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Omeershffudin UNM, Kumar S. Antibiotic resistance in Neisseria gonorrhoeae: broad-spectrum drug target identification using subtractive genomics. Genomics Inform 2023; 21:e5. [PMID: 37037463 PMCID: PMC10085745 DOI: 10.5808/gi.22066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 04/03/2023] Open
Abstract
Neisseria gonorrhoeae is a Gram-negative aerobic diplococcus bacterium that primarily causes sexually transmitted infections through direct human sexual contact. It is a major public health threat due to its impact on reproductive health, the widespread presence of antimicrobial resistance, and the lack of a vaccine. In this study, we used a bioinformatics approach and performed subtractive genomic methods to identify potential drug targets against the core proteome of N. gonorrhoeae (12 strains). In total, 12,300 protein sequences were retrieved, and paralogous proteins were removed using CD-HIT. The remaining sequences were analyzed for non-homology against the human proteome and gut microbiota, and screened for broad-spectrum analysis, druggability, and anti-target analysis. The proteins were also characterized for unique interactions between the host and pathogen through metabolic pathway analysis. Based on the subtractive genomic approach and subcellular localization, we identified one cytoplasmic protein, 2Fe-2S iron-sulfur cluster binding domain-containing protein (NGFG RS03485), as a potential drug target. This protein could be further exploited for drug development to create new medications and therapeutic agents for the treatment of N. gonorrhoeae infections.
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Affiliation(s)
| | - Suresh Kumar
- Faculty of Health and Life Sciences, Management and Science University, Seksyen 13, 40100, Shah Alam, Selangor, Malaysia
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2
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Patel KB, Kononova O, Cai S, Barsegov V, Parmar VS, Kumar R, Singh BR. Botulinum neurotoxin inhibitor binding dynamics and kinetics relevant for drug design. Biochim Biophys Acta Gen Subj 2021; 1865:129933. [PMID: 34023445 DOI: 10.1016/j.bbagen.2021.129933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/05/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND A natural product analog, 3-(4-nitrophenyl)-7H-furo[3,2-g]chromen-7-one, which is a nitrophenyl psoralen (NPP) was found to be an effective inhibitor of botulinum neurotoxin type A (BoNT/A). METHODS In this work, we performed enzyme inhibition kinetics and employed biochemical techniques such as isothermal calorimetry (ITC) and fluorescence spectroscopy as well as molecular modeling to examine the kinetics and binding mechanism of NPP inhibitor with BoNT/A LC. RESULTS Studies of inhibition mechanism and binding dynamics of NPP to BoNT/A light chain (BoNT/A LC) showed that NPP is a mixed type inhibitor for the zinc endopeptidase activity, implying that at least part of the inhibitor-enzyme binding site may be different from the substrate-enzyme binding site. By using biochemical techniques, we demonstrated NPP forms a stable complex with BoNT/A LC. These observations were confirmed by Molecular Dynamics (MD) simulation, which demonstrates that NPP binds to the site near the active site. CONCLUSION The NPP binding interferes with BoNT/A LC binding to the SNAP-25, hence, inhibits its cleavage. Based on these results, we propose a modified strategy for designing a molecule to enhance the efficiency of the inhibition against the neurotoxic effect of BoNT. GENERAL SIGNIFICANCE Insights into the interactions of NPP with BoNT/A LC using biochemical and computational approaches will aid in the future development of effective countermeasures and better pharmacological strategies against botulism.
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Affiliation(s)
- Kruti B Patel
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA; Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, USA
| | - Olga Kononova
- Department of Chemistry and Biochemistry, University of Massachusetts Lowell, Lowell, MA, USA
| | - Shuowei Cai
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, USA
| | - Valeri Barsegov
- Department of Chemistry and Biochemistry, University of Massachusetts Lowell, Lowell, MA, USA
| | - Virinder S Parmar
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA; Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Raj Kumar
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA
| | - Bal Ram Singh
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA; Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, USA; Prime Bio Inc., Dartmouth, MA, USA.
