1
|
Abdelmagid WM, Mahmoodi N, Tanner ME. A guanidinium-based inhibitor of a type I isopentenyl diphosphate isomerase. Bioorg Med Chem Lett 2020; 30:127577. [PMID: 32979487 DOI: 10.1016/j.bmcl.2020.127577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 11/19/2022]
Abstract
An inhibitor bearing a phosphinylphosphonate group appended to a guanidinium functionality was designed to inhibit enzymes that generate carbocations from dimethylallyl diphosphate. When tested against human farnesyl diphosphate synthase the inhibitor bound with high micromolar affinity and did not bind more tightly than an isosteric inhibitor lacking the guanidinium functionality. When tested against the Type I isopentenyl diphosphate:dimethylallyl diphosphate isomerase from Escherichia coli, the inhibitor bound with a Ki value of 120 nM, which was 400 times greater than its isosteric counterpart. This strategy of inhibition was much more effective with an enzyme that generates a carbocation that is not stabilized by both resonance and ion pairing, presumably because there is more evolutionary pressure on the enzyme to stabilize the cation.
Collapse
Affiliation(s)
- Walid M Abdelmagid
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Niusha Mahmoodi
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada.
| |
Collapse
|
2
|
Serkova OS, Kamkina AV, Sivkova AS, Maslennikova VI. Synthesis of oligophosphonate aromatic systems using the Michaelis-Arbuzov reaction and microwave radiation. PHOSPHORUS SULFUR 2019. [DOI: 10.1080/10426507.2019.1618299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Olga S. Serkova
- Institute of Biology and Chemistry, Moscow State University of Education, Moscow, Russia
| | - Anastasia V. Kamkina
- Institute of Biology and Chemistry, Moscow State University of Education, Moscow, Russia
| | - Anastasia S. Sivkova
- Institute of Biology and Chemistry, Moscow State University of Education, Moscow, Russia
| | - Vera I. Maslennikova
- Institute of Biology and Chemistry, Moscow State University of Education, Moscow, Russia
| |
Collapse
|
3
|
Dormán G, Nakamura H, Pulsipher A, Prestwich GD. The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore. Chem Rev 2016; 116:15284-15398. [PMID: 27983805 DOI: 10.1021/acs.chemrev.6b00342] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread applications of benzophenone (BP) photochemistry in biological chemistry, bioorganic chemistry, and material science have been prominent in both academic and industrial research. BP photophores have unique photochemical properties: upon n-π* excitation at 365 nm, a biradicaloid triplet state is formed reversibly, which can abstract a hydrogen atom from accessible C-H bonds; the radicals subsequently recombine, creating a stable covalent C-C bond. This light-directed covalent attachment process is exploited in many different ways: (i) binding/contact site mapping of ligand (or protein)-protein interactions; (ii) identification of molecular targets and interactome mapping; (iii) proteome profiling; (iv) bioconjugation and site-directed modification of biopolymers; (v) surface grafting and immobilization. BP photochemistry also has many practical advantages, including low reactivity toward water, stability in ambient light, and the convenient excitation at 365 nm. In addition, several BP-containing building blocks and reagents are commercially available. In this review, we explore the "forbidden" (transitions) and excitation-activated world of photoinduced covalent attachment of BP photophores by touring a colorful palette of recent examples. In this exploration, we will see the pros and cons of using BP photophores, and we hope that both novice and expert photolabelers will enjoy and be inspired by the breadth and depth of possibilities.
