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Hauf S, Rotrattanadumrong R, Yokobayashi Y. Analysis of the Sequence Preference of Saporin by Deep Sequencing. ACS Chem Biol 2022; 17:2619-2630. [PMID: 35969718 PMCID: PMC9486812 DOI: 10.1021/acschembio.2c00531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/29/2022] [Indexed: 01/19/2023]
Abstract
Ribosome-inactivating proteins (RIPs) are RNA:adenosine glycosidases that inactivate eukaryotic ribosomes by depurinating the sarcin-ricin loop (SRL) in 28S rRNA. The GAGA sequence at the top of the SRL or at the top of a hairpin loop is assumed to be their target motif. Saporin is a RIP widely used to develop immunotoxins for research and medical applications, but its sequence specificity has not been investigated. Here, we combine the conventional aniline cleavage assay for depurinated nucleic acids with high-throughput sequencing to study sequence-specific depurination of oligonucleotides caused by saporin. Our data reveal the sequence preference of saporin for different substrates and show that the GAGA motif is not efficiently targeted by this protein, neither in RNA nor in DNA. Instead, a preference of saporin for certain hairpin DNAs was observed. The observed sequence-specific activity of saporin may be relevant to antiviral or apoptosis-inducing effects of RIPs. The developed method could also be useful for studying the sequence specificity of depurination by other RIPs or enzymes.
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Affiliation(s)
- Samuel Hauf
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science
and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Rachapun Rotrattanadumrong
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science
and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science
and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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2
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Abstract
Transition state theory teaches that chemically stable mimics of enzymatic transition states will bind tightly to their cognate enzymes. Kinetic isotope effects combined with computational quantum chemistry provides enzymatic transition state information with sufficient fidelity to design transition state analogues. Examples are selected from various stages of drug development to demonstrate the application of transition state theory, inhibitor design, physicochemical characterization of transition state analogues, and their progress in drug development.
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Affiliation(s)
- Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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3
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Plant Ribosome-Inactivating Proteins: Progesses, Challenges and Biotechnological Applications (and a Few Digressions). Toxins (Basel) 2017; 9:toxins9100314. [PMID: 29023422 PMCID: PMC5666361 DOI: 10.3390/toxins9100314] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/29/2017] [Accepted: 10/03/2017] [Indexed: 12/11/2022] Open
Abstract
Plant ribosome-inactivating protein (RIP) toxins are EC3.2.2.22 N-glycosidases, found among most plant species encoded as small gene families, distributed in several tissues being endowed with defensive functions against fungal or viral infections. The two main plant RIP classes include type I (monomeric) and type II (dimeric) as the prototype ricin holotoxin from Ricinus communis that is composed of a catalytic active A chain linked via a disulphide bridge to a B-lectin domain that mediates efficient endocytosis in eukaryotic cells. Plant RIPs can recognize a universally conserved stem-loop, known as the α-sarcin/ ricin loop or SRL structure in 23S/25S/28S rRNA. By depurinating a single adenine (A4324 in 28S rat rRNA), they can irreversibly arrest protein translation and trigger cell death in the intoxicated mammalian cell. Besides their useful application as potential weapons against infected/tumor cells, ricin was also used in bio-terroristic attacks and, as such, constitutes a major concern. In this review, we aim to summarize past studies and more recent progresses made studying plant RIPs and discuss successful approaches that might help overcoming some of the bottlenecks encountered during the development of their biomedical applications.
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5
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Oligonucleotide transition state analogues of saporin L3. Eur J Med Chem 2016; 127:793-809. [PMID: 27823883 DOI: 10.1016/j.ejmech.2016.10.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/14/2016] [Accepted: 10/26/2016] [Indexed: 11/24/2022]
Abstract
Ribosome inactivating proteins (RIPs) are among the most toxic agents known. More than a dozen clinical trials against refractory cancers have been initiated using modified RIPs with impressive results. However, dose-limiting toxicity due to vascular leak syndrome limits success of the therapy. We have previously reported some tight-binding transition state analogues of Saporin L3 that mimic small oligonucleotide substrates in which the susceptible adenosine has been replaced by a 9-deazaadenyl hydroxypyrrolidinol derivative. They provide the first step in the development of rescue agents to prevent Saporin L3 toxicity on non-targeted cells. Here we report the synthesis, using solution phase chemistry, of these and a larger group of transition state analogues. They were tested for inhibition against Saporin L3 giving Ki values as low as 3.3 nM and indicating the structural requirements for inhibition.
