1
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Photoaffinity labeling and bioorthogonal ligation: Two critical tools for designing "Fish Hooks" to scout for target proteins. Bioorg Med Chem 2022; 62:116721. [PMID: 35358862 DOI: 10.1016/j.bmc.2022.116721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022]
Abstract
Small molecules remain an important category of therapeutic agents. Their binding to different proteins can lead to both desired and undesired biological effects. Identification of the proteins that a drug binds to has become an important step in drug development because it can lead to safer and more effective drugs. Parent bioactive molecules can be converted to appropriate probes that allow for visualization and identification of their target proteins. Typically, these probes are designed and synthesized utilizing some or all of five major tools; a photoactivatable group, a reporter tag, a linker, an affinity tag, and a bioorthogonal handle. This review covers two of the most challenging tools, photoactivation and bioorthogonal ligation. We provide a historical and theoretical background along with synthetic routes to prepare them. In addition, the review provides comparative analyses of the available tools that can assist decision making when designing such probes. A survey of most recent literature reports is included as well to identify recent trends in the field.
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Abstract
A growing theme in chemistry is the joining of multiple organic molecular building blocks to create functional molecules. Diverse derivatizable structures—here termed “scaffolds” comprised of “hubs”—provide the foundation for systematic covalent organization of a rich variety of building blocks. This review encompasses 30 tri- or tetra-armed molecular hubs (e.g., triazine, lysine, arenes, dyes) that are used directly or in combination to give linear, cyclic, or branched scaffolds. Each scaffold is categorized by graph theory into one of 31 trees to express the molecular connectivity and overall architecture. Rational chemistry with exacting numbers of derivatizable sites is emphasized. The incorporation of water-solubilization motifs, robust or self-immolative linkers, enzymatically cleavable groups and functional appendages affords immense (and often late-stage) diversification of the scaffolds. Altogether, 107 target molecules are reviewed along with 19 syntheses to illustrate the distinctive chemistries for creating and derivatizing scaffolds. The review covers the history of the field up through 2020, briefly touching on statistically derivatized carriers employed in immunology as counterpoints to the rationally assembled and derivatized scaffolds here, although most citations are from the past two decades. The scaffolds are used widely in fields ranging from pure chemistry to artificial photosynthesis and biomedical sciences.
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3
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Jia H, Wang Z, Zhang J, Feng F. γ-Secretase inhibitors for breast cancer and hepatocellular carcinoma: From mechanism to treatment. Life Sci 2021; 268:119007. [PMID: 33428878 DOI: 10.1016/j.lfs.2020.119007] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/21/2022]
Abstract
The γ-secretase complex is a key hydrolase for many type 1 transmembrane proteins. It is very important for activation of the Notch receptor and regulation of target-gene transcription. Abnormal activation and expression of the Notch pathway are closely related to the occurrence and development of many tumor types, including breast cancer and liver cancer. In this review, we elaborated on the basic situation of γ-secretase complex and the biological function and role of γ-secretase in APP and Notch signal pathway are described in detail. Subsequently, all currently known γ-secretase inhibitors and γ-secretase modulators are listed and their mechanism of action, value of IC50, chemical structure and current research stage are summarized. Next, the selection presented the treatment progress of γ-secretase inhibitors in breast cancer and hepatocellular carcinoma in the past five years. Finally, the mechanism of action of γ-secretase-mediated breast cancer and hepatocellular carcinoma and the advantages and disadvantages of γ-secretase inhibitors are discussed, and the concept of further research is proposed.
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Affiliation(s)
- Hui Jia
- Department of Pharmacy, General Hospital of Northern Theater Command, No. 83 Wenhua Road, Shenhe District, Shenyang City 110840, Liaoning Province, PR China; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110006, PR China
| | - Zuojun Wang
- Department of Pharmacy, General Hospital of Northern Theater Command, No. 83 Wenhua Road, Shenhe District, Shenyang City 110840, Liaoning Province, PR China
| | - Jingyi Zhang
- Department of Pharmacy, General Hospital of Northern Theater Command, No. 83 Wenhua Road, Shenhe District, Shenyang City 110840, Liaoning Province, PR China.
| | - Fan Feng
- Center for Clinical Laboratory, The Fifth Medical Center, General Hospital of Chinese PLA, Beijing 100039, PR China.
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4
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Nie P, Vartak A, Li YM. γ-Secretase inhibitors and modulators: Mechanistic insights into the function and regulation of γ-Secretase. Semin Cell Dev Biol 2020; 105:43-53. [PMID: 32249070 DOI: 10.1016/j.semcdb.2020.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 02/08/2023]
Abstract
Over two decades, γ-secretase has been the target for extensive therapeutic development due to its pivotal role in pathogenesis of Alzheimer's disease and cancer. However, it has proven to be a challenging task owing to its large set of substrates and our limited understanding of the enzyme's structural and mechanistic features. The scientific community is taking bigger strides towards solving this puzzle with recent advancement in techniques like cryogenic electron microscopy (cryo-EM) and photo-affinity labelling (PAL). This review highlights the significance of the PAL technique with multiple examples of photo-probes developed from γ-secretase inhibitors and modulators. The binding of these probes into active and/or allosteric sites of the enzyme has provided crucial information on the γ-secretase complex and improved our mechanistic understanding of this protease. Combining the knowledge of function and regulation of γ-secretase will be a decisive factor in developing novel γ-secretase modulators and biological therapeutics.
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Affiliation(s)
- Pengju Nie
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Pharmacology program, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
| | - Abhishek Vartak
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Pharmacology program, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA.
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5
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Sucharov J, Ray K, Brooks EP, Nichols JT. Selective breeding modifies mef2ca mutant incomplete penetrance by tuning the opposing Notch pathway. PLoS Genet 2019; 15:e1008507. [PMID: 31790396 PMCID: PMC6907857 DOI: 10.1371/journal.pgen.1008507] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 12/12/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023] Open
Abstract
Deleterious genetic mutations allow developmental biologists to understand how genes control development. However, not all loss of function genetic mutants develop phenotypic changes. Many deleterious mutations only produce a phenotype in a subset of mutant individuals, a phenomenon known as incomplete penetrance. Incomplete penetrance can confound analyses of gene function and our understanding of this widespread phenomenon remains inadequate. To better understand what controls penetrance, we capitalized on the zebrafish mef2ca mutant which produces craniofacial phenotypes with variable penetrance. Starting with a characterized mef2ca loss of function mutant allele, we used classical selective breeding methods to generate zebrafish strains in which mutant-associated phenotypes consistently appear with low or high penetrance. Strikingly, our selective breeding for low penetrance converted the mef2ca mutant allele behavior from homozygous lethal to homozygous viable. Meanwhile, selective breeding for high penetrance converted the mef2ca mutant allele from fully recessive to partially dominant. Comparing the selectively-bred low- and high-penetrance strains revealed that the strains initially respond similarly to the mutation, but then gene expression differences between strains emerge during development. Thus, altered temporal genetic circuitry can manifest through selective pressure to modify mutant penetrance. Specifically, we demonstrate differences in Notch signaling between strains, and further show that experimental manipulation of the Notch pathway phenocopies penetrance changes occurring through selective breeding. This study provides evidence that penetrance is inherited as a liability-threshold trait. Our finding that vertebrate animals can overcome a deleterious mutation by tuning genetic circuitry complements other reported mechanisms of overcoming deleterious mutations such as transcriptional adaptation of compensatory genes, alternative mRNA splicing, and maternal deposition of wild-type transcripts, which are not observed in our system. The selective breeding approach and the resultant genetic circuitry change we uncovered advances and expands our current understanding of genetic and developmental resilience. Some deleterious gene mutations only affect a subset of genetically mutant animals. This widespread phenomenon, known as mutant incomplete penetrance, complicates discovery of causative gene mutations in both model organisms and human disease. This study utilized the zebrafish mef2ca transcription factor mutant that produces craniofacial skeleton defects with incomplete penetrance. Selectively breeding zebrafish families for low- or high-penetrance mutants for many generations created different zebrafish strains with consistently low or high penetrance. Comparing these strains allowed us to gain insight into the mechanisms that control penetrance. Specifically, genes under the control of mef2ca are initially similarly expressed between the two strains, but differences between strains emerge during development. We found that genetic manipulation of these downstream genes mimics the effects of our selective breeding. Thus, selective breeding for penetrance can change the genetic circuitry downstream of the mutated gene. We propose that small differences in gene circuitry between individuals is one mechanism underlying susceptibility or resilience to genetic mutations.