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3
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Thompson JC, Dao WT, Ku A, Rodriguez-Beltran SL, Amezcua M, Palomino AY, Lien T, Salzameda NT. Synthesis and activity of isoleucine sulfonamide derivatives as novel botulinum neurotoxin serotype A light chain inhibitors. Bioorg Med Chem 2020; 28:115659. [PMID: 32828426 DOI: 10.1016/j.bmc.2020.115659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/07/2020] [Accepted: 07/10/2020] [Indexed: 11/20/2022]
Abstract
The botulinum neurotoxin (BoNT) is the most lethal protein known to man causing the deadly disease botulinum. The neurotoxin, composed of a heavy (HC) and light (LC) chain, work in concert to cause muscle paralysis. A therapeutic strategy to treat individuals infected with the neurotoxin is inhibiting the catalytic activity of the BoNT LC. We report the synthesis, inhibition study and computational docking analysis of novel small molecule BoNT/A LC inhibitors. A structure activity relationship study resulted in the discovery of d-isoleucine functionalized with a hydroxamic acid on the C-terminal and a biphenyl with chlorine at C- 2 connected by a sulfonamide linker at the N-terminus. This compound has a measured IC50 of 0.587 µM for the BoNT/A LC. Computational docking analysis indicates the sulfonamide linker adopts a geometry that is advantageous for binding to the BoNT LC active site. In addition, Arg363 is predicted to be involved in key binding interactions with the scaffold in this study.
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Affiliation(s)
- Jordan C Thompson
- Department of Chemistry & Biochemistry, California State University, 800 N. State College, Fullerton, CA, 92834, USA
| | - Wendy T Dao
- Department of Chemistry & Biochemistry, California State University, 800 N. State College, Fullerton, CA, 92834, USA
| | - Alex Ku
- Department of Chemistry & Biochemistry, California State University, 800 N. State College, Fullerton, CA, 92834, USA
| | - Sandra L Rodriguez-Beltran
- Department of Chemistry & Biochemistry, California State University, 800 N. State College, Fullerton, CA, 92834, USA
| | - Martin Amezcua
- Department of Chemistry & Biochemistry, California State University, 800 N. State College, Fullerton, CA, 92834, USA
| | - Alejandra Y Palomino
- Department of Chemistry & Biochemistry, California State University, 800 N. State College, Fullerton, CA, 92834, USA
| | - Thanh Lien
- Department of Chemistry & Biochemistry, California State University, 800 N. State College, Fullerton, CA, 92834, USA
| | - Nicholas T Salzameda
- Department of Chemistry & Biochemistry, California State University, 800 N. State College, Fullerton, CA, 92834, USA.
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4
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Kumar R, Maksudov F, Kononova O, Marx KA, Barsegov V, Singh BR. Botulinum Endopeptidase: SAXS Experiments and MD Simulations Reveal Extended Solution Structures That Account for Its Biochemical Properties. J Phys Chem B 2020; 124:5801-5812. [PMID: 32543194 DOI: 10.1021/acs.jpcb.0c02817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Development of antidotes against botulism requires understanding of the enzymatically active conformations of Botulinum neurotoxin serotype A (BoNT/A) light chain (LCA). We performed small angle X-ray scattering (SAXS) to characterize the solution structures of truncated light chain (tLCA). The 34-37 Å radius of gyration of tLCA was 1.5-times greater than the averaged 22-23-Å radius from the crystal structures. The bimodal distribution of interatomic distances P(r) indicated the two-domain tLCA structure with 129-133 Å size, and Kratky plots indicated the tLCA partial unfolding in the 25-37 °C temperature range. To interpret these data, we employed molecular dynamics simulations and machine learning. Excellent agreement between experimental and theoretical P(r) profiles helped to resolve conformational subpopulations of tLCA in solution. Partial unfolding of the C-terminal portion of tLCA (residues 339-425) results in formation of extended conformations with the larger globular domain (residues 2-298) and the smaller unstructured domain (339-425). The catalytic domain, buried 20 Å-deep inside the crystal structure, becomes accessible in extended solution conformations (8-9 Å deep). The C- and N-termini containing different functional sequence motifs are maximally separated in the extended conformations. Our results offer physical insights into the molecular basis of BoNT/A function and stress the importance of reversible unfolding-refolding transitions and hydrophobic interactions.
