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Miller ET, Tsodikov OV, Garneau-Tsodikova S. Structural insights into the diverse prenylating capabilities of DMATS prenyltransferases. Nat Prod Rep 2024; 41:113-147. [PMID: 37929638 DOI: 10.1039/d3np00036b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Covering: 2009 up to August 2023Prenyltransferases (PTs) are involved in the primary and the secondary metabolism of plants, bacteria, and fungi, and they are key enzymes in the biosynthesis of many clinically relevant natural products (NPs). The continued biochemical and structural characterization of the soluble dimethylallyl tryptophan synthase (DMATS) PTs over the past two decades have revealed the significant promise that these enzymes hold as biocatalysts for the chemoenzymatic synthesis of novel drug leads. This is a comprehensive review of DMATSs describing the structure-function relationships that have shaped the mechanistic underpinnings of these enzymes, as well as the application of this knowledge to the engineering of DMATSs. We summarize the key findings and lessons learned from these studies over the past 14 years (2009-2023). In addition, we identify current gaps in our understanding of these fascinating enzymes.
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Affiliation(s)
- Evan T Miller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
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2
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Wang J, Al-Majid D, Brenner JC, Smith JD. Mutant HRas Signaling and Rationale for Use of Farnesyltransferase Inhibitors in Head and Neck Squamous Cell Carcinoma. Target Oncol 2023; 18:643-655. [PMID: 37665491 DOI: 10.1007/s11523-023-00993-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2023] [Indexed: 09/05/2023]
Abstract
Head and neck squamous cell carcinomas (HNSCCs) are often associated with poor outcomes, due at least in part to the limited number of treatment options available for those patients who develop recurrent and/or metastatic disease (R/M HNSCC). Even with the recent validation and approval of immunotherapies in the first-line setting for these patients, the need for the development of new and alternative precision medicine strategies with survival benefit is clear. Oncogenic alterations in the HRAS (Harvey rat sarcoma virus) proto-oncogene are seen in approximately 4-8% of R/M HNSCC tumors. Recently, several preclinical and clinical advancements have been made in the implementation of small-molecule inhibitors that block post-translational farnesylation of HRas, thereby abrogating its downstream oncogenic activity. In this review, we focus on the biology of wild-type and mutant HRas signaling in HNSCC, and rationale for use and outcomes of farnesyltransferase inhibitors in patients with HRAS-mutant tumors.
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Affiliation(s)
- Jiayu Wang
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Dana Al-Majid
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan, MSRB III 1150 W. Medical Center Dr., Ann Arbor, MI, 48109, USA
| | - J Chad Brenner
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan, MSRB III 1150 W. Medical Center Dr., Ann Arbor, MI, 48109, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Joshua D Smith
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan, MSRB III 1150 W. Medical Center Dr., Ann Arbor, MI, 48109, USA
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3
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Schey GL, Buttery PH, Hildebrandt ER, Novak SX, Schmidt WK, Hougland JL, Distefano MD. MALDI-MS Analysis of Peptide Libraries Expands the Scope of Substrates for Farnesyltransferase. Int J Mol Sci 2021; 22:ijms222112042. [PMID: 34769472 PMCID: PMC8584866 DOI: 10.3390/ijms222112042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 11/16/2022] Open
Abstract
Protein farnesylation is a post-translational modification where a 15-carbon farnesyl isoprenoid is appended to the C-terminal end of a protein by farnesyltransferase (FTase). This modification typically causes proteins to associate with the membrane and allows them to participate in signaling pathways. In the canonical understanding of FTase, the isoprenoids are attached to the cysteine residue of a four-amino-acid CaaX box sequence. However, recent work has shown that five-amino-acid sequences can be recognized, including the pentapeptide CMIIM. This paper describes a new systematic approach to discover novel peptide substrates for FTase by combining the combinatorial power of solid-phase peptide synthesis (SPPS) with the ease of matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS). The workflow consists of synthesizing focused libraries containing 10-20 sequences obtained by randomizing a synthetic peptide at a single position. Incubation of the library with FTase and farnesyl pyrophosphate (FPP) followed by mass spectrometric analysis allows the enzymatic products to be clearly resolved from starting peptides due to the increase in mass that occurs upon farnesylation. Using this method, 30 hits were obtained from a series of libraries containing a total of 80 members. Eight of the above peptides were selected for further evaluation, reflecting a mixture that represented a sampling of diverse substrate space. Six of these sequences were found to be bona fide substrates for FTase, with several meeting or surpassing the in vitro efficiency of the benchmark sequence CMIIM. Experiments in yeast demonstrated that proteins bearing these sequences can be efficiently farnesylated within live cells. Additionally, a bioinformatics search showed that a variety of pentapeptide CaaaX sequences can be found in the mammalian genome, and several of these sequences display excellent farnesylation in vitro and in yeast cells, suggesting that the number of farnesylated proteins within mammalian cells may be larger than previously thought.
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Affiliation(s)
- Garrett L. Schey
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Peter H. Buttery
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Emily R. Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (E.R.H.); (W.K.S.)
| | - Sadie X. Novak
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA; (S.X.N.); (J.L.H.)
| | - Walter K. Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (E.R.H.); (W.K.S.)
| | - James L. Hougland
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA; (S.X.N.); (J.L.H.)
- BioInspired Syracuse, Syracuse University, Syracuse, NY 13244, USA
| | - Mark D. Distefano
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
- Correspondence:
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4
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Kessler L, Malik S, Leoni M, Burrows F. Potential of Farnesyl Transferase Inhibitors in Combination Regimens in Squamous Cell Carcinomas. Cancers (Basel) 2021; 13:cancers13215310. [PMID: 34771475 PMCID: PMC8582567 DOI: 10.3390/cancers13215310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
Current therapies for recurrent and metastatic SCC are associated with poor outcomes, and options for later lines of treatment are limited. Insights into potential therapeutic targets, as well as mechanisms of resistance to available therapies, have begun to be elucidated, creating the basis for exploration of combination approaches to drive better patient outcomes. Tipifarnib, a farnesyl transferase inhibitor (FTI), is a small molecule drug that has demonstrated encouraging clinical activity in a genetically-defined subset of head and neck squamous cell carcinoma (HNSCC)-specifically, tumors that express a mutation in the HRAS protooncogene. More recently, bioinformatic analyses and results from patient-derived xenograft modeling indicate that HRAS pathway dependency may extend to a broader subpopulation of SCCs beyond HRAS mutants in the context of combination with agents such as cisplatin, cetuximab, or alpelisib. In addition, tipifarnib can also inactivate additional farnesylated proteins implicated in resistance to approved therapies, including immunotherapies, through a variety of distinct mechanisms, suggesting that tipifarnib could serve as an anchor for combination regimens in SCCs and other tumor types.
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Wang Q, Chen F, Liu P, Mu Y, Sun S, Yuan X, Shang P, Ji B. Scaffold-based analysis of nonpeptide oncogenic FTase inhibitors using multiple similarity matching, binding affinity scoring and enzyme inhibition assay. J Mol Graph Model 2021; 105:107898. [PMID: 33784524 DOI: 10.1016/j.jmgm.2021.107898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/25/2021] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
Abstract
Oncogenic protein farnesyltransferase (FTase) is a key enzyme responsible for the lipid modification of a large and important number of proteins including Ras, which has been recognized as a druggable target of diverse cancers. Here, we report a systematic scaffold-based analysis to investigate the affinity, selectivity and cross-reactivity of nonpeptide inhibitors across ontology-enriched, disease-associated FTase mutants, by integrating multiple similarity matching, binding affinity scoring and enzyme inhibition assay. It is revealed that nonpeptide inhibitors are generally insensitive to FTase mutations; many of them cannot definitely select for wild-type target over mutant enzymes. Therefore, off-target is observed as a common phenomenon for the untargeted consequence of targeted therapies with FTase inhibition. This is not unexpected if considering that the enzyme active site is highly conserved in composition, configuration and function. The off-target, on the one hand, causes nonpeptide inhibitors with adverse drug reactions and, on the other hand, makes the inhibitors as promising candidates for the new use of old drugs. To practice the latter, a number of unexpected mutant-inhibitor interactions involved in cancer signaling pathways are uncovered in the created profile, from which several nonpeptide inhibitors are identified as insensitive to a drug-resistant mutation. Structural analysis suggests that the inhibitor ligands can bind to the mutant active site in a similar manner with wild-type target, although their nonbonded interactions appear to be impaired moderately upon the mutation.