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Affiliation(s)
- Juliana Sucharov
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Kuval Ray
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Elliott P. Brooks
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - James T. Nichols
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- * E-mail:
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6
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Ge SS, Chen B, Wu YY, Long QS, Zhao YL, Wang PY, Yang S. Current advances of carbene-mediated photoaffinity labeling in medicinal chemistry. RSC Adv 2018; 8:29428-29454. [PMID: 35547988 PMCID: PMC9084484 DOI: 10.1039/c8ra03538e] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/07/2018] [Indexed: 12/21/2022] Open
Abstract
Photoaffinity labeling (PAL) in combination with a chemical probe to covalently bind its target upon UV irradiation has demonstrated considerable promise in drug discovery for identifying new drug targets and binding sites. In particular, carbene-mediated photoaffinity labeling (cmPAL) has been widely used in drug target identification owing to its excellent photolabeling efficiency, minimal steric interference and longer excitation wavelength. Specifically, diazirines, which are among the precursors of carbenes and have higher carbene yields and greater chemical stability than diazo compounds, have proved to be valuable photolabile reagents in a diverse range of biological systems. This review highlights current advances of cmPAL in medicinal chemistry, with a focus on structures and applications for identifying small molecule-protein and macromolecule-protein interactions and ligand-gated ion channels, coupled with advances in the discovery of targets and inhibitors using carbene precursor-based biological probes developed in recent decades.
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Affiliation(s)
- Sha-Sha Ge
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Biao Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Yuan-Yuan Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Qing-Su Long
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Yong-Liang Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Pei-Yi Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
- College of Pharmacy, East China University of Science & Technology Shanghai 200237 China
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7
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Foray V, Pérez-Jiménez MM, Fattouh N, Landmann F. Wolbachia Control Stem Cell Behavior and Stimulate Germline Proliferation in Filarial Nematodes. Dev Cell 2018; 45:198-211.e3. [PMID: 29689195 DOI: 10.1016/j.devcel.2018.03.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/20/2018] [Accepted: 03/23/2018] [Indexed: 01/04/2023]
Abstract
Although symbiotic interactions are ubiquitous in the living world, examples of developmental symbioses are still scarce. We show here the crucial role of Wolbachia in the oogenesis of filarial nematodes, a class of parasites of biomedical and veterinary relevance. We applied newly developed techniques to demonstrate the earliest requirements of Wolbachia in the parasite germline preceding the production of faulty embryos in Wolbachia-depleted nematodes. We show that Wolbachia stimulate germline proliferation in a cell-autonomous manner, and not through nucleotide supplementation as previously hypothesized. We also found Wolbachia to maintain the quiescence of a pool of germline stem cells to ensure a constant delivery of about 1,400 eggs per day for many years. The loss of quiescence upon Wolbachia depletion as well as the disorganization of the distal germline suggest that Wolbachia are required to execute the proper germline stem cell developmental program in order to produce viable eggs and embryos.
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Affiliation(s)
- Vincent Foray
- CRBM, University of Montpellier, CNRS, Montpellier, France
| | | | - Nour Fattouh
- CRBM, University of Montpellier, CNRS, Montpellier, France
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8
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Verhelst SHL. Intramembrane proteases as drug targets. FEBS J 2017; 284:1489-1502. [PMID: 27889944 DOI: 10.1111/febs.13979] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/14/2016] [Accepted: 11/24/2016] [Indexed: 01/04/2023]
Abstract
Proteases are considered attractive drug targets. Various drugs targeting classical, soluble proteases have been approved for treatment of human disease. Intramembrane proteases (IMPs) are a more recently discovered group of proteolytic enzymes. They are embedded in lipid bilayers and their active sites are located in the plane of a membrane. All four mechanistic families of IMPs have been linked to disease, but currently, no drugs against IMPs have entered the market. In this review, I will outline the function of IMPs with a focus on the ones involved in human disease, which includes Alzheimer's disease, cancer, and infectious diseases by microorganisms. Inhibitors of IMPs are known for all mechanistic classes, but are not yet very potent or selective - aside from those targeting γ-secretase. I will here describe the different features of IMP inhibitors and discuss a list of issues that need attention in the near future in order to improve the drug development for IMPs.
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Affiliation(s)
- Steven H L Verhelst
- Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Belgium.,AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS, Dortmund, Germany
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9
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Dormán G, Nakamura H, Pulsipher A, Prestwich GD. The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore. Chem Rev 2016; 116:15284-15398. [PMID: 27983805 DOI: 10.1021/acs.chemrev.6b00342] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread applications of benzophenone (BP) photochemistry in biological chemistry, bioorganic chemistry, and material science have been prominent in both academic and industrial research. BP photophores have unique photochemical properties: upon n-π* excitation at 365 nm, a biradicaloid triplet state is formed reversibly, which can abstract a hydrogen atom from accessible C-H bonds; the radicals subsequently recombine, creating a stable covalent C-C bond. This light-directed covalent attachment process is exploited in many different ways: (i) binding/contact site mapping of ligand (or protein)-protein interactions; (ii) identification of molecular targets and interactome mapping; (iii) proteome profiling; (iv) bioconjugation and site-directed modification of biopolymers; (v) surface grafting and immobilization. BP photochemistry also has many practical advantages, including low reactivity toward water, stability in ambient light, and the convenient excitation at 365 nm. In addition, several BP-containing building blocks and reagents are commercially available. In this review, we explore the "forbidden" (transitions) and excitation-activated world of photoinduced covalent attachment of BP photophores by touring a colorful palette of recent examples. In this exploration, we will see the pros and cons of using BP photophores, and we hope that both novice and expert photolabelers will enjoy and be inspired by the breadth and depth of possibilities.
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Affiliation(s)
- György Dormán
- Targetex llc , Dunakeszi H-2120, Hungary.,Faculty of Pharmacy, University of Szeged , Szeged H-6720, Hungary
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , Yokohama 226-8503, Japan
| | - Abigail Pulsipher
- GlycoMira Therapeutics, Inc. , Salt Lake City, Utah 84108, United States.,Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| | - Glenn D Prestwich
- Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
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10
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Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Departamento de Fisicoquímica; Universidad Nacional Autónoma de México; Ciudad de México 04510 México
| | - Laura Dominguez
- Departamento de Fisicoquímica; Universidad Nacional Autónoma de México; Ciudad de México 04510 México
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11
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Tatarnikova OG, Orlov MA, Bobkova NV. Beta-Amyloid and Tau-Protein: Structure, Interaction, and Prion-Like Properties. BIOCHEMISTRY (MOSCOW) 2016; 80:1800-19. [PMID: 26878581 DOI: 10.1134/s000629791513012x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
During the last twenty years, molecular genetic investigations of Alzheimer's disease (AD) have significantly broadened our knowledge of basic mechanisms of this disorder. However, still no unambiguous concept on the molecular bases of AD pathogenesis has been elaborated, which significantly impedes the development of AD therapy. In this review, we analyze issues concerning processes of generation of two proteins (β-amyloid peptide and Tau-protein) in the cell, which are believed to play the key role in AD genesis. Until recently, these agents were considered independently of each other, but in light of the latest studies, it becomes clear that it is necessary to study their interaction and combined effects. Studies of mechanisms of toxic action of these endogenous compounds, beginning from their interaction with known receptors of main neurotransmitters to specific peculiarities of functioning of signal intracellular pathways upon development of this pathology, open the way to development of new pharmaceutical substances directed concurrently on key mechanisms of interaction of toxic proteins inside the cell and on the pathways of their propagation in the extracellular space.
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Affiliation(s)
- O G Tatarnikova
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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12
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Onodera Y, Hirota K, Suga Y, Konoki K, Yotsu-Yamashita M, Sasaki M, Fuwa H. Diastereoselective Ring-Closing Metathesis as a Means to Construct Medium-Sized Cyclic Ethers: Application to the Synthesis of a Photoactivatable Gambierol Derivative. J Org Chem 2016; 81:8234-52. [DOI: 10.1021/acs.joc.6b01302] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Onodera
- Graduate
School of Life Sciences, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai 980-8577, Japan
| | - Kazuaki Hirota
- Graduate
School of Life Sciences, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai 980-8577, Japan
| | - Yuto Suga
- Graduate
School of Life Sciences, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai 980-8577, Japan
| | - Keiichi Konoki
- Graduate
School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
| | - Mari Yotsu-Yamashita
- Graduate
School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
| | - Makoto Sasaki
- Graduate
School of Life Sciences, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai 980-8577, Japan
| | - Haruhiko Fuwa
- Graduate
School of Life Sciences, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai 980-8577, Japan
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13
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Crump CJ, Murrey HE, Ballard TE, am Ende CW, Wu X, Gertsik N, Johnson DS, Li YM. Development of Sulfonamide Photoaffinity Inhibitors for Probing Cellular γ-Secretase. ACS Chem Neurosci 2016; 7:1166-73. [PMID: 27253220 DOI: 10.1021/acschemneuro.6b00127] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
γ-Secretase is a multiprotein complex that catalyzes intramembrane proteolysis associated with Alzheimer's disease and cancer. Here, we have developed potent sulfonamide clickable photoaffinity probes that target γ-secretase in vitro and in cells by incorporating various photoreactive groups and walking the clickable alkyne handle to different positions around the molecule. We found that benzophenone is preferred over diazirine as a photoreactive group within the sulfonamide scaffold for labeling γ-secretase. Intriguingly, the placement of the alkyne at different positions has little effect on probe potency but has a significant impact on the efficiency of labeling of γ-secretase. Moreover, the optimized clickable photoprobe, 163-BP3, was utilized as a cellular probe to effectively assess the target engagement of inhibitors with γ-secretase in primary neuronal cells. In addition, biotinylated 163-BP3 probes were developed and used to capture the native γ-secretase complex in the 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate (CHAPSO) solubilized state. Taken together, these next generation clickable and biotinylated sulfonamide probes offer new tools to study γ-secretase in biochemical and cellular systems. Finally, the data provide insights into structural features of the sulfonamide inhibitor binding site in relation to the active site and into the design of clickable photoaffinity probes.