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Affiliation(s)
- Raj Kumar
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, Massachusetts 02747, United States
| | - Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
| | - Olga Kononova
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
| | - Kenneth A Marx
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
| | - Bal Ram Singh
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, Massachusetts 02747, United States
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5
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An Appraisal of Antidotes' Effectiveness: Evidence of the Use of Phyto-Antidotes and Biotechnological Advancements. Molecules 2020; 25:molecules25071516. [PMID: 32225103 PMCID: PMC7181008 DOI: 10.3390/molecules25071516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/20/2022] Open
Abstract
Poisoning is the greatest source of avoidable death in the world and can result from industrial exhausts, incessant bush burning, drug overdose, accidental toxication or snake envenomation. Since the advent of Albert Calmette’s cobra venom antidote, efforts have been geared towards antidotes development for various poisons to date. While there are resources and facilities to tackle poisoning in urban areas, rural areas and developing countries are challenged with poisoning management due to either the absence of or inadequate facilities and this has paved the way for phyto-antidotes, some of which have been scientifically validated. This review presents the scope of antidotes’ effectiveness in different experimental models and biotechnological advancements in antidote research for future applications. While pockets of evidence of the effectiveness of antidotes exist in vitro and in vivo with ample biotechnological developments, the utilization of analytic assays on existing and newly developed antidotes that have surpassed the proof of concept stage, as well as the inclusion of antidote’s short and long-term risk assessment report, will help in providing the required scientific evidence(s) prior to regulatory authorities’ approval.
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6
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Omersa N, Podobnik M, Anderluh G. Inhibition of Pore-Forming Proteins. Toxins (Basel) 2019; 11:E545. [PMID: 31546810 PMCID: PMC6784129 DOI: 10.3390/toxins11090545] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/27/2019] [Accepted: 09/10/2019] [Indexed: 12/16/2022] Open
Abstract
Perforation of cellular membranes by pore-forming proteins can affect cell physiology, tissue integrity, or immune response. Since many pore-forming proteins are toxins or highly potent virulence factors, they represent an attractive target for the development of molecules that neutralize their actions with high efficacy. There has been an assortment of inhibitors developed to specifically obstruct the activity of pore-forming proteins, in addition to vaccination and antibiotics that serve as a plausible treatment for the majority of diseases caused by bacterial infections. Here we review a wide range of potential inhibitors that can specifically and effectively block the activity of pore-forming proteins, from small molecules to more specific macromolecular systems, such as synthetic nanoparticles, antibodies, antibody mimetics, polyvalent inhibitors, and dominant negative mutants. We discuss their mechanism of inhibition, as well as advantages and disadvantages.