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Affiliation(s)
- Qifei Wang
- Department of Chest Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China
| | - Fei Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China
| | - Peng Liu
- Department of Chest Surgery, Ningyang First People's Hospital, Taian, 271400, China
| | - Yushu Mu
- Department of Chest Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China
| | - Shibin Sun
- Department of Chest Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China
| | - Xulong Yuan
- Department of Chest Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China
| | - Pan Shang
- Department of Chest Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China
| | - Bo Ji
- Department of Chest Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China.
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7
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Klimpel A, Stillger K, Wiederstein JL, Krüger M, Neundorf I. Cell-permeable CaaX-peptides affect K-Ras downstream signaling and promote cell death in cancer cells. FEBS J 2020; 288:2911-2929. [PMID: 33112492 DOI: 10.1111/febs.15612] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 08/17/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022]
Abstract
Cysteine prenylation is a post-translational modification that is used by nature to control crucial biological functions of proteins, such as membrane trafficking, signal transduction, and apoptosis. It mainly occurs in eukaryotic proteins at a C-terminal CaaX box and is mediated by prenyltransferases. Since the discovery of prenylated proteins, various tools have been developed to study the mechanisms of prenyltransferases, as well as to visualize and to identify prenylated proteins. Herein, we introduce cell-permeable peptides bearing a C-terminal CaaX motif based on Ras sequences. We demonstrate that intracellular accumulation of those peptides in different cells is controlled by the presence of their CaaX motif and that they specifically interact with intracellular prenyltransferases. As proof of concept, we further highlight their utilization to alter downstream signaling of Ras proteins, particularly of K-Ras-4B, in pancreatic cancer cells. Application of this strategy holds great promise to better understand and regulate post-translational cysteine prenylation.
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Affiliation(s)
- Annika Klimpel
- Institute for Biochemistry, University of Cologne, Germany
| | | | - Janica L Wiederstein
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
| | - Marcus Krüger
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany.,Center for Molecular Medicine (CMMC), University of Cologne, Germany
| | - Ines Neundorf
- Institute for Biochemistry, University of Cologne, Germany
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8
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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9
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Xu Y, Anderson DE, Ye Y. The HECT domain ubiquitin ligase HUWE1 targets unassembled soluble proteins for degradation. Cell Discov 2016; 2:16040. [PMID: 27867533 PMCID: PMC5102030 DOI: 10.1038/celldisc.2016.40] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/17/2016] [Indexed: 12/18/2022] Open
Abstract
In eukaryotes, many proteins function in multi-subunit complexes that require
proper assembly. To maintain complex stoichiometry, cells use the endoplasmic
reticulum-associated degradation system to degrade unassembled membrane
subunits, but how unassembled soluble proteins are eliminated is undefined. Here
we show that degradation of unassembled soluble proteins (referred to as
unassembled soluble protein degradation, USPD) requires the ubiquitin selective
chaperone p97, its co-factor nuclear protein localization protein 4 (Npl4), and
the proteasome. At the ubiquitin ligase level, the previously identified protein
quality control ligase UBR1 (ubiquitin protein ligase E3 component n-recognin 1)
and the related enzymes only process a subset of unassembled soluble proteins.
We identify the homologous to the E6-AP carboxyl terminus (homologous to the
E6-AP carboxyl terminus) domain-containing protein HUWE1 as a ubiquitin ligase
for substrates bearing unshielded, hydrophobic segments. We used a stable
isotope labeling with amino acids-based proteomic approach to identify
endogenous HUWE1 substrates. Interestingly, many HUWE1 substrates form
multi-protein complexes that function in the nucleus although HUWE1 itself is
cytoplasmically localized. Inhibition of nuclear entry enhances HUWE1-mediated
ubiquitination and degradation, suggesting that USPD occurs primarily in the
cytoplasm. Altogether, these findings establish a new branch of the cytosolic
protein quality control network, which removes surplus polypeptides to control
protein homeostasis and nuclear complex assembly.
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Affiliation(s)
- Yue Xu
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, MD, USA
| | - D Eric Anderson
- Advanced Mass Spectrometry Core Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, MD, USA
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, MD, USA
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10
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Moorthy NSHN, Sousa SF, Ramos MJ, Fernandes PA. Binding mode of conformations and structure-based pharmacophore development for farnesyltransferase inhibitors. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1578-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Moorthy NSHN, Sousa SF, Ramos MJ, Fernandes PA. Molecular dynamic simulations and structure-based pharmacophore development for farnesyltransferase inhibitors discovery. J Enzyme Inhib Med Chem 2016; 31:1428-42. [PMID: 26887913 DOI: 10.3109/14756366.2016.1144593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Farnesyltransferase is one of the enzyme targets for the development of drugs for diseases, including cancer, malaria, progeria, etc. In the present study, the structure-based pharmacophore models have been developed from five complex structures (1LD7, 1NI1, 2IEJ, 2ZIR and 2ZIS) obtained from the protein data bank. Initially, molecular dynamic (MD) simulations were performed for the complexes for 10 ns using AMBER 12 software. The conformers of the complexes (75) generated from the equilibrated protein were undergone protein-ligand interaction fingerprint (PLIF) analysis. The results showed that some important residues, such as LeuB96, TrpB102, TrpB106, ArgB202, TyrB300, AspB359 and TyrB361, are predominantly present in most of the complexes for interactions. These residues form side chain acceptor and surface (hydrophobic or π-π) kind of interactions with the ligands present in the complexes. The structure-based pharmacophore models were generated from the fingerprint bits obtained from PLIF analysis. The pharmacophore models have 3-4 pharmacophore contours consist of acceptor and metal ligation (Acc & ML), hydrophobic (HydA) and extended acceptor (Acc2) features with the radius ranging between 1-3 Å for Acc & ML and 1-2 Å for HydA. The excluded volumes of the pharmacophore contours radius are between 1-2 Å. Further, the distance between the interacting groups, root mean square deviation (RMSD), root mean square fluctuation (RMSF) and radial distribution function (RDF) analysis were performed for the MD-simulated proteins using PTRAJ module. The generated pharmacophore models were used to screen a set of natural compounds and database compounds to select significant HITs. We conclude that the developed pharmacophore model can be a significant model for the identification of HITs as FTase inhibitors.