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Affiliation(s)
- Christina J. Crump
- Chemical
Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York
Avenue, New York, New York 10065, United States
| | - Heather E. Murrey
- Pfizer Worldwide Research and Development, Worldwide Medicinal Chemistry, Cambridge, Massachusetts 02139, United States
| | - T. Eric Ballard
- Pfizer Worldwide Research and Development, Worldwide
Medicinal Chemistry Groton, Connecticut 06340, United States
| | - Christopher W. am Ende
- Pfizer Worldwide Research and Development, Worldwide
Medicinal Chemistry Groton, Connecticut 06340, United States
| | - Xianzhong Wu
- Chemical
Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York
Avenue, New York, New York 10065, United States
| | - Natalya Gertsik
- Chemical
Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York
Avenue, New York, New York 10065, United States
| | - Douglas S. Johnson
- Pfizer Worldwide Research and Development, Worldwide Medicinal Chemistry, Cambridge, Massachusetts 02139, United States
| | - Yue-Ming Li
- Chemical
Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York
Avenue, New York, New York 10065, United States
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14
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Theis T, Ortiz GX, Logan AWJ, Claytor KE, Feng Y, Huhn WP, Blum V, Malcolmson SJ, Chekmenev EY, Wang Q, Warren WS. Direct and cost-efficient hyperpolarization of long-lived nuclear spin states on universal (15)N2-diazirine molecular tags. SCIENCE ADVANCES 2016; 2:e1501438. [PMID: 27051867 PMCID: PMC4820385 DOI: 10.1126/sciadv.1501438] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/05/2016] [Indexed: 05/17/2023]
Abstract
Conventional magnetic resonance (MR) faces serious sensitivity limitations which can be overcome by hyperpolarization methods, but the most common method (dynamic nuclear polarization) is complex and expensive, and applications are limited by short spin lifetimes (typically seconds) of biologically relevant molecules. We use a recently developed method, SABRE-SHEATH, to directly hyperpolarize (15)N2 magnetization and long-lived (15)N2 singlet spin order, with signal decay time constants of 5.8 and 23 minutes, respectively. We find >10,000-fold enhancements generating detectable nuclear MR signals that last for over an hour. (15)N2-diazirines represent a class of particularly promising and versatile molecular tags, and can be incorporated into a wide range of biomolecules without significantly altering molecular function.
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Affiliation(s)
- Thomas Theis
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Corresponding author. E-mail: (W.S.W.); (Q.W.); (T.T.)
| | | | | | | | - Yesu Feng
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - William P. Huhn
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Volker Blum
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | | | - Eduard Y. Chekmenev
- Departments of Radiology and Biomedical Engineering, Vanderbilt University, Institute of Imaging Science, Nashville, TN 37232, USA
| | - Qiu Wang
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Corresponding author. E-mail: (W.S.W.); (Q.W.); (T.T.)
| | - Warren S. Warren
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Department of Physics, Duke University, Durham, NC 27708, USA
- Departments of Radiology and Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Corresponding author. E-mail: (W.S.W.); (Q.W.); (T.T.)
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15
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Shi RG, Wang XH, Liu R, Yan CG. Two-carbon ring expansion of isatin: a convenient construction of a dibenzo[b,d]azepinone scaffold. Chem Commun (Camb) 2016; 52:6280-3. [DOI: 10.1039/c6cc00525j] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A unique two-carbon ring expansion of isatin has been achieved to conveniently construct the functionalized dibenzo[b,d]azepin-6-one scaffold in moderate to high yields, and the two carbon sources are different: one carbon is from the N-substituent of pyridinium bromide and the other is from indene-1,3-dione.
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Affiliation(s)
- Rong-Guo Shi
- College of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou
- China
| | - Xiao-Hua Wang
- College of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou
- China
| | - Ruzhang Liu
- College of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou
- China
| | - Chao-Guo Yan
- College of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou
- China
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16
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Nguyen MTN, Kersavond TV, Verhelst SHL. Chemical Tools for the Study of Intramembrane Proteases. ACS Chem Biol 2015; 10:2423-34. [PMID: 26473325 DOI: 10.1021/acschembio.5b00693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intramembrane proteases (IMPs) reside inside lipid bilayers and perform peptide hydrolysis in transmembrane or juxtamembrane regions of their substrates. Many IMPs are involved in crucial regulatory pathways and human diseases, including Alzheimer's disease, Parkinson's disease, and diabetes. In the past, chemical tools have been instrumental in the study of soluble proteases, enabling biochemical and biomedical research in complex environments such as tissue lysates or living cells. However, IMPs place special challenges on probe design and applications, and progress has been much slower than for soluble proteases. In this review, we will give an overview of the available chemical tools for IMPs, including activity-based probes, affinity-based probes, and synthetic substrates. We will discuss how these have been used to increase our structural and functional understanding of this fascinating group of enzymes, and how they might be applied to address future questions and challenges.
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Affiliation(s)
- Minh T. N. Nguyen
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Tim Van Kersavond
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Steven H. L. Verhelst
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
- KU Leuven − University of Leuven, Department
of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49 Box 802, 3000 Leuven, Belgium
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17
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Naing SH, Vukoti KM, Drury JE, Johnson JL, Kalyoncu S, Hill SE, Torres MP, Lieberman RL. Catalytic Properties of Intramembrane Aspartyl Protease Substrate Hydrolysis Evaluated Using a FRET Peptide Cleavage Assay. ACS Chem Biol 2015; 10:2166-74. [PMID: 26118406 DOI: 10.1021/acschembio.5b00305] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical details of intramembrane proteolysis remain elusive despite its prevalence throughout biology. We developed a FRET peptide assay for the intramembrane aspartyl protease (IAP) from Methanoculleus marisnigri JR1 in combination with quantitative mass spectrometry cleavage site analysis. IAP can hydrolyze the angiotensinogen sequence, a substrate for the soluble aspartyl protease renin, at a predominant cut site, His-Thr. Turnover is slow (min(-1) × 10(-3)), affinity and Michaelis constant (Km) values are in the low micromolar range, and both catalytic rates and cleavage sites are the same in detergent as reconstituted into bicelles. Three well-established, IAP-directed inhibitors were directly confirmed as competitive, albeit with modest inhibitor constant (Ki) values. Partial deletion of the first transmembrane helix results in a biophysically similar but less active enzyme than full-length IAP, indicating a catalytic role. Our study demonstrates previously unappreciated similarities with soluble aspartyl proteases, provides new biochemical features of IAP and inhibitors, and offers tools to study other intramembrane protease family members in molecular detail.
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Affiliation(s)
- Swe-Htet Naing
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic
Drive Northwest, Atlanta, Georgia 30332-0400, United States
| | - Krishna M. Vukoti
- School
of Biology, Georgia Institute of Technology, 310 Ferst Drive Northwest, Atlanta, Georgia 30332-0230, United States
| | - Jason E. Drury
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic
Drive Northwest, Atlanta, Georgia 30332-0400, United States
| | - Jennifer L. Johnson
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic
Drive Northwest, Atlanta, Georgia 30332-0400, United States
| | - Sibel Kalyoncu
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic
Drive Northwest, Atlanta, Georgia 30332-0400, United States
| | - Shannon E. Hill
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic
Drive Northwest, Atlanta, Georgia 30332-0400, United States
| | - Matthew P. Torres
- School
of Biology, Georgia Institute of Technology, 310 Ferst Drive Northwest, Atlanta, Georgia 30332-0230, United States
| | - Raquel L. Lieberman
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic
Drive Northwest, Atlanta, Georgia 30332-0400, United States
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18
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Gertsik N, Chau DM, Li YM. γ-Secretase Inhibitors and Modulators Induce Distinct Conformational Changes in the Active Sites of γ-Secretase and Signal Peptide Peptidase. ACS Chem Biol 2015; 10:1925-31. [PMID: 26030233 DOI: 10.1021/acschembio.5b00321] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
γ-Secretase inhibitors (GSIs) and modulators (GSMs) are at the frontline of cancer and Alzheimer's disease research, respectively. While both are therapeutically promising, not much is known about their interactions with proteins other than γ-secretase. Signal peptide peptidase (SPP), like γ-secretase, is a multispan transmembrane aspartyl protease that catalyzes regulated intramembrane proteolysis. We used active site-directed photophore walking probes to study the effects of different GSIs and GSMs on the active sites of γ-secretase and SPP and found that nontransition state GSIs inhibit labeling of γ-secretase by activity-based probes but enhance labeling of SPP. The opposite is true of GSMs, which have little effect on the labeling of γ-secretase but diminish labeling of SPP. These results demonstrate that GSIs and GSMs are altering the structure of not only γ-secretase but also SPP, leading to potential changes in enzyme activity and specificity that may impact the clinical outcomes of these molecules.