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Affiliation(s)
- Neža Omersa
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
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7
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Agnew HD, Coppock MB, Idso MN, Lai BT, Liang J, McCarthy-Torrens AM, Warren CM, Heath JR. Protein-Catalyzed Capture Agents. Chem Rev 2019; 119:9950-9970. [PMID: 30838853 DOI: 10.1021/acs.chemrev.8b00660] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein-catalyzed capture agents (PCCs) are synthetic and modular peptide-based affinity agents that are developed through the use of single-generation in situ click chemistry screens against large peptide libraries. In such screens, the target protein, or a synthetic epitope fragment of that protein, provides a template for selectively promoting the noncopper catalyzed azide-alkyne dipolar cycloaddition click reaction between either a library peptide and a known ligand or a library peptide and the synthetic epitope. The development of epitope-targeted PCCs was motivated by the desire to fully generalize pioneering work from the Sharpless and Finn groups in which in situ click screens were used to develop potent, divalent enzymatic inhibitors. In fact, a large degree of generality has now been achieved. Various PCCs have demonstrated utility for selective protein detection, as allosteric or direct inhibitors, as modulators of protein folding, and as tools for in vivo tumor imaging. We provide a historical context for PCCs and place them within the broader scope of biological and synthetic aptamers. The development of PCCs is presented as (i) Generation I PCCs, which are branched ligands engineered through an iterative, nonepitope-targeted process, and (ii) Generation II PCCs, which are typically developed from macrocyclic peptide libraries and are precisely epitope-targeted. We provide statistical comparisons of Generation II PCCs relative to monoclonal antibodies in which the protein target is the same. Finally, we discuss current challenges and future opportunities of PCCs.
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Affiliation(s)
- Heather D Agnew
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - Matthew B Coppock
- Sensors and Electron Devices Directorate , U.S. Army Research Laboratory , Adelphi , Maryland 20783 , United States
| | - Matthew N Idso
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Bert T Lai
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - JingXin Liang
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Amy M McCarthy-Torrens
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Carmen M Warren
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - James R Heath
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
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8
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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9
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Natural Compounds and Their Analogues as Potent Antidotes against the Most Poisonous Bacterial Toxin. Appl Environ Microbiol 2018; 84:AEM.01280-18. [PMID: 30389764 DOI: 10.1128/aem.01280-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/28/2018] [Indexed: 01/30/2023] Open
Abstract
Botulinum neurotoxins (BoNTs), the most poisonous proteins known to humankind, are a family of seven (serotype A to G) immunologically distinct proteins synthesized primarily by different strains of the anaerobic bacterium Clostridium botulinum Being the causative agents of botulism, the toxins block neurotransmitter release by specifically cleaving one of the three soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) proteins, thereby inducing flaccid paralysis. The development of countermeasures and therapeutics against BoNTs is a high-priority research area for public health because of their extreme toxicity and potential for use as biowarfare agents. Extensive research has focused on designing antagonists that block the catalytic activity of BoNTs. In this study, we screened 300 small natural compounds and their analogues extracted from Indian plants for their activity against BoNT serotype A (BoNT/A) as well as its light chain (LCA) using biochemical and cellular assays. One natural compound, a nitrophenyl psoralen (NPP), was identified to be a specific inhibitor of LCA with an in vitro 50% inhibitory concentration (IC50) value of 4.74 ± 0.03 µM. NPP was able to rescue endogenous synaptosome-associated protein 25 (SNAP-25) from cleavage by BoNT/A in human neuroblastoma cells with an IC50 of 12.2 ± 1.7 µM, as well as to prolong the time to the blocking of neutrally elicited twitch tensions in isolated mouse phrenic nerve-hemidiaphragm preparations.IMPORTANCE The long-lasting endopeptidase activity of BoNT is a critical biological activity inside the nerve cell, as it prompts proteolysis of the SNARE proteins, involved in the exocytosis of the neurotransmitter acetylcholine. Thus, the BoNT endopeptidase activity is an appropriate clinical target for designing new small-molecule antidotes against BoNT with the potential to reverse the paralysis syndrome of botulism. In principle, small-molecule inhibitors (SMIs) can gain entry into BoNT-intoxicated cells if they have a suitable octanol-water partition coefficient (log P) value and other favorable characteristics (P. Leeson, Nature 481:455-456, 2012, https://doi.org/10.1038/481455a). Several efforts have been made in the past to develop SMIs, but inhibitors effective under in vitro conditions have not in general been effective in vivo or in cellular models (L. M. Eubanks, M. S. Hixon, W. Jin, S. Hong, et al., Proc Natl Acad Sci U S A 104:2602-2607, 2007, https://doi.org/10.1073/pnas.0611213104). The difference between the in vitro and cellular efficacy presumably results from difficulties experienced by the compounds in crossing the cell membrane, in conjunction with poor bioavailability and high cytotoxicity. The screened nitrophenyl psoralen (NPP) effectively antagonized BoNT/A in both in vitro and ex vivo assays. Importantly, NPP inhibited the BoNT/A light chain but not other general zinc endopeptidases, such as thermolysin, suggesting high selectivity for its target. Small-molecule (nonpeptidic) inhibitors have better oral bioavailability, better stability, and better tissue and cell permeation than antitoxins or peptide inhibitors.