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6
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Yuan H, Stratton CF, Schramm VL. Transition State Structure of RNA Depurination by Saporin L3. ACS Chem Biol 2016; 11:1383-90. [PMID: 26886255 DOI: 10.1021/acschembio.5b01069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Saporin L3 from the leaves of the common soapwort is a catalyst for hydrolytic depurination of adenine from RNA. Saporin L3 is a type 1 ribosome inactivating protein (RIP) composed only of a catalytic domain. Other RIPs have been used in immunotoxin cancer therapy, but off-target effects have limited their development. In the current study, we use transition state theory to understand the chemical mechanism and transition state structure of saporin L3. In favorable cases, transition state structures guide the design of transition state analogues as inhibitors. Kinetic isotope effects (KIEs) were determined for an A14C mutant of saporin L3. To permit KIE measurements, small stem-loop RNAs that contain an AGGG tetraloop structure were enzymatically synthesized with the single adenylate bearing specific isotopic substitutions. KIEs were measured and corrected for forward commitment to obtain intrinsic values. A model of the transition state structure for depurination of stem-loop RNA (5'-GGGAGGGCCC-3') by saporin L3 was determined by matching KIE values predicted via quantum chemical calculations to a family of intrinsic KIEs. This model indicates saporin L3 displays a late transition state with the N-ribosidic bond to the adenine nearly cleaved, and the attacking water nucleophile weakly bonded to the ribosyl anomeric carbon. The transition state retains partial ribocation character, a feature common to most N-ribosyl transferases. However, the transition state geometry for saporin L3 is distinct from ricin A-chain, the only other RIP whose transition state is known.
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Affiliation(s)
- Hongling Yuan
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Christopher F. Stratton
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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7
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Hohn C, Härtsch A, Ehrmann FR, Pfaffeneder T, Trapp N, Dumele O, Klebe G, Diederich F. An Immucillin-Based Transition-State-Analogous Inhibitor of tRNA-Guanine Transglycosylase (TGT). Chemistry 2016; 22:6750-4. [PMID: 26991861 DOI: 10.1002/chem.201600883] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Indexed: 11/06/2022]
Abstract
Shigellosis is one of the most severe diarrheal diseases worldwide without any efficient treatment so far. The enzyme tRNA-guanine transglycosylase (TGT) has been identified as a promising target for small-molecule drug design. Herein, we report a transition-state analogue, a small, immucillin-derived inhibitor, as a new lead structure with a novel mode of action. The complex inhibitor synthesis was accomplished in 18 steps with an overall yield of 3 %. A co-crystal structure of the inhibitor bound to Z. mobilis TGT confirmed the predicted conformation of the immucillin derivative in the enzyme active site.
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Affiliation(s)
- Christoph Hohn
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Adrian Härtsch
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Frederik Rainer Ehrmann
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Toni Pfaffeneder
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Oliver Dumele
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland.