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Affiliation(s)
- N S Hari Narayana Moorthy
- a UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Universidade do Porto , 687, Rua do Campo Alegre , Porto , Portugal
| | - Sergio F Sousa
- a UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Universidade do Porto , 687, Rua do Campo Alegre , Porto , Portugal
| | - Maria J Ramos
- a UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Universidade do Porto , 687, Rua do Campo Alegre , Porto , Portugal
| | - Pedro A Fernandes
- a UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Universidade do Porto , 687, Rua do Campo Alegre , Porto , Portugal
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12
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Ho MH, De Vivo M, Peraro MD, Klein ML. Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation. J Chem Theory Comput 2015; 5:1657-66. [PMID: 26609858 DOI: 10.1021/ct8004722] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The protein farnesyltransferase (FTase) is a Zn(2+)-metalloenzyme that catalyzes the farnesylation reaction, i.e., the transfer of the 15-carbon atom farnesyl group from farnesyl diphosphate (FPP) to a specific cysteine of protein substrates. Oncogenic Ras proteins, which are among the FTase substrates, are observed in about 20-30% of human cancer cells. Thus, FTase represents a target for anticancer drug design. Herein, we present a classical force-field-based and quantum mechanics/molecular mechanics (QM/MM) computational study of the FTase reaction mechanism. Our findings offer a detailed picture of the FTase catalytic pathway, describing structural features and the energetics of its saddle points. A moderate dissociation of the diphosphate group from the FPP is observed during the nucleophilic attack of the zinc-bound thiolate. At the transition state, a resonance structure is observed, which indicates the formation of a metastable carbocation. However, no stable intermediate is found along the reaction pathway. Thus, the reaction occurs via an associative mechanism with dissociative character, in agreement with the mechanism proposed by Fierke et al. ( Biochemistry 2000, 39, 2593-2602 and Biochemistry 2003, 42, 9741-9748 ). Moreover, a fluorine-substituted FPP analogue (CF3-FPP) is used to investigate the inhibitory effect of fluorine, which in turn provides additional agreement with experimental data.
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Affiliation(s)
- Ming-Hsun Ho
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy, and Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, CH-1015 Lausanne, Switzerland
| | - Marco De Vivo
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy, and Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, CH-1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy, and Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, CH-1015 Lausanne, Switzerland
| | - Michael L Klein
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy, and Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, CH-1015 Lausanne, Switzerland
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13
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Zinc-binding cysteines: diverse functions and structural motifs. Biomolecules 2014; 4:419-34. [PMID: 24970223 PMCID: PMC4101490 DOI: 10.3390/biom4020419] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 03/19/2014] [Accepted: 03/20/2014] [Indexed: 12/13/2022] Open
Abstract
Cysteine residues are known to perform essential functions within proteins, including binding to various metal ions. In particular, cysteine residues can display high affinity toward zinc ions (Zn2+), and these resulting Zn2+-cysteine complexes are critical mediators of protein structure, catalysis and regulation. Recent advances in both experimental and theoretical platforms have accelerated the identification and functional characterization of Zn2+-bound cysteines. Zn2+-cysteine complexes have been observed across diverse protein classes and are known to facilitate a variety of cellular processes. Here, we highlight the structural characteristics and diverse functional roles of Zn2+-cysteine complexes in proteins and describe structural, computational and chemical proteomic technologies that have enabled the global discovery of novel Zn2+-binding cysteines.
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14
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Mabanglo MF, Hast MA, Lubock NB, Hellinga HW, Beese LS. Crystal structures of the fungal pathogen Aspergillus fumigatus protein farnesyltransferase complexed with substrates and inhibitors reveal features for antifungal drug design. Protein Sci 2014; 23:289-301. [PMID: 24347326 PMCID: PMC3945837 DOI: 10.1002/pro.2411] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/11/2013] [Accepted: 12/11/2013] [Indexed: 11/07/2022]
Abstract
Species of the fungal genus Aspergillus are significant human and agricultural pathogens that are often refractory to existing antifungal treatments. Protein farnesyltransferase (FTase), a critical enzyme in eukaryotes, is an attractive potential target for antifungal drug discovery. We report high-resolution structures of A. fumigatus FTase (AfFTase) in complex with substrates and inhibitors. Comparison of structures with farnesyldiphosphate (FPP) bound in the absence or presence of peptide substrate, corresponding to successive steps in ordered substrate binding, revealed that the second substrate-binding step is accompanied by motions of a loop in the catalytic site. Re-examination of other FTase structures showed that this motion is conserved. The substrate- and product-binding clefts in the AfFTase active site are wider than in human FTase (hFTase). Widening is a consequence of small shifts in the α-helices that comprise the majority of the FTase structure, which in turn arise from sequence variation in the hydrophobic core of the protein. These structural effects are key features that distinguish fungal FTases from hFTase. Their variation results in differences in steady-state enzyme kinetics and inhibitor interactions and presents opportunities for developing selective anti-fungal drugs by exploiting size differences in the active sites. We illustrate the latter by comparing the interaction of ED5 and Tipifarnib with hFTase and AfFTase. In AfFTase, the wider groove enables ED5 to bind in the presence of FPP, whereas in hFTase it binds only in the absence of substrate. Tipifarnib binds similarly to both enzymes but makes less extensive contacts in AfFTase with consequently weaker binding.
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Affiliation(s)
- Mark F Mabanglo
- Department of Biochemistry, Duke University Medical CenterDurham, North Carolina, 27710
| | - Michael A Hast
- Department of Biochemistry, Duke University Medical CenterDurham, North Carolina, 27710
| | - Nathan B Lubock
- Department of Biochemistry, Duke University Medical CenterDurham, North Carolina, 27710
| | - Homme W Hellinga
- Department of Biochemistry, Duke University Medical CenterDurham, North Carolina, 27710
| | - Lorena S Beese
- Department of Biochemistry, Duke University Medical CenterDurham, North Carolina, 27710
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Expression of functional Plasmodium falciparum enzymes using a wheat germ cell-free system. EUKARYOTIC CELL 2013; 12:1653-63. [PMID: 24123271 DOI: 10.1128/ec.00222-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
One decade after the sequencing of the Plasmodium falciparum genome, 95% of malaria proteins in the genome cannot be expressed in traditional cell-based expression systems, and the targets of the best new leads for antimalarial drug discovery are either not known or not available in functional form. For a disease that kills up to 1 million people per year, routine expression of recombinant malaria proteins in functional form is needed both for the discovery of new therapeutics and for identification of targets of new drugs. We tested the general utility of cell-free systems for expressing malaria enzymes. Thirteen test enzyme sequences were reverse amplified from total RNA, cloned into a plant-like expression vector, and subjected to cell-free expression in a wheat germ system. Protein electrophoresis and autoradiography confirmed the synthesis of products of expected molecular masses. In rare problematic cases, truncated products were avoided by using synthetic genes carrying wheat codons. Scaled-up production generated 39 to 354 μg of soluble protein per 10 mg of translation lysate. Compared to rare proteins where cell-based systems do produce functional proteins, the cell-free yields are comparable or better. All 13 test products were enzymatically active, without failure. This general path to produce functional malaria proteins should now allow the community to access new tools, such as biologically active protein arrays, and lead to the discovery of new chemical functions, structures, and inhibitors of previously inaccessible malaria gene products.
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Bosc D, Mouray E, Grellier P, Cojean S, Loiseau PM, Dubois J. Introduction of methionine mimics on 3-arylthiophene: influence on protein farnesyltransferase inhibition and on antiparasitic activity. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00065f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Subramanian T, Pais JE, Liu S, Troutman JM, Suzuki Y, Leela Subramanian K, Fierke CA, Andres DA, Spielmann HP. Farnesyl diphosphate analogues with aryl moieties are efficient alternate substrates for protein farnesyltransferase. Biochemistry 2012; 51:8307-19. [PMID: 22989235 DOI: 10.1021/bi3011362] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Farnesylation is an important post-translational modification essential for the proper localization and function of many proteins. Transfer of the farnesyl group from farnesyl diphosphate (FPP) to proteins is catalyzed by protein farnesyltransferase (FTase). We employed a library of FPP analogues with a range of aryl groups substituting for individual isoprene moieties to examine some of the structural and electronic properties of the transfer of an analogue to the peptide catalyzed by FTase. Analysis of steady-state kinetics for modification of peptide substrates revealed that the multiple-turnover activity depends on the analogue structure. Analogues in which the first isoprene is replaced with a benzyl group and an analogue in which each isoprene is replaced with an aryl group are good substrates. In sharp contrast with the steady-state reaction, the single-turnover rate constant for dansyl-GCVLS alkylation was found to be the same for all analogues, despite the increased chemical reactivity of the benzyl analogues and the increased steric bulk of other analogues. However, the single-turnover rate constant for alkylation does depend on the Ca(1)a(2)X peptide sequence. These results suggest that the isoprenoid transition-state conformation is preferred over the inactive E·FPP·Ca(1)a(2)X ternary complex conformation. Furthermore, these data suggest that the farnesyl binding site in the exit groove may be significantly more selective for the farnesyl diphosphate substrate than the active site binding pocket and therefore might be a useful site for the design of novel inhibitors.