Collapse
Affiliation(s)
- György Dormán
- Targetex llc , Dunakeszi H-2120, Hungary.,Faculty of Pharmacy, University of Szeged , Szeged H-6720, Hungary
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , Yokohama 226-8503, Japan
| | - Abigail Pulsipher
- GlycoMira Therapeutics, Inc. , Salt Lake City, Utah 84108, United States.,Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| | - Glenn D Prestwich
- Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| |
Collapse
|
4
|
Palsuledesai CC, Distefano MD. Protein prenylation: enzymes, therapeutics, and biotechnology applications. ACS Chem Biol 2015; 10:51-62. [PMID: 25402849 PMCID: PMC4301080 DOI: 10.1021/cb500791f] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Protein
prenylation is a ubiquitous covalent post-translational modification
found in all eukaryotic cells, comprising attachment of either a farnesyl
or a geranylgeranyl isoprenoid. It is essential for the proper cellular
activity of numerous proteins, including Ras family GTPases and heterotrimeric
G-proteins. Inhibition of prenylation has been extensively investigated
to suppress the activity of oncogenic Ras proteins to achieve antitumor
activity. Here, we review the biochemistry of the prenyltransferase
enzymes and numerous isoprenoid analogs synthesized to investigate
various aspects of prenylation and prenyltransferases. We also give
an account of the current status of prenyltransferase inhibitors as
potential therapeutics against several diseases including cancers,
progeria, aging, parasitic diseases, and bacterial and viral infections.
Finally, we discuss recent progress in utilizing protein prenylation
for site-specific protein labeling for various biotechnology applications.
Collapse
Affiliation(s)
- Charuta C. Palsuledesai
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
5
|
Martinez Farias MA, Kincaid VA, Annamalai VR, Kiessling LL. Isoprenoid phosphonophosphates as glycosyltransferase acceptor substrates. J Am Chem Soc 2014; 136:8492-5. [PMID: 24866828 PMCID: PMC4073833 DOI: 10.1021/ja500622v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Glycosyltransferases that act on
polyprenol pyrophosphate substrates
are challenging to study because their lipid-linked substrates are
difficult to isolate from natural sources and arduous to synthesize.
To facilitate access to glycosyl acceptors, we assembled phosphonophosphate
analogues and showed these are effective substrate surrogates for
GlfT1, the essential product of mycobacterial gene Rv3782. Under chemically defined conditions, the galactofuranosyltransferase
GlfT1 catalyzes the formation of a tetrasaccharide sequence en route
to assembly of the mycobacterial galactan.
Collapse
Affiliation(s)
- Mario A Martinez Farias
- Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | | | | | | |
Collapse
|
6
|
Vervacke J, Funk AL, Wang YC, Strom M, Hrycyna CA, Distefano MD. Diazirine-containing photoactivatable isoprenoid: synthesis and application in studies with isoprenylcysteine carboxyl methyltransferase. J Org Chem 2014; 79:1971-8. [PMID: 24502619 PMCID: PMC3985442 DOI: 10.1021/jo402600b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Indexed: 12/19/2022]
Abstract
Photoaffinity labeling is a useful technique employed to identify protein-ligand and protein-protein noncovalent interactions. Photolabeling experiments have been particularly informative for probing membrane-bound proteins where structural information is difficult to obtain. The most widely used classes of photoactive functionalities include aryl azides, diazocarbonyls, diazirines, and benzophenones. Diazirines are intrinsically smaller than benzophenones and generate carbenes upon photolysis that react with a broader range of amino acid side chains compared with the benzophenone-derived diradical; this makes diazirines potentially more general photoaffinity-labeling agents. In this article, we describe the development and application of a new isoprenoid analogue containing a diazirine moiety that was prepared in six steps and incorporated into an a-factor-derived peptide produced via solid-phase synthesis. In addition to the diazirine moiety, fluorescein and biotin groups were also incorporated into the peptide to aid in the detection and enrichment of photo-cross-linked products. This multifuctional diazirine-containing peptide was a substrate for Ste14p, the yeast homologue of the potential anticancer target Icmt, with K(m) (6.6 μM) and V(max) (947 pmol min(-1) mg(-1)) values comparable or better than a-factor peptides functionalized with benzophenone-based isoprenoids. Photo-cross-linking experiments demonstrated that the diazirine probe photo-cross-linked to Ste14p with observably higher efficiency than benzophenone-containing a-factor peptides.