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8
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Yuan H, Du Q, Sturm MB, Schramm VL. Soapwort Saporin L3 Expression in Yeast, Mutagenesis, and RNA Substrate Specificity. Biochemistry 2015; 54:4565-74. [PMID: 26091305 DOI: 10.1021/acs.biochem.5b00405] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Saporin L3 from Saponaria officinalis (soapwort) leaves is a type 1 ribosome-inactivating protein. It catalyzes the hydrolysis of oligonucleotide adenylate N-ribosidic bonds to release adenine from rRNA. Depurination sites include both adenines in the GAGA tetraloop of short sarcin-ricin stem-loops and multiple adenines within eukaryotic rRNA, tRNAs, and mRNAs. Multiple Escherichia coli vector designs for saporin L3 expression were attempted but demonstrated high toxicity even during plasmid maintenance and selection in E. coli nonexpression strains. Saporin L3 is >10(3) times more efficient at RNA deadenylation on short GAGA stem-loops than saporin S6, the saporin isoform currently used in immunotoxin clinical trials. We engineered a construct for the His-tagged saporin L3 to test for expression in Pichia pastoris when it is linked to the protein export system for the yeast α-mating factor. DNA encoding saporin L3 was cloned into a pPICZαB expression vector and expressed in P. pastoris under the alcohol dehydrogenase AOX1 promoter. A fusion protein of saporin L3 containing the pre-pro-sequence of the α-mating factor, the c-myc epitope, and the His tag was excreted from the P. pastoris cells and isolated from the culture medium. Autoprocessing of the α-mating factor yielded truncated saporin L3 (amino acids 22-280), the c-myc epitope, and the His tag expressed optimally as a 32 kDa construct following methanol induction. Saporin L3 was also expressed with specific alanines and/or serines mutated to cysteine. Native and Cys mutant saporins are kinetically similar. The recombinant expression of saporin L3 and its mutants permits the production and investigation of this high-activity ribosome-inactivating protein.
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Affiliation(s)
- Hongling Yuan
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Quan Du
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Matthew B Sturm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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9
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Schrot J, Weng A, Melzig MF. Ribosome-inactivating and related proteins. Toxins (Basel) 2015; 7:1556-615. [PMID: 26008228 PMCID: PMC4448163 DOI: 10.3390/toxins7051556] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 04/23/2015] [Accepted: 04/28/2015] [Indexed: 01/15/2023] Open
Abstract
Ribosome-inactivating proteins (RIPs) are toxins that act as N-glycosidases (EC 3.2.2.22). They are mainly produced by plants and classified as type 1 RIPs and type 2 RIPs. There are also RIPs and RIP related proteins that cannot be grouped into the classical type 1 and type 2 RIPs because of their different sizes, structures or functions. In addition, there is still not a uniform nomenclature or classification existing for RIPs. In this review, we give the current status of all known plant RIPs and we make a suggestion about how to unify those RIPs and RIP related proteins that cannot be classified as type 1 or type 2 RIPs.
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Affiliation(s)
- Joachim Schrot
- Institute of Pharmacy, Freie Universitaet Berlin, Koenigin-Luise-Str. 2 + 4, 14195 Berlin, Germany.
| | - Alexander Weng
- Institute of Pharmacy, Freie Universitaet Berlin, Koenigin-Luise-Str. 2 + 4, 14195 Berlin, Germany.
| | - Matthias F Melzig
- Institute of Pharmacy, Freie Universitaet Berlin, Koenigin-Luise-Str. 2 + 4, 14195 Berlin, Germany.
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Abstract
Enzymes achieve their transition states by dynamic conformational searches on the femtosecond to picosecond time scale. Mimics of reactants at enzymatic transition states bind tightly to enzymes by stabilizing the conformation optimized through evolution for transition state formation. Instead of forming the transient transition state geometry, transition state analogues convert the short-lived transition state to a stable thermodynamic state. Enzymatic transition states are understood by combining kinetic isotope effects and computational chemistry. Analogues of the transition state can bind millions of times more tightly than substrates and show promise for drug development for several targets.
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Affiliation(s)
- Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx New York 10461, United States.