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Affiliation(s)
- Thangaiah Subramanian
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536-0084, USA
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18
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Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif. J Mol Model 2012; 19:673-88. [DOI: 10.1007/s00894-012-1590-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 08/29/2012] [Indexed: 10/27/2022]
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19
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Abate-Pella D, Zeliadt NA, Ochocki JD, Warmka JK, Dore TM, Blank DA, Wattenberg EV, Distefano MD. Photochemical modulation of Ras-mediated signal transduction using caged farnesyltransferase inhibitors: activation by one- and two-photon excitation. Chembiochem 2012; 13:1009-16. [PMID: 22492666 PMCID: PMC3436068 DOI: 10.1002/cbic.201200063] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Indexed: 01/04/2023]
Abstract
The creation of caged molecules involves the attachment of protecting groups to biologically active compounds such as ligands, substrates and drugs that can be removed under specific conditions. Photoremovable caging groups are the most common due to their ability to be removed with high spatial and temporal resolution. Here, the synthesis and photochemistry of a caged inhibitor of protein farnesyltransferase is described. The inhibitor, FTI, was caged by alkylation of a critical thiol group with a bromohydroxycoumarin (Bhc) moiety. While Bhc is well established as a protecting group for carboxylates and phosphates, it has not been extensively used to cage sulfhydryl groups. The resulting caged molecule, Bhc-FTI, can be photolyzed with UV light to release the inhibitor that prevents Ras farnesylation, Ras membrane localization and downstream signaling. Finally, it is shown that Bhc-FTI can be uncaged by two-photon excitation to produce FTI at levels sufficient to inhibit Ras localization and alter cell morphology. Given the widespread involvement of Ras proteins in signal transduction pathways, this caged inhibitor should be useful in a plethora of studies.
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Affiliation(s)
- Daniel Abate-Pella
- Departments of Chemistry and Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455 (USA)
| | - Nicholette A. Zeliadt
- Division of Environmental Health Sciences, University of Minnesota, Minneapolis, MN 55455 (USA)
| | - Joshua D. Ochocki
- Departments of Chemistry and Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455 (USA)
| | - Janel K. Warmka
- Division of Environmental Health Sciences, University of Minnesota, Minneapolis, MN 55455 (USA)
| | - Timothy M. Dore
- Department of Chemistry, University of Georgia, Athens, GA 30602 (USA)
| | - David A. Blank
- Departments of Chemistry and Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455 (USA)
| | - Elizabeth V. Wattenberg
- Division of Environmental Health Sciences, University of Minnesota, Minneapolis, MN 55455 (USA)
| | - Mark D. Distefano
- Departments of Chemistry and Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455 (USA)
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21
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Yang Y, Wang B, Ucisik MN, Cui G, Fierke CA, Merz KM. Insights into the mechanistic dichotomy of the protein farnesyltransferase peptide substrates CVIM and CVLS. J Am Chem Soc 2012; 134:820-3. [PMID: 22206225 DOI: 10.1021/ja209650h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein farnesyltransferase (FTase) catalyzes farnesylation of a variety of peptide substrates. (3)H α-secondary kinetic isotope effect (α-SKIE) measurements of two peptide substrates, CVIM and CVLS, are significantly different and have been proposed to reflect a rate-limiting S(N)2-like transition state with dissociative characteristics for CVIM, while, due to the absence of an isotope effect, CVLS was proposed to have a rate-limiting peptide conformational change. Potential of mean force quantum mechanical/molecular mechanical studies coupled with umbrella sampling techniques were performed to further probe this mechanistic dichotomy. We observe the experimentally proposed transition state (TS) for CVIM but find that CVLS has a symmetric S(N)2 TS, which is also consistent with the absence of a (3)H α-SKIE. These calculations demonstrate facile substrate-dependent alterations in the transition state structure catalyzed by FTase.
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Affiliation(s)
- Yue Yang
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435, USA
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22
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Perez MAS, Sousa SF, Oliveira EFT, Fernandes PA, Ramos MJ. Detection of Farnesyltransferase Interface Hot Spots through Computational Alanine Scanning Mutagenesis. J Phys Chem B 2011; 115:15339-54. [DOI: 10.1021/jp205481y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Marta A. S. Perez
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Sérgio F. Sousa
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Eduardo F. T. Oliveira
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
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Hast MA, Nichols CB, Armstrong SM, Kelly SM, Hellinga HW, Alspaugh JA, Beese LS. Structures of Cryptococcus neoformans protein farnesyltransferase reveal strategies for developing inhibitors that target fungal pathogens. J Biol Chem 2011; 286:35149-62. [PMID: 21816822 DOI: 10.1074/jbc.m111.250506] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cryptococcus neoformans is a fungal pathogen that causes life-threatening infections in immunocompromised individuals, including AIDS patients and transplant recipients. Few antifungals can treat C. neoformans infections, and drug resistance is increasing. Protein farnesyltransferase (FTase) catalyzes post-translational lipidation of key signal transduction proteins and is essential in C. neoformans. We present a multidisciplinary study validating C. neoformans FTase (CnFTase) as a drug target, showing that several anticancer FTase inhibitors with disparate scaffolds can inhibit C. neoformans and suggesting structure-based strategies for further optimization of these leads. Structural studies are an essential element for species-specific inhibitor development strategies by revealing similarities and differences between pathogen and host orthologs that can be exploited. We, therefore, present eight crystal structures of CnFTase that define the enzymatic reaction cycle, basis of ligand selection, and structurally divergent regions of the active site. Crystal structures of clinically important anticancer FTase inhibitors in complex with CnFTase reveal opportunities for optimization of selectivity for the fungal enzyme by modifying functional groups that interact with structurally diverse regions. A substrate-induced conformational change in CnFTase is observed as part of the reaction cycle, a feature that is mechanistically distinct from human FTase. Our combined structural and functional studies provide a framework for developing FTase inhibitors to treat invasive fungal infections.