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Affiliation(s)
- Natalya Gertsik
- Molecular
Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
| | - De-Ming Chau
- Molecular
Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
- Clinical
Genetics Unit Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Yue-Ming Li
- Molecular
Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
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19
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Bohm C, Chen F, Sevalle J, Qamar S, Dodd R, Li Y, Schmitt-Ulms G, Fraser PE, St George-Hyslop PH. Current and future implications of basic and translational research on amyloid-β peptide production and removal pathways. Mol Cell Neurosci 2015; 66:3-11. [PMID: 25748120 PMCID: PMC4503820 DOI: 10.1016/j.mcn.2015.02.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 02/26/2015] [Accepted: 02/27/2015] [Indexed: 01/12/2023] Open
Abstract
Inherited variants in multiple different genes are associated with increased risk for Alzheimer's disease (AD). In many of these genes, the inherited variants alter some aspect of the production or clearance of the neurotoxic amyloid β-peptide (Aβ). Thus missense, splice site or duplication mutants in the presenilin 1 (PS1), presenilin 2 (PS2) or the amyloid precursor protein (APP) genes, which alter the levels or shift the balance of Aβ produced, are associated with rare, highly penetrant autosomal dominant forms of Familial Alzheimer's Disease (FAD). Similarly, the more prevalent late-onset forms of AD are associated with both coding and non-coding variants in genes such as SORL1, PICALM and ABCA7 that affect the production and clearance of Aβ. This review summarises some of the recent molecular and structural work on the role of these genes and the proteins coded by them in the biology of Aβ. We also briefly outline how the emerging knowledge about the pathways involved in Aβ generation and clearance can be potentially targeted therapeutically. This article is part of Special Issue entitled "Neuronal Protein".
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Affiliation(s)
- C Bohm
- Tanz Centre for Research in Neurodegenerative Diseases, Departments of Medicine, Laboratory Medicine and Pathobiology and Medical Biophysics, University of Toronto, Krembil Discovery Tower, 6th Floor-6KD417, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - F Chen
- Tanz Centre for Research in Neurodegenerative Diseases, Departments of Medicine, Laboratory Medicine and Pathobiology and Medical Biophysics, University of Toronto, Krembil Discovery Tower, 6th Floor-6KD417, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - J Sevalle
- Tanz Centre for Research in Neurodegenerative Diseases, Departments of Medicine, Laboratory Medicine and Pathobiology and Medical Biophysics, University of Toronto, Krembil Discovery Tower, 6th Floor-6KD417, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - S Qamar
- Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Addenbrookes Hospital, Hills Road, Cambridge CB2 0XY, UK
| | - R Dodd
- Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Addenbrookes Hospital, Hills Road, Cambridge CB2 0XY, UK
| | - Y Li
- Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Addenbrookes Hospital, Hills Road, Cambridge CB2 0XY, UK
| | - G Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, Departments of Medicine, Laboratory Medicine and Pathobiology and Medical Biophysics, University of Toronto, Krembil Discovery Tower, 6th Floor-6KD417, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - P E Fraser
- Tanz Centre for Research in Neurodegenerative Diseases, Departments of Medicine, Laboratory Medicine and Pathobiology and Medical Biophysics, University of Toronto, Krembil Discovery Tower, 6th Floor-6KD417, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - P H St George-Hyslop
- Tanz Centre for Research in Neurodegenerative Diseases, Departments of Medicine, Laboratory Medicine and Pathobiology and Medical Biophysics, University of Toronto, Krembil Discovery Tower, 6th Floor-6KD417, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada; Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Addenbrookes Hospital, Hills Road, Cambridge CB2 0XY, UK.
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20
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Yang P, Liu K. Activity-based protein profiling: recent advances in probe development and applications. Chembiochem 2015; 16:712-24. [PMID: 25652106 DOI: 10.1002/cbic.201402582] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Indexed: 11/08/2022]
Abstract
The completion of the human genome sequencing project has provided a wealth of new information regarding the genomic blueprint of the cell. Although, to date, there are roughly 20,000 genes in the human genome, the functions of only a handful of proteins are clear. The major challenge lies in translating genomic information into an understanding of their cellular functions. The recently developed activity-based protein profiling (ABPP) is an unconventional approach that is complementary for gene expression analysis and an ideal utensil in decoding this overflow of genomic information. This approach makes use of synthetic small molecules that covalently modify a set of related proteins and subsequently facilitates identification of the target protein, enabling rapid biochemical analysis and inhibitor discovery. This tutorial review introduces recent advances in the field of ABPP and its applications.
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Affiliation(s)
- Pengyu Yang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037 (USA)
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21
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Li Y, Bohm C, Dodd R, Chen F, Qamar S, Schmitt-Ulms G, Fraser PE, St George-Hyslop PH. Structural biology of presenilin 1 complexes. Mol Neurodegener 2014; 9:59. [PMID: 25523933 PMCID: PMC4326451 DOI: 10.1186/1750-1326-9-59] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/12/2014] [Indexed: 11/17/2022] Open
Abstract
The presenilin genes were first identified as the site of missense mutations causing early onset autosomal dominant familial Alzheimer's disease. Subsequent work has shown that the presenilin proteins are the catalytic subunits of a hetero-tetrameric complex containing APH1, nicastrin and PEN-2. This complex (variously termed presenilin complex or gamma-secretase complex) performs an unusual type of proteolysis in which the transmembrane domains of Type I proteins are cleaved within the hydrophobic compartment of the membrane. This review describes some of the molecular and structural biology of this unusual enzyme complex. The presenilin complex is a bilobed structure. The head domain contains the ectodomain of nicastrin. The base domain contains a central cavity with a lateral cleft that likely provides the route for access of the substrate to the catalytic cavity within the centre of the base domain. There are reciprocal allosteric interactions between various sites in the complex that affect its function. For instance, binding of Compound E, a peptidomimetic inhibitor to the PS1 N-terminus, induces significant conformational changes that reduces substrate binding at the initial substrate docking site, and thus inhibits substrate cleavage. However, there is a reciprocal allosteric interaction between these sites such that prior binding of the substrate to the initial docking site paradoxically increases the binding of the Compound E peptidomimetic inhibitor. Such reciprocal interactions are likely to form the basis of a gating mechanism that underlies access of substrate to the catalytic site. An increasingly detailed understanding of the structural biology of the presenilin complex is an essential step towards rational design of substrate- and/or cleavage site-specific modulators of presenilin complex function.
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Affiliation(s)
| | | | | | | | | | | | | | - Peter H St George-Hyslop
- Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Addenbrookes Hospital, Hills Road, Cambridge CB2 0XY, UK.
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22
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Ishikawa R, Yoshida N, Akao Y, Kawabe Y, Inai M, Asakawa T, Hamashima Y, Kan T. Total Syntheses of (+)-Sesamin and (+)-Sesaminol. CHEM LETT 2014. [DOI: 10.1246/cl.140613] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ryo Ishikawa
- School of Pharmaceutical Sciences, University of Shizuoka
| | - Naoto Yoshida
- School of Pharmaceutical Sciences, University of Shizuoka
| | - Yusuke Akao
- School of Pharmaceutical Sciences, University of Shizuoka
| | - Yusuke Kawabe
- School of Pharmaceutical Sciences, University of Shizuoka
| | - Makoto Inai
- School of Pharmaceutical Sciences, University of Shizuoka
| | | | | | - Toshiyuki Kan
- School of Pharmaceutical Sciences, University of Shizuoka
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23
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Abstract
Presenilin is a membrane-embedded intramembrane-cleaving protease with a conserved catalytic G×GD motif. It is the catalytic subunit of γ-secretase, which plays critical roles in developmental biology and the molecular etiology of Alzheimer disease, together with three membrane protein cofactors, nicastrin, Aph-1 and Pen-2. Biochemical and enzymatic analyses have revealed that γ-secretase executes two types of proteolytic activities on a single substrate; an endopeptidase-like cleavage followed by carboxypeptidase-like processive cleavage. Utilizing small molecule inhibitors/modulators together with the substituted cysteine accessibility method, we identified certain residues and regions of presenilin that contribute to the formation of a catalytic pore structure within the lipid bilayer required for its intramembrane-cleaving activity. Recently, determination of the crystal structure of the archaeal presenilin homologue has confirmed the intramembranous location of the two conserved and essential aspartates. In this review, I will introduce the recent progresses in the understanding of the molecular mechanisms of action of this atypical protease.