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10
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McLauchlan CC, Murakami HA, Wallace CA, Crans DC. Coordination environment changes of the vanadium in vanadium-dependent haloperoxidase enzymes. J Inorg Biochem 2018; 186:267-279. [PMID: 29990751 DOI: 10.1016/j.jinorgbio.2018.06.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 06/11/2018] [Accepted: 06/14/2018] [Indexed: 11/17/2022]
Abstract
Vanadium-dependent haloperoxidases are a class of enzymes that catalyze oxidation reactions with halides to form halogenated organic products and water. These enzymes include chloroperoxidase and bromoperoxidase, which have very different protein sequences and sizes, but regardless the coordination environment of the active sites is surprisingly constant. In this manuscript, the comparison of the coordination chemistry of V-containing-haloperoxidases of the trigonal bipyramidal geometry was done by data mining. The catalytic cycle imposes changes in the coordination geometry of the vanadium to accommodate the peroxidovanadium(V) intermediate in an environment we describe as a distorted square pyramidal geometry. During the catalytic cycle, this intermediate converts to a trigonal bipyramidal intermediate before losing the halogen and forming a tetrahedral vanadium-protein intermediate. Importantly, the catalysis is facilitated by a proton-relay system supplied by the second sphere coordination environment and the changes in the coordination environment of the vanadium(V) making this process unique among protein catalyzed processes. The analysis of the coordination chemistry shows that the active site is very tightly regulated with only minor changes in the coordination geometry. The coordination geometry in the protein structures deviates from that found for both small molecules crystalized in the absence of protein and the reported functional small molecule model compounds. At this time there are no examples reported of a structurally similar small molecule with the geometry observed for the peroxidovanadium(V) in the active site of the vanadium-containing haloperoxidases.
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Affiliation(s)
- Craig C McLauchlan
- Department of Chemistry, Illinois State University, Campus Box 4160, Normal, IL 61790, USA.
| | - Heide A Murakami
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Craig A Wallace
- Department of Chemistry, Illinois State University, Campus Box 4160, Normal, IL 61790, USA
| | - Debbie C Crans
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA; Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA.
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11
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Jacobson AR, Adler M, Silvaggi NR, Allen KN, Smith GM, Fredenburg RA, Stein RL, Park JB, Feng X, Shoemaker CB, Deshpande SS, Goodnough MC, Malizio CJ, Johnson EA, Pellett S, Tepp WH, Tzipori S. Small molecule metalloprotease inhibitor with in vitro, ex vivo and in vivo efficacy against botulinum neurotoxin serotype A. Toxicon 2017; 137:36-47. [PMID: 28698055 DOI: 10.1016/j.toxicon.2017.06.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 01/08/2023]
Abstract
Botulinum neurotoxins (BoNTs) are the most toxic substances known to mankind and are the causative agents of the neuroparalytic disease botulism. Their ease of production and extreme toxicity have caused these neurotoxins to be classified as Tier 1 bioterrorist threat agents and have led to a sustained effort to develop countermeasures to treat intoxication in case of a bioterrorist attack. While timely administration of an approved antitoxin is effective in reducing the severity of botulism, reversing intoxication requires different strategies. In the present study, we evaluated ABS 252 and other mercaptoacetamide small molecule active-site inhibitors of BoNT/A light chain using an integrated multi-assay approach. ABS 252 showed inhibitory activity in enzymatic, cell-based and muscle activity assays, and importantly, produced a marked delay in time-to-death in mice. The results suggest that a multi-assay approach is an effective strategy for discovery of potential BoNT therapeutic candidates.