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Affiliation(s)
- Michael A Hast
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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24
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Qiao Y, Gao J, Qiu Y, Wu L, Guo F, Kam-Wing Lo K, Li D. Design, synthesis, and characterization of piperazinedione-based dual protein inhibitors for both farnesyltransferase and geranylgeranyltransferase-I. Eur J Med Chem 2011; 46:2264-73. [DOI: 10.1016/j.ejmech.2011.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/25/2011] [Accepted: 03/02/2011] [Indexed: 01/13/2023]
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25
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Yang Y, Chakravorty DK, Merz KM. Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase. Biochemistry 2011; 49:9658-66. [PMID: 20923173 DOI: 10.1021/bi1008358] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies aimed at elucidating the unknown Mg2+ binding site in protein farnesyltransferase (FTase) are reported. FTase catalyzes the transfer of a farnesyl group to a conserved cysteine residue (Cys1p) on a target protein, an important step for proteins in the signal transduction pathways (e.g., Ras). Mg2+ ions accelerate the protein farnesylation reaction by up to 700-fold. The exact function of Mg2+ in catalysis and the structural characteristics of its binding remain unresolved to date. Molecular dynamics (MD) simulations addressing the role of magnesium ions in FTase are presented, and relevant octahedral binding motifs for Mg2+ in wild-type (WT) FTase and the Dβ352A mutant are explored. Our simulations suggest that the addition of Mg2+ ions causes a conformational change to occur in the FTase active site, breaking interactions known to keep FPP in its inactive conformation. Two relevant Mg2+ ion binding motifs were determined in WT FTase. In the first binding motif, WT1, the Mg2+ ion is coordinated to D352β, zinc-bound D297β, two water molecules, and one oxygen atom from the α- and β-phosphates of farnesyl diphosphate (FPP). The second binding motif, WT2, is identical with the exception of the zinc-bound D297β being replaced by a water molecule in the Mg2+ coordination complex. In the Dβ352A mutant Mg2+ binding motif, D297β, three water molecules, and one oxygen atom from the α- and β-phosphates of FPP complete the octahedral coordination sphere of Mg2+. Simulations of WT FTase, in which Mg2+ was replaced by water in the active site, recreated the salt bridges and hydrogen-bonding patterns around FPP, validating these simulations. In all Mg2+ binding motifs, a key hydrogen bond was identified between a magnesium-bound water and Cys1p, bridging the two metallic binding sites and, thereby, reducing the equilibrium distance between the reacting atoms of FPP Cys1p. The free energy profiles calculated for these systems provide a qualitative understanding of experimental results. They demonstrate that the two reactive atoms approach each other more readily in the presence of Mg2+ in WT FTase and mutant. The flexible WT2 model was found to possess the lowest barrier toward the conformational change, suggesting it is the preferred Mg2+ binding motif in WT FTase. In the mutant, the absence of D352β makes the transition toward a conformational change harder. Our calculations find support for the proposal that D352β performs a critical role in Mg2+ binding and Mg2+ plays an important role in the conformational transition step.
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Affiliation(s)
- Yue Yang
- Department of Chemistry and the Quantum Theory Project, University of Florida, Gainesville, FL 32611-8435, USA
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26
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Hari Narayana Moorthy NS, Sousa SF, Ramos MJ, Fernandes PA. Structural feature study of benzofuran derivatives as farnesyltransferase inhibitors. J Enzyme Inhib Med Chem 2011; 26:777-91. [DOI: 10.3109/14756366.2011.552885] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- N. S. Hari Narayana Moorthy
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
| | - Sergio F. Sousa
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
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Wlodarczyk N, Le Broc-Ryckewaert D, Gilleron P, Lemoine A, Farce A, Chavatte P, Dubois J, Pommery N, Hénichart JP, Furman C, Millet R. Potent Farnesyltransferase Inhibitors with 1,4-Diazepane Scaffolds as Novel Destabilizing Microtubule Agents in Hormone-Resistant Prostate Cancer. J Med Chem 2011; 54:1178-90. [DOI: 10.1021/jm101067y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicolas Wlodarczyk
- Institut de Chimie Pharmaceutique Albert Lespagnol, Université Lille-Nord de France, EA4481, IFR114, 3 Rue du Pr Laguesse, B.P. 83, F-59006 Lille, France
| | - Delphine Le Broc-Ryckewaert
- Faculté des Sciences Pharmaceutiques et Biologiques de Lille, Université Lille-Nord de France, EA4483, IFR114, 3 Rue du Pr Laguesse, B.P. 83, F-59006 Lille, France
| | - Pauline Gilleron
- Institut de Chimie Pharmaceutique Albert Lespagnol, Université Lille-Nord de France, EA4481, IFR114, 3 Rue du Pr Laguesse, B.P. 83, F-59006 Lille, France
| | - Amélie Lemoine
- Institut de Chimie Pharmaceutique Albert Lespagnol, Université Lille-Nord de France, EA4481, IFR114, 3 Rue du Pr Laguesse, B.P. 83, F-59006 Lille, France
| | - Amaury Farce
- Institut de Chimie Pharmaceutique Albert Lespagnol, Université Lille-Nord de France, EA4481, IFR114, 3 Rue du Pr Laguesse, B.P. 83, F-59006 Lille, France
| | - Philippe Chavatte
- Institut de Chimie Pharmaceutique Albert Lespagnol, Université Lille-Nord de France, EA4481, IFR114, 3 Rue du Pr Laguesse, B.P. 83, F-59006 Lille, France
| | - Joëlle Dubois
- Institut de Chimie des Substances Naturelles, UPR2301 CNRS, Centre de Recherche de Gif, Avenue de la Terrasse, F-91198 Gif-sur-Yvette Cedex, France
| | - Nicole Pommery
- Faculté des Sciences Pharmaceutiques et Biologiques de Lille, Université Lille-Nord de France, EA4483, IFR114, 3 Rue du Pr Laguesse, B.P. 83, F-59006 Lille, France
| | - Jean-Pierre Hénichart
- Institut de Chimie Pharmaceutique Albert Lespagnol, Université Lille-Nord de France, EA4481, IFR114, 3 Rue du Pr Laguesse, B.P. 83, F-59006 Lille, France
| | - Christophe Furman
- Faculté des Sciences Pharmaceutiques et Biologiques de Lille, Université Lille-Nord de France, EA4483, IFR114, 3 Rue du Pr Laguesse, B.P. 83, F-59006 Lille, France
| | - Régis Millet
- Institut de Chimie Pharmaceutique Albert Lespagnol, Université Lille-Nord de France, EA4481, IFR114, 3 Rue du Pr Laguesse, B.P. 83, F-59006 Lille, France
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28
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Global Identification of Protein Prenyltransferase Substrates. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/b978-0-12-381339-8.00012-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
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29
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Fletcher S, Keaney EP, Cummings CG, Blaskovich MA, Hast MA, Glenn MP, Chang SY, Bucher CJ, Floyd RJ, Katt WP, Gelb MH, Van Voorhis WC, Beese LS, Sebti SM, Hamilton AD. Structure-based design and synthesis of potent, ethylenediamine-based, mammalian farnesyltransferase inhibitors as anticancer agents. J Med Chem 2010; 53:6867-88. [PMID: 20822181 DOI: 10.1021/jm1001748] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A potent class of anticancer, human farnesyltransferase (hFTase) inhibitors has been identified by "piggy-backing" on potent, antimalarial inhibitors of Plasmodium falciparum farnesyltransferase (PfFTase). On the basis of a 4-fold substituted ethylenediamine scaffold, the inhibitors are structurally simple and readily derivatized, facilitating the extensive structure-activity relationship (SAR) study reported herein. Our most potent inhibitor is compound 1f, which exhibited an in vitro hFTase IC(50) value of 25 nM and a whole cell H-Ras processing IC(50) value of 90 nM. Moreover, it is noteworthy that several of our inhibitors proved highly selective for hFTase (up to 333-fold) over the related prenyltransferase enzyme geranylgeranyltransferase-I (GGTase-I). A crystal structure of inhibitor 1a co-crystallized with farnesyl pyrophosphate (FPP) in the active site of rat FTase illustrates that the para-benzonitrile moiety of 1a is stabilized by a π-π stacking interaction with the Y361β residue, suggesting a structural explanation for the observed importance of this component of our inhibitors.