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Affiliation(s)
- Taisuke Tomita
- Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
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24
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Notch inhibition allows oncogene-independent generation of iPS cells. Nat Chem Biol 2014; 10:632-639. [PMID: 24952596 PMCID: PMC4310751 DOI: 10.1038/nchembio.1552] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 05/13/2014] [Indexed: 12/17/2022]
Abstract
The reprogramming of somatic cells to pluripotency using defined transcription factors holds great promise for biomedicine. However, human reprogramming remains inefficient and relies either on the use of the potentially dangerous oncogenes KLF4 and CMYC or the genetic inhibition of the tumor suppressor gene p53. We hypothesized that inhibition of signal transduction pathways that promote differentiation of the target somatic cells during development might relieve the requirement for non-core pluripotency factors during iPSC reprogramming. Here, we show that inhibition of Notch significantly improves the efficiency of iPSC generation from mouse and human keratinocytes by suppressing p21 in a p53-independent manner and thereby enriching for undifferentiated cells capable of long-term self-renewal. Pharmacological inhibition of Notch enabled routine production of human iPSCs without KLF4 and CMYC while leaving p53 activity intact. Thus, restricting the development of somatic cells by altering intercellular communication enables the production of safer human iPSCs.
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25
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Sakurai K, Ozawa S, Yamada R, Yasui T, Mizuno S. Comparison of the Reactivity of Carbohydrate Photoaffinity Probes with Different Photoreactive Groups. Chembiochem 2014; 15:1399-403. [DOI: 10.1002/cbic.201402051] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Indexed: 01/12/2023]
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26
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Sasaki S, Suzuki H, Ouchi H, Asakawa T, Inai M, Sakai R, Shimamoto K, Hamashima Y, Kan T. Practical synthesis of kainoids: a new chemical probe precursor and a fluorescent probe. Org Lett 2014; 16:564-7. [PMID: 24397779 DOI: 10.1021/ol403434e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A practical total synthesis of kainoid MFPA (5) was achieved in only six steps, via a novel Ni-catalyst-mediated asymmetric conjugate addition reaction. Furthermore, a fluorescein-based fluorescent ionotropic glutamate receptor probe 28 was efficiently synthesized from a precursor derived from a synthetic intermediate of 5.
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Affiliation(s)
- Shingo Sasaki
- School of Pharmaceutical Sciences, University of Shizuoka , 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
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27
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Tomita T. Secretase inhibitors and modulators for Alzheimer’s disease treatment. Expert Rev Neurother 2014; 9:661-79. [DOI: 10.1586/ern.09.24] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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28
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Ikeuchi K, Fujii R, Sugiyama S, Asakawa T, Inai M, Hamashima Y, Choi JH, Suzuki T, Kawagishi H, Kan T. Practical synthesis of natural plant-growth regulator 2-azahypoxanthine, its derivatives, and biotin-labeled probes. Org Biomol Chem 2014; 12:3813-5. [DOI: 10.1039/c4ob00705k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
AHX derivatives and their probe molecules.
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Affiliation(s)
- Kazutada Ikeuchi
- School of Pharmaceutical Sciences
- University of Shizuoka
- Suruga-ku, Japan
| | - Ryosuke Fujii
- School of Pharmaceutical Sciences
- University of Shizuoka
- Suruga-ku, Japan
| | - Shimpei Sugiyama
- School of Pharmaceutical Sciences
- University of Shizuoka
- Suruga-ku, Japan
| | - Tomohiro Asakawa
- School of Pharmaceutical Sciences
- University of Shizuoka
- Suruga-ku, Japan
| | - Makoto Inai
- School of Pharmaceutical Sciences
- University of Shizuoka
- Suruga-ku, Japan
| | | | - Jae-Hoon Choi
- Research Institute of Green Science and Technology
- Shizuoka University
- Suruga-ku, Japan
| | - Tomohiro Suzuki
- Research Institute of Green Science and Technology
- Shizuoka University
- Suruga-ku, Japan
| | - Hirokazu Kawagishi
- Research Institute of Green Science and Technology
- Shizuoka University
- Suruga-ku, Japan
- Graduate School of Science and Technology
- Shizuoka University
| | - Toshiyuki Kan
- School of Pharmaceutical Sciences
- University of Shizuoka
- Suruga-ku, Japan
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29
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Li Y, Lu SHJ, Tsai CJ, Bohm C, Qamar S, Dodd RB, Meadows W, Jeon A, McLeod A, Chen F, Arimon M, Berezovska O, Hyman BT, Tomita T, Iwatsubo T, Johnson CM, Farrer LA, Schmitt-Ulms G, Fraser PE, St George-Hyslop PH. Structural interactions between inhibitor and substrate docking sites give insight into mechanisms of human PS1 complexes. Structure 2013; 22:125-35. [PMID: 24210759 PMCID: PMC3887256 DOI: 10.1016/j.str.2013.09.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/28/2013] [Accepted: 09/21/2013] [Indexed: 11/18/2022]
Abstract
Presenilin-mediated endoproteolysis of transmembrane proteins plays a key role in physiological signaling and in the pathogenesis of Alzheimer disease and some cancers. Numerous inhibitors have been found via library screens, but their structural mechanisms remain unknown. We used several biophysical techniques to investigate the structure of human presenilin complexes and the effects of peptidomimetic γ-secretase inhibitors. The complexes are bilobed. The head contains nicastrin ectodomain. The membrane-embedded base has a central channel and a lateral cleft, which may represent the initial substrate docking site. Inhibitor binding induces widespread structural changes, including rotation of the head and closure of the lateral cleft. These changes block substrate access to the catalytic pocket and inhibit the enzyme. Intriguingly, peptide substrate docking has reciprocal effects on the inhibitor binding site. Similar reciprocal shifts may underlie the mechanisms of other inhibitors and of the “lateral gate” through which substrates access to the catalytic site. The head contains nicastrin ectodomain and overhangs a solute-accessible cavity in base The base has a central channel and a lateral cleft (putative substrate docking site) Inhibitors close the cleft and channel and rotate the head, blocking substrate access
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Affiliation(s)
- Yi Li
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Stephen Hsueh-Jeng Lu
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Ching-Ju Tsai
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Christopher Bohm
- Tanz Centre for Research in Neurodegenerative Diseases, and Departments of Medicine, Laboratory Medicine and Pathobiology, and Medical Biophysics, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Seema Qamar
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Roger B Dodd
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - William Meadows
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Amy Jeon
- Tanz Centre for Research in Neurodegenerative Diseases, and Departments of Medicine, Laboratory Medicine and Pathobiology, and Medical Biophysics, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Adam McLeod
- Tanz Centre for Research in Neurodegenerative Diseases, and Departments of Medicine, Laboratory Medicine and Pathobiology, and Medical Biophysics, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Fusheng Chen
- Tanz Centre for Research in Neurodegenerative Diseases, and Departments of Medicine, Laboratory Medicine and Pathobiology, and Medical Biophysics, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Muriel Arimon
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Oksana Berezovska
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Bradley T Hyman
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Taisuke Tomita
- Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, and Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeshi Iwatsubo
- Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, and Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Christopher M Johnson
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Lindsay A Farrer
- Departments of Medicine (Biomedical Genetics), Neurology, Ophthalmology, Genetics and Genomics, Biostatistics, and Epidemiology, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, and Departments of Medicine, Laboratory Medicine and Pathobiology, and Medical Biophysics, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Paul E Fraser
- Tanz Centre for Research in Neurodegenerative Diseases, and Departments of Medicine, Laboratory Medicine and Pathobiology, and Medical Biophysics, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Peter H St George-Hyslop
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Tanz Centre for Research in Neurodegenerative Diseases, and Departments of Medicine, Laboratory Medicine and Pathobiology, and Medical Biophysics, University of Toronto, Toronto, ON M5S 3H2, Canada.
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30
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Recent advances in target characterization and identification by photoaffinity probes. Molecules 2013; 18:10425-51. [PMID: 23994969 PMCID: PMC6270116 DOI: 10.3390/molecules180910425] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 08/23/2013] [Accepted: 08/23/2013] [Indexed: 11/17/2022] Open
Abstract
Target identification of biologically active molecules such as natural products, synthetic small molecules, peptides, and oligonucleotides mainly relies on affinity chromatography, activity-based probes, or photoaffinity labeling (PAL). Amongst them, activity-based probes and PAL have offered great advantages in target identification technology due to their ability to form covalent bonds with the corresponding targets. Activity-based probe technology mainly relies on the chemical reactivity of the target proteins, thereby limiting the majority of the biological targets to enzymes or proteins which display reactive residues at the probe-binding site. In general, the probes should bear a reactive moiety such as an epoxide, a Michael acceptor, or a reactive alkyl halide in their structures. On the other hand, photoaffinity probes (PAPs) are composed of a target-specific ligand and a photoactivatable functional group. When bound to the corresponding target proteins and activated with wavelength-specific light, PAPs generate highly reactive chemical species that covalently cross-link proximal amino acid residues. This process is better known as PAL and is widely employed to identify cellular targets of biologically active molecules. This review highlights recent advances in target identification by PAL, with a focus on the structure and chemistry of the photoaffinity probes developed in the recent decade, coupled to the target proteins identified using these probes.