Collapse
Affiliation(s)
- Jeffrey
S. Vervacke
- Departments
of Chemistry and Medicinal Chemistry, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Amy L. Funk
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907−2084, United States
| | - Yen-Chih Wang
- Departments
of Chemistry and Medicinal Chemistry, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mark Strom
- Departments
of Chemistry and Medicinal Chemistry, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christine A. Hrycyna
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907−2084, United States
| | - Mark D. Distefano
- Departments
of Chemistry and Medicinal Chemistry, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
7
|
Synthesis of isoprenoid chain-contained chemical probes for an investigation of molecular interactions by using quartz crystal microbalance. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
8
|
Wang R, Yan F, Qiu D, Jeong JS, Jin Q, Kim TY, Chen L. Traceless cross-linker for photocleavable bioconjugation. Bioconjug Chem 2012; 23:705-13. [PMID: 22432929 DOI: 10.1021/bc200343u] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photoresponsive bioconjugation empowers the development of novel methods for drug discovery, disease diagnosis, and high-throughput screening, among others. In this paper, we report on the characteristics of a traceless photocleavable cross-linker, di-6-(3-succinimidyl carbonyloxymethyl-4-nitro-phenoxy)-hexanoic acid disulfide diethanol ester (SCNE). The traceless feature and the biocompatibility of this photocleavable cross-linking reagent were corroborated. Consequently, we demonstrated its application in reversible phage particle immobilization that could provide a platform for direct single-phage screening. We also applied it in protein-photoprinting, where SCNE acts as a "photo-eraser" to remove the cross-linked protein molecules at a desired region in a simple, clean, and light-controllable fashion. We further demonstrated the two-tier atomic force microscopic (AFM) method that uses SCNE to carry out two subsequent AFM tasks in situ. The approach allows guided protein delivery and subsequent high-resolution imaging at the same local area, thus opening up the possibility of monitoring protein functions in live cells. The results imply that SCNE is a versatile cross-linker that can be used for a wide range of applications where photocleavage ensures clean and remote-controllable release of biological molecules from a substrate.
Collapse
Affiliation(s)
- Rong Wang
- Department of Biological, Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA.
| | | | | | | | | | | | | |
Collapse
|
9
|
Abstract
Rubber biosynthesis in plants is a fascinating biochemical system, which evolved at the dawn of the dicotyledoneae and is present in at least four of the dictolydonous superorders. Rubber biosynthesis is catalyzed by a membrane complex in a monolayer membrane envelope, requires two distinct substrates and a divalent cation cofactor, and produces a high-molecular-weight isoprenoid polymer. A solid understanding of this system underpins valuable papers in the literature. However, the published literature is rife with unreliable reports in which the investigators have fallen into traps created by the current incomplete understanding of the biochemistry of rubber synthesis. In this chapter, we attempt to guide both new and more established researchers around these pitfalls.
Collapse
|
10
|
Placzek AT, Krzysiak AJ, Gibbs RA. Chemical Probes of Protein Prenylation. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/b978-0-12-415922-8.00005-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
|
11
|
Mullen DG, Kyro K, Hauser M, Gustavsson M, Veglia G, Becker JM, Naider F, Distefano MD. Synthesis of a-factor peptide from Saccharomyces cerevisiae and photoactive analogues via Fmoc solid phase methodology. Bioorg Med Chem 2010; 19:490-7. [PMID: 21134758 DOI: 10.1016/j.bmc.2010.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 10/29/2010] [Accepted: 11/02/2010] [Indexed: 11/28/2022]
Abstract
a-Factor from Saccharomyces cerevisiae is a farnesylated dodecapeptide involved in mating. The molecule binds to a G-protein coupled receptor and hence serves as a simple system for studying the interactions between prenylated molecules and their cognate receptors. Here, we describe the preparation of a-factor and two photoactive analogues via Fmoc solid-phase peptide synthesis using hydrazinobenzoyl AM NovaGel™ resin; the structure of the synthetic a-factor was confirmed by MS-MS analysis and NMR; the structures of the analogues were confirmed by MS-MS analysis. Using a yeast growth arrest assay, the analogues were found to have activity comparable to a-factor itself.