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Affiliation(s)
- Steven Fletcher
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, USA
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Khan AH, Prakash A, Kumar D, Rawat AK, Srivastava R, Srivastava S. Virtual screening and pharmacophore studies for ftase inhibitors using Indian plant anticancer compounds database. Bioinformation 2010; 5:62-6. [PMID: 21346865 PMCID: PMC3039991 DOI: 10.6026/97320630005062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 04/29/2010] [Accepted: 06/08/2010] [Indexed: 11/23/2022] Open
Abstract
Farnesyl transferase (FTase) is an enzyme responsible for post-translational modification in proteins having a carboxy-terminal CaaX motif in
human. It catalyzes the attachment of a lipid group in proteins of RAS superfamily, which is essential in signal transduction. FTase has been recognized
as an important target for anti cancer therapeutics. In this work, we performed virtual screening against FTase with entire 125 compounds from Indian
Plant Anticancer Database using AutoDock 3.0.5 software. All compounds were docked within binding pocket containing Lys164, Tyr300, His248 and
Tyr361 residues in crystal structure of FTase. These complexes were ranked according to their docking score, using methodology that was shown
to achieve maximum accuracy. Finally we got three potent compounds with the best Autodock docking Score (Vinorelbine: -21.28 Kcal/mol,
Vincristine: -21.74 Kcal/mol and Vinblastine: -22.14 Kcal/mol) and their energy scores were better than the FTase bound co-crystallized ligand (L-
739: ―7.9 kcal/mol). These three compounds belong to Vinca alkaloids were analyzed through Python Molecular Viewer for their interaction studies. It
predicted similar orientation and binding modes for these compounds with L-739 in FTase.Thus from the complex scoring and binding ability it is
concluded that these Vinca alkaloids could be promising inhibitors for FTase. A 2-D pharmacophore was generated for these alkaloids using LigandScout
to confirm it. A shared feature pharmacophore was also constructed that shows four common features (one hydogen bond Donar, Two hydrogen bond
Acceptor and one ionizable area) help compounds to interact with this enzyme.
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Affiliation(s)
- Abdul Hafeez Khan
- Biotechnology and Bioinformatics Division, BIOBRAINZ, 566/29 J, Jai Prakash Nagar, Alambagh, Lucknow 226005, U.P., India
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Hougland JL, Lamphear CL, Scott SA, Gibbs RA, Fierke CA. Context-dependent substrate recognition by protein farnesyltransferase. Biochemistry 2010; 48:1691-701. [PMID: 19199818 DOI: 10.1021/bi801710g] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Prenylation is a posttranslational modification whereby C-terminal lipidation leads to protein localization to membranes. A C-terminal "Ca(1)a(2)X" sequence has been proposed as the recognition motif for two prenylation enzymes, protein farnesyltransferase (FTase) and protein geranylgeranyltransferase type I. To define the parameters involved in recognition of the a(2) residue, we performed structure-activity analysis which indicates that FTase discriminates between peptide substrates based on both the hydrophobicity and steric volume of the side chain at the a(2) position. For nonpolar side chains, the dependence of the reactivity on side chain volume at this position forms a pyramidal pattern with a maximal activity near the steric volume of valine. This discrimination occurs at a step in the kinetic mechanism that is at or before the farnesylation step. Furthermore, a(2) selectivity is also affected by the identity of the adjacent X residue, leading to context-dependent substrate recognition. Context-dependent a(2) selectivity suggests that FTase recognizes the sequence downstream of the conserved cysteine as a set of two or three cooperative, interconnected recognition elements as opposed to three independent amino acids. These findings expand the pool of proposed FTase substrates in cells. A better understanding of the molecular recognition of substrates performed by FTase will aid in both designing new FTase inhibitors as therapeutic agents and characterizing proteins involved in prenylation-dependent cellular pathways.
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Affiliation(s)
- James L Hougland
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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32
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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.
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Affiliation(s)
- Marisa L Hovlid
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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Hougland JL, Hicks KA, Hartman HL, Kelly RA, Watt TJ, Fierke CA. Identification of novel peptide substrates for protein farnesyltransferase reveals two substrate classes with distinct sequence selectivities. J Mol Biol 2010; 395:176-90. [PMID: 19878682 PMCID: PMC2916699 DOI: 10.1016/j.jmb.2009.10.038] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 10/15/2009] [Accepted: 10/16/2009] [Indexed: 10/20/2022]
Abstract
Prenylation is a posttranslational modification essential for the proper localization and function of many proteins. Farnesylation, the attachment of a 15-carbon farnesyl group near the C-terminus of protein substrates, is catalyzed by protein farnesyltransferase (FTase). Farnesylation has received significant interest as a target for pharmaceutical development, and farnesyltransferase inhibitors are in clinical trials as cancer therapeutics. However, as the total complement of prenylated proteins is unknown, the FTase substrates responsible for farnesyltransferase inhibitor efficacy are not yet understood. Identifying novel prenylated proteins within the human proteome constitutes an important step towards understanding prenylation-dependent cellular processes. Based on sequence preferences for FTase derived from analysis of known farnesylated proteins, we selected and screened a library of small peptides representing the C-termini of 213 human proteins for activity with FTase. We identified 77 novel FTase substrates that exhibit multiple-turnover (MTO) reactivity within this library; our library also contained 85 peptides that can be farnesylated by FTase only under single-turnover (STO) conditions. Based on these results, a second library was designed that yielded an additional 29 novel MTO FTase substrates and 45 STO substrates. The two classes of substrates exhibit different specificity requirements. Efficient MTO reactivity correlates with the presence of a nonpolar amino acid at the a(2) position and a Phe, Met, or Gln at the terminal X residue, consistent with the proposed Ca(1)a(2)X sequence model. In contrast, the sequences of the STO substrates vary significantly more at both the a(2) and the X residues and are not well described by current farnesylation algorithms. These results improve the definition of prenyltransferase substrate specificity, test the efficacy of substrate algorithms, and provide valuable information about therapeutic targets. Finally, these data illuminate the potential for in vivo regulation of prenylation through modulation of STO versus MTO peptide reactivity with FTase.
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Affiliation(s)
- James L. Hougland
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Katherine A. Hicks
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Heather L. Hartman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Rebekah A. Kelly
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Terry J. Watt
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Carol A. Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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Molecular Dynamics Simulations: Difficulties, Solutions and Strategies for Treating Metalloenzymes. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-90-481-3034-4_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Hast MA, Fletcher S, Cummings CG, Pusateri EE, Blaskovich MA, Rivas K, Gelb MH, Van Voorhis WC, Sebti SM, Hamilton AD, Beese LS. Structural basis for binding and selectivity of antimalarial and anticancer ethylenediamine inhibitors to protein farnesyltransferase. ACTA ACUST UNITED AC 2009; 16:181-92. [PMID: 19246009 DOI: 10.1016/j.chembiol.2009.01.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 01/21/2009] [Accepted: 01/26/2009] [Indexed: 11/24/2022]
Abstract
Protein farnesyltransferase (FTase) catalyzes an essential posttranslational lipid modification of more than 60 proteins involved in intracellular signal transduction networks. FTase inhibitors have emerged as a significant target for development of anticancer therapeutics and, more recently, for the treatment of parasitic diseases caused by protozoan pathogens, including malaria (Plasmodium falciparum). We present the X-ray crystallographic structures of complexes of mammalian FTase with five inhibitors based on an ethylenediamine scaffold, two of which exhibit over 1000-fold selective inhibition of P. falciparum FTase. These structures reveal the dominant determinants in both the inhibitor and enzyme that control binding and selectivity. Comparison to a homology model constructed for the P. falciparum FTase suggests opportunities for further improving selectivity of a new generation of antimalarial inhibitors.
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Affiliation(s)
- Michael A Hast
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC 27710, USA
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36
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Sousa SF, Fernandes PA, Ramos MJ. Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme. Bioorg Med Chem 2009; 17:3369-78. [DOI: 10.1016/j.bmc.2009.03.055] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 03/16/2009] [Accepted: 03/20/2009] [Indexed: 10/20/2022]
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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.