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Affiliation(s)
| | - Michael Adler
- Neuroscience Branch, Medical Toxicology Division, USAMRICD, APG, MD, 21010, United States.
| | - Nicholas R Silvaggi
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
| | | | - Ross A Fredenburg
- Center for Neurologic Diseases, Brigham & Women's Hospital and Harvard Medical School, Cambridge, MA, 02139, United States
| | - Ross L Stein
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women's Hospital and Harvard Medical School, Cambridge, MA, 02139, United States
| | - Jong-Beak Park
- Division of Infectious Diseases, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, 01536, United States
| | - Xiaochuan Feng
- Division of Infectious Diseases, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, 01536, United States
| | - Charles B Shoemaker
- Division of Infectious Diseases, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, 01536, United States
| | - Sharad S Deshpande
- Neuroscience Branch, Medical Toxicology Division, USAMRICD, APG, MD, 21010, United States
| | | | | | - Eric A Johnson
- Department of Bacteriology, University of Wisconsin at Madison, Madison, WI, 53706, United States
| | - Sabine Pellett
- Department of Bacteriology, University of Wisconsin at Madison, Madison, WI, 53706, United States
| | - William H Tepp
- Department of Bacteriology, University of Wisconsin at Madison, Madison, WI, 53706, United States
| | - Saul Tzipori
- Division of Infectious Diseases, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, 01536, United States
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12
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Burnett JC, Lim C, Peyser BD, Samankumara LP, Kovaliov M, Colombo R, Bulfer SL, LaPorte MG, Hermone AR, McGrath CF, Arkin MR, Gussio R, Huryn DM, Wipf P. A threonine turnstile defines a dynamic amphiphilic binding motif in the AAA ATPase p97 allosteric binding site. Org Biomol Chem 2017; 15:4096-4114. [PMID: 28352916 PMCID: PMC5472064 DOI: 10.1039/c7ob00526a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The turnstile motion of two neighboring threonines sets up a dynamic side chain interplay that can accommodate both polar and apolar ligands in a small molecule allosteric protein binding site. A computational model based on SAR data and both X-ray and cryo-EM structures of the AAA ATPase p97 was used to analyze the effects of paired threonines at the inhibitor site. Specifically, the Thr side chain hydroxyl groups form a hydrogen bonding network that readily accommodates small, highly polar ligand substituents. Conversely, diametric rotation of the χ1 torsion by 150-180° orients the side chain β-methyl groups into the binding cleft, creating a hydrophobic pocket that can accommodate small, apolar substituents. This motif was found to be critical for rationalizing the affinities of a structurally focused set of inhibitors of p97 covering a > 2000-fold variation in potencies, with a preference for either small-highly polar or small-apolar groups. The threonine turnstile motif was further validated by a PDB search that identified analogous binding modes in ligand interactions in PKB, as well as by an analysis of NMR structures demonstrating additional gear-like interactions between adjacent Thr pairs. Combined, these data suggest that the threonine turnstile motif may be a general feature of interest in protein binding pockets.