Collapse
Affiliation(s)
- Daniel G Mullen
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Abrunhosa-Thomas I, Coudray L, Montchamp JL. Synthesis and Reactivity Studies of α,α-Difluoromethylphosphinates. Tetrahedron 2010; 66:4434-4440. [PMID: 20725593 PMCID: PMC2921993 DOI: 10.1016/j.tet.2010.04.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The preparation and reactivity of some α,α-difluorophosphinates is investigated. Alkylation of H-phosphinates with LiHMDS and ClCF(2)H gives the corresponding α,α-difluorophosphinates in good yield. Deprotonation of these reagents with alkyllithium or LDA is then studied. Subtle electronic effects translate into significant differences in the deprotonation/alkylation of the two "Ciba-Geigy reagents" (EtO)(2)CRP(O)(OEt)H (R = H, Me). On the other hand, attempted methylation of difluoromethyl-octyl-phosphinic acid butyl ester resulted in the exclusive alkylation of the octyl chain. Finally, reaction with carbonyl compounds results in the formation of 1,1-difluoro-2-phosphinoyl compounds.
Collapse
|
13
|
Kyro K, Manandhar SP, Mullen D, Schmidt WK, Distefano MD. Photoaffinity labeling of Ras converting enzyme 1 (Rce1p) using a benzophenone-containing peptide substrate. Bioorg Med Chem 2010; 18:5675-84. [PMID: 20619662 DOI: 10.1016/j.bmc.2010.06.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 06/04/2010] [Accepted: 06/07/2010] [Indexed: 11/30/2022]
Abstract
Isoprenylation is a post-translational modification that increases protein hydrophobicity and helps target certain proteins to membranes. Ras converting enzyme 1 (Rce1p) is an endoprotease that catalyzes the removal of a three residue fragment from the C-terminus of isoprenylated proteins. To obtain structural information about this membrane protein, photoaffinity labeling agents are being prepared and employed. Here, we describe the synthesis of a benzophenone-containing peptide substrate analogue for Rce1p. Using a continuous spectrofluorometric assay, this peptide was shown to be a substrate for Rce1p. Mass spectrometry was performed to confirm the site of cleavage and structure of the processed probe. Photolysis of the biotinylated compound in the presence of membranes containing Rce1p followed by streptavidin pull-down and Western blot analysis indicated that Rce1p had been labeled by the probe. Photolysis in the presence of both the biotinylated, benzophenone-containing probe and a farnesylated peptide competitor reduced the extent of labeling, suggesting that labeling is occurring in the active site.