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31
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Crump CJ, Johnson DS, Li YM. Development and mechanism of γ-secretase modulators for Alzheimer's disease. Biochemistry 2013; 52:3197-216. [PMID: 23614767 DOI: 10.1021/bi400377p] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
γ-Secretase is an aspartyl intramembranal protease composed of presenilin, Nicastrin, Aph1, and Pen2 with 19 transmembrane domains. γ-Secretase cleaves the amyloid precursor proteins (APP) to release Aβ peptides that likely play a causative role in the pathogenesis of Alzheimer's disease (AD). In addition, γ-secretase cleaves Notch and other type I membrane proteins. γ-Secretase inhibitors (GSIs) have been developed and used for clinical studies. However, clinical trials have shown adverse effects of GSIs that are potentially linked with nondiscriminatory inhibition of Notch signaling, overall APP processing, and other substrate cleavages. Therefore, these findings call for the development of disease-modifying agents that target γ-secretase activity to lower levels of Aβ42 production without blocking the overall processing of γ-secretase substrates. γ-Secretase modulators (GSMs) originally derived from nonsteroidal anti-inflammatory drugs (NSAIDs) display such characteristics and are the focus of this review. However, first-generation GSMs have limited potential because of the low potency and undesired neuropharmacokinetic properties. This generation of GSMs has been suggested to interact with the APP substrate, γ-secretase, or both. To improve the potency and brain availability, second-generation GSMs, including NSAID-derived carboxylic acid and non-NSAID-derived heterocyclic chemotypes, as well as natural product-derived GSMs have been developed. Animal studies of this generation of GSMs have shown encouraging preclinical profiles. Moreover, using potent GSM photoaffinity probes, multiple studies unambiguously have showed that both carboxylic acid and heterocyclic GSMs specifically target presenilin, the catalytic subunit of γ-secretase. In addition, two types of GSMs have distinct binding sites within the γ-secretase complex and exhibit different Aβ profiles. GSMs induce a conformational change of γ-secretase to achieve modulation. Various models are proposed and discussed. Despite the progress of GSM research, many outstanding issues remain to be investigated to achieve the ultimate goal of developing GSMs as effective AD therapies.
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Affiliation(s)
- Christina J Crump
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center , 1275 York Avenue, New York, New York 10065, United States
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32
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Tomita T, Iwatsubo T. Structural biology of presenilins and signal peptide peptidases. J Biol Chem 2013; 288:14673-80. [PMID: 23585568 DOI: 10.1074/jbc.r113.463281] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Presenilin and signal peptide peptidase are multispanning intramembrane-cleaving proteases with a conserved catalytic GxGD motif. Presenilin comprises the catalytic subunit of γ-secretase, a protease responsible for the generation of amyloid-β peptides causative of Alzheimer disease. Signal peptide peptidase proteins are implicated in the regulation of the immune system. Both protease family proteins have been recognized as druggable targets for several human diseases, but their detailed structure still remains unknown. Recently, the x-ray structures of some archaeal GxGD proteases have been determined. We review the recent progress in biochemical and biophysical probing of the structure of these atypical proteases.
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Affiliation(s)
- Taisuke Tomita
- Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan.
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Thirumurugan P, Matosiuk D, Jozwiak K. Click Chemistry for Drug Development and Diverse Chemical–Biology Applications. Chem Rev 2013; 113:4905-79. [DOI: 10.1021/cr200409f] [Citation(s) in RCA: 1309] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Prakasam Thirumurugan
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Dariusz Matosiuk
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Krzysztof Jozwiak
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
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34
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Imamura Y, Umezawa N, Osawa S, Shimada N, Higo T, Yokoshima S, Fukuyama T, Iwatsubo T, Kato N, Tomita T, Higuchi T. Effect of Helical Conformation and Side Chain Structure on γ-Secretase Inhibition by β-Peptide Foldamers: Insight into Substrate Recognition. J Med Chem 2013; 56:1443-54. [DOI: 10.1021/jm301306c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuki Imamura
- Department of Bioorganic-Inorganic
Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku,
Nagoya, Aichi, Japan
| | - Naoki Umezawa
- Department of Bioorganic-Inorganic
Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku,
Nagoya, Aichi, Japan
| | - Satoko Osawa
- Department
of Neuropathology
and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo,
Japan
| | - Naoaki Shimada
- Department of Synthetic
Natural
Products Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo,
Japan
| | - Takuya Higo
- Department of Synthetic
Natural
Products Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo,
Japan
| | - Satoshi Yokoshima
- Department of Synthetic
Natural
Products Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo,
Japan
| | - Tohru Fukuyama
- Department of Synthetic
Natural
Products Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo,
Japan
| | - Takeshi Iwatsubo
- Department
of Neuropathology
and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo,
Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan
- Department of Neuropathology,
Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Nobuki Kato
- Department of Bioorganic-Inorganic
Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku,
Nagoya, Aichi, Japan
| | - Taisuke Tomita
- Department
of Neuropathology
and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo,
Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan
| | - Tsunehiko Higuchi
- Department of Bioorganic-Inorganic
Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku,
Nagoya, Aichi, Japan
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35
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Bulic B, Ness J, Hahn S, Rennhack A, Jumpertz T, Weggen S. Chemical Biology, Molecular Mechanism and Clinical Perspective of γ-Secretase Modulators in Alzheimer's Disease. Curr Neuropharmacol 2012; 9:598-622. [PMID: 22798753 PMCID: PMC3391656 DOI: 10.2174/157015911798376352] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 10/25/2010] [Accepted: 11/01/2010] [Indexed: 12/25/2022] Open
Abstract
Comprehensive evidence supports that oligomerization and accumulation of amyloidogenic Aβ42 peptides in brain is crucial in the pathogenesis of both familial and sporadic forms of Alzheimer's disease. Imaging studies indicate that the buildup of Aβ begins many years before the onset of clinical symptoms, and that subsequent neurodegeneration and cognitive decline may proceed independently of Aβ. This implies the necessity for early intervention in cognitively normal individuals with therapeutic strategies that prioritize safety. The aspartyl protease γ-secretase catalyses the last step in the cellular generation of Aβ42 peptides, and is a principal target for anti-amyloidogenic intervention strategies. Due to the essential role of γ-secretase in the NOTCH signaling pathway, overt mechanism-based toxicity has been observed with the first generation of γ-secretase inhibitors, and safety of this approach has been questioned. However, two new classes of small molecules, γ-secretase modulators (GSMs) and NOTCH-sparing γ-secretase inhibitors, have revitalized γ-secretase as a drug target in AD. GSMs are small molecules that cause a product shift from Aβ42 towards shorter and less toxic Ab peptides. Importantly, GSMs spare other physiologically important substrates of the γ-secretase complex like NOTCH. Recently, GSMs with nanomolar potency and favorable in vivo properties have been described. In this review, we summarize the knowledge about the unusual proteolytic activity of γ-secretase, and the chemical biology, molecular mechanisms and clinical perspective of compounds that target the γ-secretase complex, with a particular focus on GSMs.
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Affiliation(s)
- Bruno Bulic
- Research Group Chemical Biology of Neurodegenerative Diseases, Center of Advanced European Studies and Research, D-53175 Bonn, Germany
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36
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Crump CJ, am Ende CW, Ballard TE, Pozdnyakov N, Pettersson M, Chau DM, Bales KR, Li YM, Johnson DS. Development of clickable active site-directed photoaffinity probes for γ-secretase. Bioorg Med Chem Lett 2012; 22:2997-3000. [PMID: 22418280 DOI: 10.1016/j.bmcl.2012.02.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 02/08/2012] [Accepted: 02/10/2012] [Indexed: 12/31/2022]
Abstract
We have developed clickable active site-directed photoaffinity probes for γ-secretase which incorporate a photoreactive benzophenone group and an alkyne handle for subsequent click chemistry mediated conjugation with azide-linked reporter tags for visualization (e.g., TAMRA-azide) or enrichment (e.g., biotin-azide) of labeled proteins. Specifically, we synthesized clickable analogs of L646 (2) and L505 (3) and validated specific labeling to presenilin-1N-terminal fragment (PS1-NTF), the active site aspartyl protease component within the γ-secretase complex. Additionally, we were able to identify signal peptide peptidase (SPP) by Western blot analysis. Furthermore, we analyzed the photo-labeled proteins in an unbiased fashion by click chemistry with TAMRA-azide followed by in-gel fluorescence detection. This approach expands the utility of γ-secretase inhibitor (GSI) photoaffinity probes in that labeled proteins can be tagged with any number of azide-linked reporters groups using a single clickable photoaffinity probe for target pull down and/or fluorescent imaging applications.