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11
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Antonucci F, Alpár A, Kacza J, Caleo M, Verderio C, Giani A, Martens H, Chaudhry FA, Allegra M, Grosche J, Michalski D, Erck C, Hoffmann A, Harkany T, Matteoli M, Härtig W. Cracking down on inhibition: selective removal of GABAergic interneurons from hippocampal networks. J Neurosci 2012; 32:1989-2001. [PMID: 22323713 PMCID: PMC3742881 DOI: 10.1523/jneurosci.2720-11.2012] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 12/07/2011] [Accepted: 12/14/2011] [Indexed: 12/12/2022] Open
Abstract
Inhibitory (GABAergic) interneurons entrain assemblies of excitatory principal neurons to orchestrate information processing in the hippocampus. Disrupting the dynamic recruitment as well as the temporally precise activity of interneurons in hippocampal circuitries can manifest in epileptiform seizures, and impact specific behavioral traits. Despite the importance of GABAergic interneurons during information encoding in the brain, experimental tools to selectively manipulate GABAergic neurotransmission are limited. Here, we report the selective elimination of GABAergic interneurons by a ribosome inactivation approach through delivery of saporin-conjugated anti-vesicular GABA transporter antibodies (SAVAs) in vitro as well as in the mouse and rat hippocampus in vivo. We demonstrate the selective loss of GABAergic--but not glutamatergic--synapses, reduced GABA release, and a shift in excitation/inhibition balance in mixed cultures of hippocampal neurons exposed to SAVAs. We also show the focal and indiscriminate loss of calbindin(+), calretinin(+), parvalbumin/system A transporter 1(+), somatostatin(+), vesicular glutamate transporter 3 (VGLUT3)/cholecystokinin/CB(1) cannabinoid receptor(+) and neuropeptide Y(+) local-circuit interneurons upon SAVA microlesions to the CA1 subfield of the rodent hippocampus, with interneuron debris phagocytosed by infiltrating microglia. SAVA microlesions did not affect VGLUT1(+) excitatory afferents. Yet SAVA-induced rearrangement of the hippocampal circuitry triggered network hyperexcitability associated with the progressive loss of CA1 pyramidal cells and the dispersion of dentate granule cells. Overall, our data identify SAVAs as an effective tool to eliminate GABAergic neurons from neuronal circuits underpinning high-order behaviors and cognition, and whose manipulation can recapitulate pathogenic cascades of epilepsy and other neuropsychiatric illnesses.
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Affiliation(s)
- Flavia Antonucci
- Department of Medical Pharmacology, CNR Institute of Neuroscience, Università di Milano and
- Fondazione Filarete, I-20129 Milan, Italy
| | - Alán Alpár
- Division of Molecular Neurobiology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden
| | - Johannes Kacza
- Institute of Veterinary Anatomy, University of Leipzig, D-04103 Leipzig, Germany
| | - Matteo Caleo
- CNR Institute of Neuroscience, I-51600 Pisa, Italy
| | - Claudia Verderio
- Department of Medical Pharmacology, CNR Institute of Neuroscience, Università di Milano and
| | - Alice Giani
- Department of Medical Pharmacology, CNR Institute of Neuroscience, Università di Milano and
| | | | - Farrukh A. Chaudhry
- The Biotechnology Centre of Oslo & Centre for Molecular Biology and Neuroscience, University of Oslo, N-0317 Oslo, Norway
| | | | - Jens Grosche
- Paul Flechsig Institute for Brain Research, University of Leipzig, D-04109 Leipzig, Germany
| | - Dominik Michalski
- Department of Neurology, University of Leipzig, D-04103 Leipzig, Germany
| | | | - Anke Hoffmann
- Institute of Veterinary Anatomy, University of Leipzig, D-04103 Leipzig, Germany
| | - Tibor Harkany
- Division of Molecular Neurobiology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden
- European Neuroscience Institute, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom, and
| | - Michela Matteoli
- Department of Medical Pharmacology, CNR Institute of Neuroscience, Università di Milano and
- Instituto Clinico Humanitas, IRCCS, Rozzano, I-20089 Milan, Italy
| | - Wolfgang Härtig
- Paul Flechsig Institute for Brain Research, University of Leipzig, D-04109 Leipzig, Germany
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12
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Schramm VL. Enzymatic transition states, transition-state analogs, dynamics, thermodynamics, and lifetimes. Annu Rev Biochem 2011; 80:703-32. [PMID: 21675920 DOI: 10.1146/annurev-biochem-061809-100742] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Experimental analysis of enzymatic transition-state structures uses kinetic isotope effects (KIEs) to report on bonding and geometry differences between reactants and the transition state. Computational correlation of experimental values with chemical models permits three-dimensional geometric and electrostatic assignment of transition states formed at enzymatic catalytic sites. The combination of experimental and computational access to transition-state information permits (a) the design of transition-state analogs as powerful enzymatic inhibitors, (b) exploration of protein features linked to transition-state structure, (c) analysis of ensemble atomic motions involved in achieving the transition state, (d) transition-state lifetimes, and (e) separation of ground-state (Michaelis complexes) from transition-state effects. Transition-state analogs with picomolar dissociation constants have been achieved for several enzymatic targets. Transition states of closely related isozymes indicate that the protein's dynamic architecture is linked to transition-state structure. Fast dynamic motions in catalytic sites are linked to transition-state generation. Enzymatic transition states have lifetimes of femtoseconds, the lifetime of bond vibrations. Binding isotope effects (BIEs) reveal relative reactant and transition-state analog binding distortion for comparison with actual transition states.
