows for proper orientation of the enzyme on interfaces and should facilitate processive catalysis.
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Affiliation(s)
- Yang Wei
- From the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467 and
| | - Boguslaw Stec
- From the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467 and
| | - Alfred G Redfield
- the Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454
| | - Eranthie Weerapana
- From the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467 and
| | - Mary F Roberts
- From the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467 and
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