Collapse
Affiliation(s)
- Kelly Kyro
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | | | | | | | | |
Collapse
|
14
|
Hovlid ML, Edelstein RL, Henry O, Ochocki J, DeGraw A, Lenevich S, Talbot T, Young VG, Hruza AW, Lopez-Gallego F, Labello NP, Strickland CL, Schmidt-Dannert C, Distefano MD. Synthesis, properties, and applications of diazotrifluropropanoyl-containing photoactive analogs of farnesyl diphosphate containing modified linkages for enhanced stability. Chem Biol Drug Des 2010; 75:51-67. [PMID: 19954434 DOI: 10.1111/j.1747-0285.2009.00914.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photoactive analogs of farnesyl diphosphate (FPP) are useful probes in studies of enzymes that employ this molecule as a substrate. Here, we describe the preparation and properties of two new FPP analogs that contain diazotrifluoropropanoyl photophores linked to geranyl diphosphate via amide or ester linkages. The amide-linked analog (3) was synthesized in 32P-labeled form from geraniol in seven steps. Experiments with Saccharomyces cerevisiae protein farnesyltransferase (ScPFTase) showed that 3 is an alternative substrate for the enzyme. Photolysis experiments with [(32)P]3 demonstrate that this compound labels the beta-subunits of both farnesyltransferase and geranylgeranyltransferase (types 1 and 2). However, the amide-linked probe 3 undergoes a rearrangement to a photochemically unreactive isomeric triazolone upon long term storage making it inconvenient to use. To address this stability issue, the ester-linked analog 4 was prepared in six steps from geraniol. Computational analysis and X-ray crystallographic studies suggest that 4 binds to protein farnesyl transferase (PFTase) in a similar fashion as FPP. Compound 4 is also an alternative substrate for PFTase, and a 32P-labeled form selectively photocrosslinks the beta-subunit of ScPFTase as well as E. coli farnesyldiphosphate synthase and a germacrene-producing sesquiterpene synthase from Nostoc sp. strain PCC7120 (a cyanobacterial source). Finally, nearly exclusive labeling of ScPFTase in crude E. coli extract was observed, suggesting that [32P]4 manifests significant selectivity and should hence be useful for identifying novel FPP-utilizing enzymes in crude protein preparations.
Collapse
Affiliation(s)
- Marisa L Hovlid
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Lodewyk MW, Lui VG, Tantillo DJ. Synthesis of (sulfonyl)methylphosphonate analogs of prenyl diphosphates. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2009.10.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
16
|
Synthesis and application of photoaffinity probe containing an intact isoprenoid chain. Bioorg Med Chem Lett 2009; 19:4824-6. [DOI: 10.1016/j.bmcl.2009.06.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 05/20/2009] [Accepted: 06/10/2009] [Indexed: 01/06/2023]
|
17
|
LI L, TANG W, ZHAO Z. Synthesis and Application of Prenyl-Derived Photoaffinity Probes. CHINESE J CHEM 2009. [DOI: 10.1002/cjoc.200990233] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
18
|
Henry O, Lopez-Gallego F, Agger SA, Schmidt-Dannert C, Sen S, Shintani D, Cornish K, Distefano MD. A versatile photoactivatable probe designed to label the diphosphate binding site of farnesyl diphosphate utilizing enzymes. Bioorg Med Chem 2009; 17:4797-805. [PMID: 19447628 DOI: 10.1016/j.bmc.2009.04.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 04/01/2009] [Accepted: 04/09/2009] [Indexed: 10/20/2022]
Abstract
Farnesyl diphosphate (FPP) is a substrate for a diverse number of enzymes found in nature. Photoactive analogues of isoprenoid diphosphates containing either benzophenone, diazotrifluoropropionate or azide groups have been useful for studying both the enzymes that synthesize FPP as well as those that employ FPP as a substrate. Here we describe the synthesis and properties of a new class of FPP analogues that links an unmodified farnesyl group to a diphosphate mimic containing a photoactive benzophenone moiety; thus, importantly, these compounds are photoactive FPP analogues that contain no modifications of the isoprenoid portion of the molecule that may interfere with substrate binding in the active site of an FPP utilizing enzyme. Two isomeric compounds containing meta- and para-substituted benzophenones were prepared. These two analogues inhibit Saccharomyces cerevisiae protein farnesyltransferase (ScPFTase) with IC(50) values of 5.8 (meta isomer) and 3.0 microM (para isomer); the more potent analogue, the para isomer, was shown to be a competitive inhibitor of ScPFTase with respect to FPP with a K(I) of 0.46 microM. Radiolabeled forms of both analogues selectively labeled the beta-subunit of ScPFTase. The para isomer was also shown to label Escherichia coli farnesyl diphosphate synthase and Drosophila melanogaster farnesyl diphosphate synthase. Finally, the para isomer was shown to be an alternative substrate for a sesquiterpene synthase from Nostoc sp. strain PCC7120, a cyanobacterial source; the compound also labeled the purified enzyme upon photolysis. Taken together, these results using a number of enzymes demonstrate that this new class of probes should be useful for a plethora of studies of FPP-utilizing enzymes.