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Affiliation(s)
- Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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13
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Chu AM, Fettinger JC, David SS. Profiling base excision repair glycosylases with synthesized transition state analogs. Bioorg Med Chem Lett 2011; 21:4969-72. [PMID: 21689934 DOI: 10.1016/j.bmcl.2011.05.085] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 05/20/2011] [Accepted: 05/23/2011] [Indexed: 11/28/2022]
Abstract
Two base excision repair glycosylase (BER) transition state (TS) mimics, (3R,4R)-1-benzyl (hydroxymethyl) pyrrolidin-3-ol (1NBn) and (3R,4R)-(hydroxymethyl) pyrrolidin-3-ol (1N), were synthesized using an improved method. Several BER glycosylases that repair oxidized DNA bases, bacterial formamidopyrimdine glycosylase (Fpg), human OG glycosylase (hOGG1) and human Nei-like glycosylase 1 (hNEIL1) exhibit exceptionally high affinity (K(d)∼pM) with DNA duplexes containing the 1NBn and 1N nucleotide. Notably, comparison of the K(d) values of both TS mimics relative to an abasic analog (THF) in duplex contexts paired opposite C or A suggest that these DNA repair enzymes use distinctly different mechanisms for damaged base recognition and catalysis despite having overlapping substrate specificities.
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Affiliation(s)
- Aurea M Chu
- Department of Chemistry, University of California, Davis, Building 143, One Shields Avenue, Davis, CA 95616, United States
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14
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Pang YP, Park JG, Wang S, Vummenthala A, Mishra RK, McLaughlin JE, Di R, Kahn JN, Tumer NE, Janosi L, Davis J, Millard CB. Small-molecule inhibitor leads of ribosome-inactivating proteins developed using the doorstop approach. PLoS One 2011; 6:e17883. [PMID: 21455295 PMCID: PMC3063779 DOI: 10.1371/journal.pone.0017883] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 02/16/2011] [Indexed: 11/19/2022] Open
Abstract
Ribosome-inactivating proteins (RIPs) are toxic because they bind to 28S rRNA and depurinate a specific adenine residue from the α-sarcin/ricin loop (SRL), thereby inhibiting protein synthesis. Shiga-like toxins (Stx1 and Stx2), produced by Escherichia coli, are RIPs that cause outbreaks of foodborne diseases with significant morbidity and mortality. Ricin, produced by the castor bean plant, is another RIP lethal to mammals. Currently, no US Food and Drug Administration-approved vaccines nor therapeutics exist to protect against ricin, Shiga-like toxins, or other RIPs. Development of effective small-molecule RIP inhibitors as therapeutics is challenging because strong electrostatic interactions at the RIP•SRL interface make drug-like molecules ineffective in competing with the rRNA for binding to RIPs. Herein, we report small molecules that show up to 20% cell protection against ricin or Stx2 at a drug concentration of 300 nM. These molecules were discovered using the doorstop approach, a new approach to protein•polynucleotide inhibitors that identifies small molecules as doorstops to prevent an active-site residue of an RIP (e.g., Tyr80 of ricin or Tyr77 of Stx2) from adopting an active conformation thereby blocking the function of the protein rather than contenders in the competition for binding to the RIP. This work offers promising leads for developing RIP therapeutics. The results suggest that the doorstop approach might also be applicable in the development of other protein•polynucleotide inhibitors as antiviral agents such as inhibitors of the Z-DNA binding proteins in poxviruses. This work also calls for careful chemical and biological characterization of drug leads obtained from chemical screens to avoid the identification of irrelevant chemical structures and to avoid the interference caused by direct interactions between the chemicals being screened and the luciferase reporter used in screening assays.