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Affiliation(s)
- Christina J Crump
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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Shi H, Zhang CJ, Chen GYJ, Yao SQ. Cell-based proteome profiling of potential dasatinib targets by use of affinity-based probes. J Am Chem Soc 2012; 134:3001-14. [PMID: 22242683 DOI: 10.1021/ja208518u] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein kinases (PKs) play an important role in the development and progression of cancer by regulating cell growth, survival, invasion, metastasis, and angiogenesis. Dasatinib (BMS-354825), a dual Src/Abl inhibitor, is a promising therapeutic agent with oral bioavailability. It has been used for the treatment of imatinib-resistant chronic myelogenous leukemia (CML). Most kinase inhibitors, including Dasatinib, inhibit multiple cellular targets and do not possess exquisite cellular specificity. Recent efforts in kinase research thus focus on the development of large-scale, proteome-wide chemical profiling methods capable of rapid identification of potential cellular (on- and off-) targets of kinase inhibitors. Most existing approaches, however, are still problematic and in many cases not compatible with live-cell studies. In this work, we have successfully developed a cell-permeable kinase probe (DA-2) capable of proteome-wide profiling of potential cellular targets of Dasatinib. In this way, highly regulated, compartmentalized kinase-drug interactions were maintained. By comparing results obtained from different proteomic setups (live cells, cell lysates, and immobilized affinity matrix), we found DA-2 was able to identify significantly more putative kinase targets. In addition to Abl and Src family tyrosine kinases, a number of previously unknown Dasatinib targets have been identified, including several serine/threonine kinases (PCTK3, STK25, eIF-2A, PIM-3, PKA C-α, and PKN2). They were further validated by pull-down/immunoblotting experiments as well as kinase inhibition assays. Further studies are needed to better understand the exact relevance of Dasatinib and its pharmacological effects in relation to these newly identified cellular targets. The approach developed herein should be amenable to the study of many of the existing reversible drugs/drug candidates.
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Affiliation(s)
- Haibin Shi
- Department of Chemistry, National University of Singapore, Singapore 117543
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38
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Jumpertz T, Rennhack A, Ness J, Baches S, Pietrzik CU, Bulic B, Weggen S. Presenilin is the molecular target of acidic γ-secretase modulators in living cells. PLoS One 2012; 7:e30484. [PMID: 22238696 PMCID: PMC3253113 DOI: 10.1371/journal.pone.0030484] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 12/16/2011] [Indexed: 01/19/2023] Open
Abstract
The intramembrane-cleaving protease γ-secretase catalyzes the last step in the generation of toxic amyloid-β (Aβ) peptides and is a principal therapeutic target in Alzheimer's disease. Both preclinical and clinical studies have demonstrated that inhibition of γ-secretase is associated with prohibitive side effects due to suppression of Notch processing and signaling. Potentially safer are γ-secretase modulators (GSMs), which are small molecules that selectively lower generation of the highly amyloidogenic Aβ42 peptides but spare Notch processing. GSMs with nanomolar potency and favorable pharmacological properties have been described, but the molecular mechanism of GSMs remains uncertain and both the substrate amyloid precursor protein (APP) and subunits of the γ-secretase complex have been proposed as the molecular target of GSMs. We have generated a potent photo-probe based on an acidic GSM that lowers Aβ42 generation with an IC50 of 290 nM in cellular assays. By combining in vivo photo-crosslinking with affinity purification, we demonstrated that this probe binds the N-terminal fragment of presenilin (PSEN), the catalytic subunit of the γ-secretase complex, in living cells. Labeling was not observed for APP or any of the other γ-secretase subunits. Binding was readily competed by structurally divergent acidic and non-acidic GSMs suggesting a shared mode of action. These findings indicate that potent acidic GSMs target presenilin to modulate the enzymatic activity of the γ-secretase complex.
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Affiliation(s)
- Thorsten Jumpertz
- Department of Neuropathology, Heinrich-Heine-University, Duesseldorf, Germany
| | - Andreas Rennhack
- Research Group Chemical Biology of Neurodegenerative Diseases, Center of Advanced European Studies and Research, Bonn, Germany
| | - Julia Ness
- Department of Neuropathology, Heinrich-Heine-University, Duesseldorf, Germany
| | - Sandra Baches
- Department of Neuropathology, Heinrich-Heine-University, Duesseldorf, Germany
| | - Claus U. Pietrzik
- Molecular Neurodegeneration Group, Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Bruno Bulic
- Research Group Chemical Biology of Neurodegenerative Diseases, Center of Advanced European Studies and Research, Bonn, Germany
- * E-mail: (BB); (SW)
| | - Sascha Weggen
- Department of Neuropathology, Heinrich-Heine-University, Duesseldorf, Germany
- * E-mail: (BB); (SW)
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39
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Wolfe MS. γ-Secretase as a target for Alzheimer's disease. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2012; 64:127-53. [PMID: 22840746 DOI: 10.1016/b978-0-12-394816-8.00004-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
γ-Secretase is a protease complex responsible for cutting the transmembrane domain of the amyloid β-protein precursor (APP) to form the amyloid β-protein (Aβ), an aggregation-prone product that accumulates in the brain in Alzheimer's disease. As evidence suggests that Aβ is critical to Alzheimer pathogenesis, γ-secretase is considered a key target for the development of disease-modifying therapeutics. The protease complex cuts many other substrates, and some of these proteolytic events are part of signaling pathways or other important cellular functions. Among these, proteolysis of the Notch receptor is essential for signaling that is involved in a number of cell-fate determinations. Many inhibitors of γ-secretase have been identified, but it is clear that drug candidates for Alzheimer's disease should have minimal effects on the Notch signaling pathway, as serious safety issues have arisen with nonselective inhibitors. Two types of promising candidates that target this protease complex have emerged: the so-called "Notch-sparing" γ-secretase inhibitors, which block cleavage of APP selectively over that of Notch, and γ-secretase modulators, which shift the proportion of Aβ peptides produced in favor of shorter, less aggregation-prone species. The current status and prospects for these two general types of candidates will be discussed.
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Affiliation(s)
- Michael S Wolfe
- Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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40
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Abstract
γ-Secretase is a membrane embedded aspartyl protease complex with presenilin as the catalytic component. Along with β-secretase, this enzyme produces the amyloid β-protein of Alzheimer's disease (AD) from the amyloid β-protein precursor. Because of its key role in the pathogenesis of AD, γ-secretase has been a prime target for drug discovery, and many inhibitors of this protease have been developed. The therapeutic potential of these inhibitors is virtually negated by the fact that γ-secretase is an essential part of the Notch signaling pathway, rendering the compounds unacceptably toxic upon chronic exposure. However, these compounds have served as useful chemical tools for biological investigations. In contrast, γ-secretase modulators continue to be of keen interest as possible AD therapeutics. These modulators either shift amyloid β-protein production to shorter, less pathogenic peptides or inhibit the proteolysis of amyloid β-protein precursor selectively compared to that of Notch. The various chemical types of inhibitors and modulators will be discussed, along with their use as probes for basic biology and their potential as AD therapeutics.
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Affiliation(s)
- Michael S Wolfe
- Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
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41
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Crump CJ, Fish BA, Castro SV, Chau DM, Gertsik N, Ahn K, Stiff C, Pozdnyakov N, Bales KR, Johnson DS, Li YM. Piperidine acetic acid based γ-secretase modulators directly bind to Presenilin-1. ACS Chem Neurosci 2011; 2:705-710. [PMID: 22229075 DOI: 10.1021/cn200098p] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Aβ42 is believed to play a causative role in Alzheimer's disease (AD) pathogenesis. γ-Secretase modulators (GSMs) are actively being pursued as potential AD therapeutics because they selectively alter the cleavage site of the amyloid precursor protein (APP) to reduce the formation of Aβ42. However, the binding partner of acid based GSMs was unresolved until now. We have developed clickable photoaffinity probes based on piperidine acetic acid GSM-1 and identified PS1 as the target within the γ-secretase complex. Furthermore, we provide evidence that allosteric interaction of GSMs with PS1 results in a conformational change in the active site of the γ-secretase complex leading to the observed modulation of γ-secretase activity.
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Affiliation(s)
- Christina J. Crump
- Molecular Pharmacology
and Chemistry
Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
| | - Benjamin A. Fish
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340,
United States
| | - Suita V. Castro
- Molecular Pharmacology
and Chemistry
Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
| | - De-Ming Chau
- Molecular Pharmacology
and Chemistry
Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
| | - Natalya Gertsik
- Molecular Pharmacology
and Chemistry
Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
| | - Kwangwook Ahn
- Molecular Pharmacology
and Chemistry
Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
| | - Cory Stiff
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340,
United States
| | - Nikolay Pozdnyakov
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340,
United States
| | - Kelly R. Bales
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340,
United States
| | - Douglas S. Johnson
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340,
United States
| | - Yue-Ming Li
- Molecular Pharmacology
and Chemistry
Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
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42
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Ohki Y, Higo T, Uemura K, Shimada N, Osawa S, Berezovska O, Yokoshima S, Fukuyama T, Tomita T, Iwatsubo T. Phenylpiperidine-type γ-secretase modulators target the transmembrane domain 1 of presenilin 1. EMBO J 2011; 30:4815-24. [PMID: 22002539 DOI: 10.1038/emboj.2011.372] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Accepted: 09/21/2011] [Indexed: 01/30/2023] Open
Abstract
Amyloid-β peptide ending at the 42nd residue (Aβ42) is implicated in the pathogenesis of Alzheimer's disease (AD). Small compounds that exhibit selective lowering effects on Aβ42 production are termed γ-secretase modulators (GSMs) and are deemed as promising therapeutic agents against AD, although the molecular target as well as the mechanism of action remains controversial. Here, we show that a phenylpiperidine-type compound GSM-1 directly targets the transmembrane domain (TMD) 1 of presenilin 1 (PS1) by photoaffinity labelling experiments combined with limited digestion. Binding of GSM-1 affected the structure of the initial substrate binding and the catalytic sites of the γ-secretase, thereby decreasing production of Aβ42, possibly by enhancing its conversion to Aβ38. These data indicate an allosteric action of GSM-1 by directly binding to the TMD1 of PS1, pinpointing the target structure of the phenylpiperidine-type GSMs.