Collapse
Affiliation(s)
- Olivier Henry
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Köpke T, Pink M, Zaleski JM. Expansion by Contraction: Diversifying the Photochemical Reactivity Scope of Diazo-oxochlorins toward Development of in Situ Alkylating Agents. J Am Chem Soc 2008; 130:15864-71. [DOI: 10.1021/ja800094e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tillmann Köpke
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Maren Pink
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | | |
Collapse
|
20
|
Kawamura A, Hindi S, Mihai DM, James L, Aminova O. Binding is not enough: flexibility is needed for photocrosslinking of Lck kinase by benzophenone photoligands. Bioorg Med Chem 2008; 16:8824-9. [PMID: 18799314 PMCID: PMC2581794 DOI: 10.1016/j.bmc.2008.08.077] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 08/27/2008] [Accepted: 08/29/2008] [Indexed: 10/21/2022]
Abstract
Benzophenone photophores are employed widely for photoaffinity-labeling studies. Photolabeling with benzophenone, however, is hardly a routine experiment. Even when a photoprobe binds to its target, photocrosslinking does not necessarily occur. This is because photolabeling by benzophenone is affected by many factors other than target-binding, such as conformational flexibility of photoligand. Despite the widespread recognition of such complications, there has been no systematic study to assess the relative importance of individual factors that can affect photolabeling efficiency. In order to gain an insight into this problem, we conducted a structure-activity relationship (SAR) study of benzophenone photoligands for Lck kinase, in which photoligands with varying target-binding affinity and conformational flexibility were compared. The study found that binding-affinity, as indicated by kinase inhibitory potency, did not correlate with photolabeling efficiency. Instead, conformational flexibility was found to be the determining factor for efficient photolabeling by our photoligands. Implication of the current findings, in particular, with regard to selection and optimization of benzophenone photoligands, is discussed.
Collapse
Affiliation(s)
- Akira Kawamura
- Department of Chemistry, Hunter College of CUNY, 695 Park Avenue, New York, NY 10065, USA.
| | | | | | | | | |
Collapse
|
21
|
Xie W, McMahan CM, Degraw AJ, Distefano MD, Cornish K, Whalen MC, Shintani DK. Initiation of rubber biosynthesis: In vitro comparisons of benzophenone-modified diphosphate analogues in three rubber-producing species. PHYTOCHEMISTRY 2008; 69:2539-2545. [PMID: 18799172 DOI: 10.1016/j.phytochem.2008.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2008] [Revised: 07/25/2008] [Accepted: 07/25/2008] [Indexed: 05/26/2023]
Abstract
Natural rubber, cis-1,4-polyisoprene, is a vital industrial material synthesized by plants via a side branch of the isoprenoid pathway by the enzyme rubber transferase. While the specific structure of this enzyme is not yet defined, based on activity it is probably a cis-prenyl transferase. Photoactive functionalized substrate analogues have been successfully used to identify isoprenoid-utilizing enzymes such as cis- and trans-prenyltransferases, and initiator binding of an allylic pyrophosphate molecule in rubber transferase has similar features to these systems. In this paper, a series of benzophenone-modified initiator analogues were shown to successfully initiate rubber biosynthesis in vitro in enzymatically-active washed rubber particles from Ficus elastica, Heveabrasiliensis and Parthenium argentatum. Rubber transferases from all three species initiated rubber biosynthesis most efficiently with farnesyl pyrophosphate. However, rubber transferase had a higher affinity for benzophenone geranyl pyrophosphate (Bz-GPP) and dimethylallyl pyrophosphate (Bz-DMAPP) analogues with ether-linkages than the corresponding GPP or DMAPP. In contrast, ester-linked Bz-DMAPP analogues were less efficient initiators than DMAPP. Thus, rubber biosynthesis depends on both the size and the structure of Bz-initiator molecules. Kinetic studies thereby inform selection of specific probes for covalent photolabeling of the initiator binding site of rubber transferase.