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Affiliation(s)
- Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail: (YPP, chemistry); (NET, biology); (CBM, biology)
| | - Jewn Giew Park
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Shaohua Wang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Anuradha Vummenthala
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Rajesh K. Mishra
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
| | - John E. McLaughlin
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Rong Di
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Jennifer Nielsen Kahn
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Nilgun E. Tumer
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail: (YPP, chemistry); (NET, biology); (CBM, biology)
| | - Laszlo Janosi
- Division of Biochemistry, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Jon Davis
- Division of Biochemistry, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Charles B. Millard
- Division of Biochemistry, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- * E-mail: (YPP, chemistry); (NET, biology); (CBM, biology)
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15
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de Virgilio M, Lombardi A, Caliandro R, Fabbrini MS. Ribosome-inactivating proteins: from plant defense to tumor attack. Toxins (Basel) 2010; 2:2699-737. [PMID: 22069572 PMCID: PMC3153179 DOI: 10.3390/toxins2112699] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 10/29/2010] [Accepted: 11/04/2010] [Indexed: 12/02/2022] Open
Abstract
Ribosome-inactivating proteins (RIPs) are EC3.2.32.22 N-glycosidases that recognize a universally conserved stem-loop structure in 23S/25S/28S rRNA, depurinating a single adenine (A4324 in rat) and irreversibly blocking protein translation, leading finally to cell death of intoxicated mammalian cells. Ricin, the plant RIP prototype that comprises a catalytic A subunit linked to a galactose-binding lectin B subunit to allow cell surface binding and toxin entry in most mammalian cells, shows a potency in the picomolar range. The most promising way to exploit plant RIPs as weapons against cancer cells is either by designing molecules in which the toxic domains are linked to selective tumor targeting domains or directly delivered as suicide genes for cancer gene therapy. Here, we will provide a comprehensive picture of plant RIPs and discuss successful designs and features of chimeric molecules having therapeutic potential.
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Affiliation(s)
| | - Alessio Lombardi
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Milan, Italy;
| | - Rocco Caliandro
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Bari, Italy;
| | - Maria Serena Fabbrini
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Milan, Italy;
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16
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Lombardi A, Marshall RS, Savino C, Fabbrini MS, Ceriotti A. Type I Ribosome-Inactivating Proteins from Saponaria officinalis. TOXIC PLANT PROTEINS 2010. [DOI: 10.1007/978-3-642-12176-0_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins. Proc Natl Acad Sci U S A 2009; 106:20276-81. [PMID: 19920175 DOI: 10.1073/pnas.0911606106] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ricin A-chain (RTA) and saporin-L1 (SAP) catalyze adenosine depurination of 28S rRNA to inhibit protein synthesis and cause cell death. We present the crystal structures of RTA and SAP in complex with transition state analogue inhibitors. These tight-binding inhibitors mimic the sarcin-ricin recognition loop of 28S rRNA and the dissociative ribocation transition state established for RTA catalysis. RTA and SAP share unique purine-binding geometry with quadruple pi-stacking interactions between adjacent adenine and guanine bases and 2 conserved tyrosines. An arginine at one end of the pi-stack provides cationic polarization and enhanced leaving group ability to the susceptible adenine. Common features of these ribosome-inactivating proteins include adenine leaving group activation, a remarkable lack of ribocation stabilization, and conserved glutamates as general bases for activation of the H(2)O nucleophile. Catalytic forces originate primarily from leaving group activation evident in both RTA and SAP in complex with transition state analogues.
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