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Affiliation(s)
- Olivier Henry
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
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38
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Sousa S, Fernandes P, Ramos M. The Search for the Mechanism of the Reaction Catalyzed by Farnesyltransferase. Chemistry 2009; 15:4243-7. [DOI: 10.1002/chem.200802745] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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39
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Subramanian T, Liu S, Troutman JM, Andres DA, Spielmann HP. Protein farnesyltransferase-catalyzed isoprenoid transfer to peptide depends on lipid size and shape, not hydrophobicity. Chembiochem 2009; 9:2872-82. [PMID: 18985644 DOI: 10.1002/cbic.200800248] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein farnesyl transferase (FTase) catalyzes transfer of a 15-carbon farnesyl group from farnesyl diphosphate (FPP) to a conserved cysteine in the C-terminal Ca(1)a(2)X motif of a range of proteins, including the oncoprotein H-Ras ("C" refers to the cysteine, "a" to any aliphatic amino acid, and "X" to any amino acid) and the lipid chain interacts with, and forms part of the Ca(1)a(2)X peptide binding site. Previous studies have shown that H-Ras biological function is ablated when it is modified with lipids that are 3-5 orders of magnitude less hydrophobic than FPP. Here, we employed a library of anilinogeranyl diphosphate (AGPP) and phenoxygeranyl diphosphate (PGPP) derivatives with a range of polarities (log P (lipid alcohol) = 0.7-6.8, log P (farnesol) = 6.1) and shapes to examine whether FTase-catalyzed transfer to peptide is dependent on the hydrophobicity of the lipid. Analysis of steady-state transfer kinetics for analogues to dansyl-GCVLS peptide revealed that the efficiency of lipid transfer was highly dependent on both the shape and size, but was independent of the polarity of the analogue. These observations indicate that hydrophobic features of isoprenoids critical for their association with membranes and/or protein receptors are not required for efficient transfer to Ca(1)a(2)X peptides by FTase. Furthermore, the results of these studies indicate that the role played by the farnesyl lipid in the FTase mechanism is primarily structural. To explain these results we propose a model in which the FTase active site stabilizes a membrane interface-like environment.
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Affiliation(s)
- Thangaiah Subramanian
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536-0084, USA
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40
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Hast MA, Beese LS. Structure of protein geranylgeranyltransferase-I from the human pathogen Candida albicans complexed with a lipid substrate. J Biol Chem 2008; 283:31933-40. [PMID: 18713740 DOI: 10.1074/jbc.m805330200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein geranylgeranyltransferase-I (GGTase-I) catalyzes the transfer of a 20-carbon isoprenoid lipid to the sulfur of a cysteine residue located near the C terminus of numerous cellular proteins, including members of the Rho superfamily of small GTPases and other essential signal transduction proteins. In humans, GGTase-I and the homologous protein farnesyltransferase (FTase) are targets of anticancer therapeutics because of the role small GTPases play in oncogenesis. Protein prenyltransferases are also essential for many fungal and protozoan pathogens that infect humans, and have therefore become important targets for treating infectious diseases. Candida albicans, a causative agent of systemic fungal infections in immunocompromised individuals, is one pathogen for which protein prenylation is essential for survival. Here we present the crystal structure of GGTase-I from C. albicans (CaGGTase-I) in complex with its cognate lipid substrate, geranylgeranylpyrophosphate. This structure provides a high-resolution picture of a non-mammalian protein prenyltransferase. There are significant variations between species in critical areas of the active site, including the isoprenoid-binding pocket, as well as the putative product exit groove. These differences indicate the regions where specific protein prenyltransferase inhibitors with antifungal activity can be designed.
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Affiliation(s)
- Michael A Hast
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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41
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Fletcher S, Cummings CG, Rivas K, Katt WP, Hornéy C, Buckner FS, Chakrabarti D, Sebti SM, Gelb MH, Van Voorhis WC, Hamilton AD. Potent, Plasmodium-selective farnesyltransferase inhibitors that arrest the growth of malaria parasites: structure-activity relationships of ethylenediamine-analogue scaffolds and homology model validation. J Med Chem 2008; 51:5176-97. [PMID: 18686940 DOI: 10.1021/jm800113p] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New chemotherapeutics are urgently needed to combat malaria. We previously reported on a novel series of antimalarial, ethylenediamine-based inhibitors of protein farnesyltransferase (PFT). In the current study, we designed and synthesized a series of second generation inhibitors, wherein the core ethylenediamine scaffold was varied in order to examine both the homology model of Plasmodium falciparum PFT (PfPFT) and our predicted inhibitor binding mode. We identified several PfPFT inhibitors (PfPFTIs) that are selective for PfPFT versus the mammalian isoform of the enzyme (up to 136-fold selectivity), that inhibit the malarial enzyme with IC50 values down to 1 nM, and that block the growth of P. falciparum in infected whole cells (erythrocytes) with ED50 values down to 55 nM. The structure-activity data for these second generation, ethylenediamine-inspired PFT inhibitors were rationalized by consideration of the X-ray crystal structure of mammalian PFT and the homology model of the malarial enzyme.
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Affiliation(s)
- Steven Fletcher
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, USA
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42
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Sousa SF, Fernandes PA, Ramos MJ. Enzyme Flexibility and the Catalytic Mechanism of Farnesyltransferase: Targeting the Relation. J Phys Chem B 2008; 112:8681-91. [DOI: 10.1021/jp711214j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sérgio F. Sousa
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Maria João Ramos
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
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43
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Machida S, Usuba K, Blaskovich MA, Yano A, Harada K, Sebti SM, Kato N, Ohkanda J. Module assembly for protein-surface recognition: geranylgeranyltransferase I bivalent inhibitors for simultaneous targeting of interior and exterior protein surfaces. Chemistry 2008; 14:1392-401. [PMID: 18200641 DOI: 10.1002/chem.200701634] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Synthetic chemical probes designed to simultaneously targeting multiple sites of protein surfaces are of interest owing to their potential application as site specific modulators of protein-protein interactions. A new approach toward bivalent inhibitors of mammalian type I geranylgeranyltransferase (GGTase I) based on module assembly for simultaneous recognition of both interior and exterior protein surfaces is reported. The inhibitors synthesized in this study consist of two modules linked by an alkyl spacer; one is the tetrapeptide CVIL module for binding to the interior protein surface (active pocket) and the other is a 3,4,5-alkoxy substituted benzoyl motif that contains three aminoalkyl groups designed to bind to the negatively charged protein exterior surface near the active site. The compounds were screened by two distinct enzyme inhibition assays based on fluorescence spectroscopy and incorporation of a [(3)H]-labeled prenyl group onto a protein substrate. The bivalent inhibitors block GGTase I enzymatic activity with K(i) values in the submicromolar range and are approximately one order of magnitude and more than 150 times more effective than the tetrapeptide CVIL and the methyl benzoate derivatives, respectively. The bivalent compounds 6 and 8 were shown to be competitive inhibitors, suggesting that the CVIL module anchors the whole molecule to the GGTase I active site and delivers the other module to the targeting protein surface. Thus, our module-assembly approach resulted in simultaneous multiple-site recognition, and as a consequence, synergetic inhibition of GGTase I activity, thereby providing a new approach in designing protein-surface-directed inhibitors for targeting protein-protein interactions.
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Affiliation(s)
- Shinnosuke Machida
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, Japan
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44
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Raucher D, Massodi I, Bidwell GL. Thermally targeted delivery of chemotherapeutics and anti-cancer peptides by elastin-like polypeptide. Expert Opin Drug Deliv 2008; 5:353-69. [DOI: 10.1517/17425247.5.3.353] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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45
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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.