Collapse
Affiliation(s)
- Wenshuang Xie
- University of Nevada, Department of Biochemistry and Molecular Biology/MS200, Reno, NV 89557, United States
| | | | | | | | | | | | | |
Collapse
|
22
|
Purification of prenylated proteins by affinity chromatography on cyclodextrin-modified agarose. Anal Biochem 2008; 386:1-8. [PMID: 18834849 DOI: 10.1016/j.ab.2008.09.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Revised: 08/26/2008] [Accepted: 09/06/2008] [Indexed: 01/19/2023]
Abstract
Although protein prenylation is widely studied, there are few good methods for isolating prenylated proteins from their nonprenylated relatives. We report that crosslinked agarose (e.g., Sepharose) chromatography medium that has been chemically functionalized with beta-cyclodextrin (beta-CD) is extremely effective in affinity chromatography of prenylated proteins. In this study, a variety of proteins with C-terminal prenylation target ("CAAX box") sequences were enzymatically prenylated in vitro with natural and nonnatural prenyl diphosphate substrates. The prenylated protein products could then be isolated from starting materials by gravity chromatography or fast protein liquid chromatography (FPLC) on a beta-CD-Sepharose column. One particular prenylation reaction, farnesylation of an mCherry-CAAX fusion construct, was studied in detail. In this case, purified farnesylated product was unambiguously identified by electrospray mass spectrometry. In addition, when mCherry-CAAX was prenylated with a nonnatural, functional isoprenoid substrate, the functional group was maintained by chromatography on beta-CD-Sepharose, such that the resulting protein could be selectively bound at its C terminus to complementary functionality on a solid substrate. Finally, beta-CD-Sepharose FPLC was used to isolate prenylated mCherry-CAAX from crude HeLa cell lysate as a model for purifying prenylated proteins from cell extracts. We propose that this method could be generally useful to the community of researchers studying protein prenylation.
Collapse
|
23
|
Tian R, Li L, Tang W, Liu H, Ye M, Zhao ZK, Zou H. Chemical proteomic study of isoprenoid chain interactome with a synthetic photoaffinity probe. Proteomics 2008; 8:3094-104. [DOI: 10.1002/pmic.200800021] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
24
|
Yu X, Wang S, Chen F. Solid-phase synthesis of solanesol. JOURNAL OF COMBINATORIAL CHEMISTRY 2008; 10:605-10. [PMID: 18558751 DOI: 10.1021/cc800069t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient and convergent solid-phase strategy for the total synthesis of All- E solanesol is described. This method features avoidance of iterative and difficult purifications comparing with solution-phase synthesis and is suitable for the preparation of other oligoprenols.
Collapse
Affiliation(s)
- Xiongjie Yu
- Department of Chemistry, Fudan University, No. 220 HanDan Road, Shanghai 200433, P. R. China
| | | | | |
Collapse
|
25
|
Labadie GR, Viswanathan R, Poulter CD. Farnesyl diphosphate analogues with omega-bioorthogonal azide and alkyne functional groups for protein farnesyl transferase-catalyzed ligation reactions. J Org Chem 2007; 72:9291-7. [PMID: 17979291 DOI: 10.1021/jo7017747] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Eleven farnesyl diphosphate analogues, which contained omega-azide or alkyne substituents suitable for bioorthogonal Staudinger and Huisgen [3 + 2] cycloaddition coupling reactions, were synthesized. The analogues were evaluated as substrates for the alkylation of peptide cosubstrates by yeast protein farnesyl transferase. Five of the diphosphates were good alternative substrates for farnesyl diphosphate (FPP). Steady-state kinetic constants were measured for the active compounds, and the products were characterized by HPLC and LC-MS. Two of the analogues gave steady-state kinetic parameters (kcat and Km) very similar to those of the natural substrate.
Collapse
|