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Affiliation(s)
- Yu Ohki
- Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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43
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Shi H, Uttamchandani M, Yao SQ. Applying Small Molecule Microarrays and Resulting Affinity Probe Cocktails for Proteome Profiling of Mammalian Cell Lysates. Chem Asian J 2011; 6:2803-15. [DOI: 10.1002/asia.201100523] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Indexed: 12/22/2022]
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Dubinsky L, Krom BP, Meijler MM. Diazirine based photoaffinity labeling. Bioorg Med Chem 2011; 20:554-70. [PMID: 21778062 DOI: 10.1016/j.bmc.2011.06.066] [Citation(s) in RCA: 283] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 06/19/2011] [Accepted: 06/24/2011] [Indexed: 10/17/2022]
Abstract
Diazirines are among the smallest photoreactive groups that form a reactive carbene upon light irradiation. This feature has been widely utilized in photoaffinity labeling to study ligand-receptor, ligand-enzyme and protein-protein interactions, and in the isolation and identification of unknown proteins. This review summarizes recent advances in the use of diazirines in photoaffinity labeling.
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Affiliation(s)
- Luba Dubinsky
- Department of Chemistry and National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
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45
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Ling S, Zhou J, Rudd JA, Hu Z, Fang M. The recent updates of therapeutic approaches against aβ for the treatment of Alzheimer's disease. Anat Rec (Hoboken) 2011; 294:1307-18. [PMID: 21717585 DOI: 10.1002/ar.21425] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 04/30/2011] [Indexed: 12/21/2022]
Abstract
One of the main neuropathological lesions observed in brain autopsy of Alzheimer's disease (AD) patients is the extracellular senile plaques mainly composed of amyloid-beta (Aβ) peptide. Recently, treatment strategies have focused on modifying the formation, clearance, and accumulation of this potentially neurotoxic peptide. β- and γ-secretase are responsible for the cleavage of amyloid precursor protein (APP) and the generation of Aβ peptide. Treatments targeting these two critical secretases may therefore reduce Aβ peptide levels and positive impact on AD. Vaccination is also an advanced approach against Aβ. This review focuses on recent advances of our understanding of this key peptide, with emphasis on Aβ peptide synthesis, accumulation and neurotoxicity, and current therapies including vaccination and two critical secretase inhibitors. MicroRNAs (miRNAs) are a class of conserved endogenous small noncoding RNAs, known to regulate the expression of complementary messenger RNAs, involved in AD development. We therefore address the relationship of miRNAs in the brain and Aβ generation, as a novel therapeutic approach to the treatment of AD while also providing new insights on the etiology of this neurological disorder.
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Affiliation(s)
- Shucai Ling
- Institute of Anatomy and Cell Biology, Medical College, Zhejiang University, Hangzhou, China
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Miyashita H, Maruyama Y, Isshiki H, Osawa S, Ogura T, Mio K, Sato C, Tomita T, Iwatsubo T. Three-dimensional structure of the signal peptide peptidase. J Biol Chem 2011; 286:26188-97. [PMID: 21636854 DOI: 10.1074/jbc.m111.260273] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Signal peptide peptidase (SPP) is an atypical aspartic protease that hydrolyzes peptide bonds within the transmembrane domain of substrates and is implicated in several biological and pathological functions. Here, we analyzed the structure of human SPP by electron microscopy and reconstructed the three-dimensional structure at a resolution of 22 Å. Enzymatically active SPP forms a slender, bullet-shaped homotetramer with dimensions of 85 × 85 × 130 Å. The SPP complex has four concaves on the rhombus-like sides, connected to a large chamber inside the molecule. Intriguingly, the N-terminal region of SPP is sufficient for the tetrameric assembly. Moreover, overexpression of the N-terminal region inhibited the formation of the endogenous SPP tetramer and the proteolytic activity within cells. These data suggest that the homotetramer is the functional unit of SPP and that its N-terminal region, which works as the structural scaffold, has a novel modulatory function for the intramembrane-cleaving activity of SPP.
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Affiliation(s)
- Hiroyuki Miyashita
- Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
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47
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Geurink PP, Prely LM, van der Marel GA, Bischoff R, Overkleeft HS. Photoaffinity labeling in activity-based protein profiling. Top Curr Chem (Cham) 2011; 324:85-113. [PMID: 22028098 DOI: 10.1007/128_2011_286] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Activity-based protein profiling has come to the fore in recent years as a powerful strategy for studying enzyme activities in their natural surroundings. Substrate analogs that bind covalently and irreversibly to an enzyme active site and that are equipped with an identification or affinity tag can be used to unearth new enzyme activities, to establish whether and at what subcellular location the enzymes are active, and to study the inhibitory effects of small compounds. A specific class of activity-based protein probes includes those that employ a photo-activatable group to create the covalent bond. Such probes are targeted to those enzymes that do not employ a catalytic nucleophile that is part of the polypeptide backbone. An overview of the various photo-activatable groups that are available to chemical biology researchers is presented, with a focus on their (photo)chemistry and their application in various research fields. A number of comparative studies are described in which the efficiency of various photo-activatable groups are compared.
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Affiliation(s)
- Paul P Geurink
- Leiden Institute of Chemistry and the Netherlands Proteomics Centre, Leiden University, The Netherlands
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48
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Shi H, Cheng X, Sze SK, Yao SQ. Proteome profiling reveals potential cellular targets of staurosporine using a clickable cell-permeable probe. Chem Commun (Camb) 2011; 47:11306-8. [DOI: 10.1039/c1cc14824a] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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49
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Participation of transmembrane domain 1 of presenilin 1 in the catalytic pore structure of the γ-secretase. J Neurosci 2010; 30:15943-50. [PMID: 21106832 DOI: 10.1523/jneurosci.3318-10.2010] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
γ-Secretase is an intramembrane-cleaving protease that is responsible for the generation of amyloid-β peptides linked to the pathogenesis of Alzheimer's disease. Using a substituted cysteine accessibility method, we have previously shown that the hydrophilic "catalytic pore" structure of γ-secretase is formed by the transmembrane domains (TMDs) 6, 7, and 9 of presenilin 1 (PS1), the catalytic subunit of γ-secretase, within the membrane. Here, we analyzed the structure in and around the first hydrophobic region, the putative TMD1, of PS1, of which the precise function as well as three-dimensional location within γ-secretase remained unknown. We found that TMD1 is located in proximity to the catalytic GxGD and PAL motifs within the C-terminal fragment of PS1, facing directly the catalytic pore. Competition experiments using known γ-secretase inhibitors suggested that the N-terminal region of TMD1 functions as a subsite during proteolytic action of the γ-secretase. Intriguingly, binding of inhibitors affected water accessibility of residues at the membrane border of TMD1, suggesting the possibility of a dynamic motion of TMD1 during the catalytic process. Our results provide mechanistic insights into the functional role of TMD1 of PS1 in the intramembrane-cleaving activity of the γ-secretase.
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50
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Tomita T. [Alzheimer's disease treatment by inhibition/modulation of the gamma-secretase activity]. Rinsho Shinkeigaku 2010; 49:845-7. [PMID: 20030227 DOI: 10.5692/clinicalneurol.49.845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Several lines of evidence indicate that the production and deposition of amyloid-beta peptides (Abeta) contribute to the etiology of Alzheimer's disease. Inhibition or modulation of gamma-secretase, that is a responsible enzyme for the Abeta production, is one of the plausible therapeutics for Alzheimer's disease. However, the gamma-secretase is an unusual aspartic protease that cleaves the scissile bond within the transmembrane domain of several membrane protein including APP and Notch receptor. Thus, development of drugs that regulate the production of Abeta without affecting the Notch signaling is now demanding. Extensive drug screening and development allow that some secretase inhibitors and modulators have advanced into late-phase clinical trials, whereas the molecular mechanisms of Notch-sparing effect by these compounds effect still remain unknown. Identification of the molecular targets and mechanisms of these compounds using chemical biological approaches is currently underway. This review focuses on the recent development of inhibitors/modulators and provides a direction for the effective treatment of AD through inhibition/modulation of the gamma-secretase activity.
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Affiliation(s)
- Taisuke Tomita
- Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo
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