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46
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Cui G, Merz KM. Computational studies of the farnesyltransferase ternary complex part II: the conformational activation of farnesyldiphosphate. Biochemistry 2007; 46:12375-81. [PMID: 17918965 DOI: 10.1021/bi701324t] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Studies aimed at elucidating the reaction mechanism of farnesyltransferase (FTase), which catalyzes the prenylation of many cellular signaling proteins including Ras, has been an active area of research. Much is known regarding substrate binding and the impact of various catalytic site residues on catalysis. However, the molecular level details regarding the conformational rearrangement of farnesyldiphosphate (FPP), which has been proposed via structural analysis and mutagenesis studies to occur prior to the chemical step, is still poorly understood. Following on our previous computational characterization of the resting state of the FTase ternary complex, the thermodynamics of the conformational rearrangement step in the absence of magnesium was investigated for the wild type FTase and the Y300Fbeta mutant complexed with the peptide CVIM. In addition, we also explored the target dependence of the conformational activation step by perturbing isoleucine into a leucine (CVLM). The calculated free energy profiles of the proposed conformational transition confirm the presence of a stable intermediate state, which was identified only when the diphosphate is monoprotonated (FPP2-). The farnesyl group in the computed intermediate state assumes a conformation similar to that of the product complex, particularly for the first two isoprene units. We found that Y300beta can readily form hydrogen bonds with either of the phosphates of FPP. Removing the hydroxyl group on Y300beta does not significantly alter the thermodynamics of the conformational transition, but shifts the location of the intermediate farther away from the nucleophile by 0.5 A, which suggests that Y300beta facilitate the reaction by stabilizing the chemical step. Our results also showed an increased transition barrier height for CVLM (1.5 kcal/mol higher than that of CVIM). Although qualitatively consistent with the findings from the recent kinetic isotope experiments by Fierke and co-workers, the magnitude is not large enough to affect the rate-limiting step.
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Affiliation(s)
- Guanglei Cui
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435, USA
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47
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Penner-Hahn J. Zinc-promoted alkyl transfer: a new role for zinc. Curr Opin Chem Biol 2007; 11:166-71. [PMID: 17376731 DOI: 10.1016/j.cbpa.2007.02.038] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 02/20/2007] [Indexed: 10/23/2022]
Abstract
The roles of zinc in biology are often thought to be limited to activating water, as in hydrolytic enzymes, and conferring structure, as in the zinc finger proteins. Over the past 15 years, it has been shown that there are many zinc-containing proteins that have 'structural-like' zinc sites with multiple cysteine ligands but in which the site promotes the alkylation of a zinc-bound thiolate. Recent work continues to extend the range of proteins showing zinc-promoted alkytransfer activity, and has refined the structural details of these sites. Of particular interest are recent crystal structures suggesting that in most cases the endogenous ligand that is displaced when the substrate thiol bind is an endogenous amino acid and not water, as had been previously thought. Despite extensive study, it remains unclear whether these enzymes function via an associative mechanism (direct alkylation of a zinc-bound thiolate) or a dissociate mechanism (nucleophilic attack by a free thiolate that has dissociated from the zinc).
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Affiliation(s)
- James Penner-Hahn
- Department of Chemistry and Biophysics Research Division, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055 USA.
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48
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de Figueiredo RM, Coudray L, Dubois J. Synthesis and biological evaluation of potential bisubstrate inhibitors of protein farnesyltransferase. Design and synthesis of functionalized imidazoles. Org Biomol Chem 2007; 5:3299-309. [PMID: 17912382 DOI: 10.1039/b709854e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel series of compounds, derived from 2,5-functionalized imidazoles, have been synthesized as potential bisubstrate inhibitors of protein farnesyltransferase (FTase) using structure-based design. These compounds have a 1,4-diacid chain and a tripeptide connected by an imidazole ring. The synthetic strategy relies on the functionalization at the C-2 position of the heterocycle with the diacid side chain and peptide coupling at the C-5 position. Several new compounds were synthesized in good yields. Kinetic experiments on the most active compounds revealed different binding modes depending on the diacid chain length.
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Affiliation(s)
- Renata Marcia de Figueiredo
- Institut de Chimie des Substances Naturelles, CNRS, Avenue de la Terrasse, 91198, Gif-sur-Yvette cedex, France
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Pentheroudakis G, Pavlidis N. Perspectives for targeted therapies in cancer of unknown primary site. Cancer Treat Rev 2006; 32:637-44. [PMID: 17046164 DOI: 10.1016/j.ctrv.2006.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 08/25/2006] [Accepted: 08/28/2006] [Indexed: 02/03/2023]
Abstract
Cancer of unknown primary site (CUP) ranks as the fourth most common cause of cancer deaths. Regression of the primary, early development of systemic metastases and resistance to therapy are hallmarks of this heterogeneous clinical entity. Targeted therapy offers promise for improvement of outcome of such patients, but it is currently hindered by lack of known molecular targets on which tumours are dependent for growth. In this review, we present the gene and protein profiling studies done on expression of oncogenes, tumour-suppressor genes and angiogenesis effectors and discuss the therapeutic potential of developed targeted agents. Existing data show occasional overexpression of Ras, BCL2 oncoproteins, absence of active EGFR/c-KIT/PDGFR signalling, uncommon presence of tumour-suppressor gene mutations and highly active angiogenesis in CUP. High-throughput multi-gene, multi-protein platforms offer promise for unravelling the complex molecular pathophysiology of CUP, for identification of targets suitable for modulation and ultimately hope for abrogation of its aggressive natural history.
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Affiliation(s)
- George Pentheroudakis
- Department of Medical Oncology, Ioannina University Hospital, Niarxou Avenue, 45110 Ioannina, Greece
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50
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Xie A, Sivaprakasam P, Doerksen RJ. 3D-QSAR analysis of antimalarial farnesyltransferase inhibitors based on a 2,5-diaminobenzophenone scaffold. Bioorg Med Chem 2006; 14:7311-23. [PMID: 16837204 DOI: 10.1016/j.bmc.2006.06.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2006] [Revised: 06/20/2006] [Accepted: 06/21/2006] [Indexed: 01/30/2023]
Abstract
With annual death tolls in the millions and emerging resistance to existing drugs, novel therapies are needed against malaria. Wiesner et al. recently developed a novel class of antimalarials derived from farnesyltransferase inhibitors based on a 2,5-diaminobenzophenone scaffold. The compounds displayed a wide range of activity, including submicromolar, against the multi-drug resistant Plasmodium falciparum strain Dd2. In order to investigate quantitatively the local physicochemical properties involved in the interaction between drug and biotarget, we used the 3D-QSAR methods CoMFA and CoMSIA to study some of the series, including the screened lead compound 2,5-bis-acylaminobenzophenone, 28 cinnamic acid derivatives, 29 N-(3-benzoyl-4-tolylacetylaminophenyl)-3-(5-aryl-2-furyl)acrylic acid amides, and 34 N-(4-substituted-amino-3-benzoylphenyl)-[5-(4-nitrophenyl)-2-furyl]acrylic acid amides. We found that steric, electrostatic, and hydrophobic properties of substituent groups play key roles in the bioactivity of the series of compounds, while hydrogen bonding interactions show no obvious impact. We built several highly predictive 3D-QSAR models, including a CoMSIA one composed of steric, electrostatic, and hydrophobic fields, with r(2)=0.94, q(2)=0.63, and r(pred)(2)=0.63. The results provide insight for optimization of this class of antimalarials for better activity and may prove helpful for further lead optimization.
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Affiliation(s)
- Aihua Xie
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, 38677-1848, USA
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