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Affiliation(s)
- James C. Burnett
- Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, United States
| | - Chaemin Lim
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Brian D. Peyser
- Frederick National Laboratory for Cancer Research, Developmental Therapeutics Program, P.O. Box B, Frederick, MD 21702, United States
| | - Lalith P. Samankumara
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Marina Kovaliov
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Raffaele Colombo
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Stacie L. Bulfer
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, CA 94158, United States
| | - Matthew G. LaPorte
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Ann R. Hermone
- Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, United States
| | - Connor F. McGrath
- Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, United States
| | - Michelle R. Arkin
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, CA 94158, United States
| | - Rick Gussio
- Frederick National Laboratory for Cancer Research, Developmental Therapeutics Program, P.O. Box B, Frederick, MD 21702, United States
| | - Donna M. Huryn
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA 15260, United States
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, United States
| | - Peter Wipf
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA 15260, United States
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, United States
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13
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The Effect of Albumin and Platelet-Poor Plasma Supplemented Botulinum A Toxin on Bioavaliability. Ann Plast Surg 2017; 78:436-442. [DOI: 10.1097/sap.0000000000000957] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Affiliation(s)
- Megan Garland
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Sebastian Loscher
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Matthew Bogyo
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
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15
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Bompiani KM, Caglič D, Krutein MC, Benoni G, Hrones M, Lairson LL, Bian H, Smith GR, Dickerson TJ. High-Throughput Screening Uncovers Novel Botulinum Neurotoxin Inhibitor Chemotypes. ACS COMBINATORIAL SCIENCE 2016; 18:461-74. [PMID: 27314875 DOI: 10.1021/acscombsci.6b00033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Botulism is caused by potent and specific bacterial neurotoxins that infect host neurons and block neurotransmitter release. Treatment for botulism is limited to administration of an antitoxin within a short time window, before the toxin enters neurons. Alternatively, current botulism drug development targets the toxin light chain, which is a zinc-dependent metalloprotease that is delivered into neurons and mediates long-term pathology. Several groups have identified inhibitory small molecules, peptides, or aptamers, although no molecule has advanced to the clinic due to a lack of efficacy in advanced models. Here we used a homogeneous high-throughput enzyme assay to screen three libraries of drug-like small molecules for new chemotypes that modulate recombinant botulinum neurotoxin light chain activity. High-throughput screening of 97088 compounds identified numerous small molecules that activate or inhibit metalloprotease activity. We describe four major classes of inhibitory compounds identified, detail their structure-activity relationships, and assess their relative inhibitory potency. A previously unreported chemotype in any context of enzyme inhibition is described with potent submicromolar inhibition (Ki = 200-300 nM). Additional detailed kinetic analyses and cellular cytotoxicity assays indicate the best compound from this series is a competitive inhibitor with cytotoxicity values around 4-5 μM. Given the potency and drug-like character of these lead compounds, further studies, including cellular activity assays and DMPK analysis, are justified.
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Affiliation(s)
- Kristin M. Bompiani
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dejan Caglič
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michelle C. Krutein
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Galit Benoni
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Morgan Hrones
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Luke L. Lairson
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Haiyan Bian
- Fox Chase Chemical Diversity Center, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Garry R. Smith
- Fox Chase Chemical Diversity Center, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Tobin J. Dickerson
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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16
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Guo J, Wang J, Gao S, Ji B, Waichi Chan E, Chen S. Substrate-based inhibitors exhibiting excellent protective and therapeutic effects against Botulinum Neurotoxin A intoxication. Sci Rep 2015; 5:16981. [PMID: 26584873 PMCID: PMC4653808 DOI: 10.1038/srep16981] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/22/2015] [Indexed: 12/18/2022] Open
Abstract
Potent inhibitors to reverse Botulinum neurotoxins (BoNTs) activity in neuronal cells are currently not available. A better understanding of the substrate recognition mechanism of BoNTs enabled us to design a novel class of peptide inhibitors which were derivatives of the BoNT/A substrate, SNAP25. Through a combination of in vitro, cellular based, and in vivo mouse assays, several potent inhibitors of approximately one nanomolar inhibitory strength both in vitro and in vivo have been identified. These compounds represent the first set of inhibitors that exhibited full protection against BoNT/A intoxication in mice model with undetectable toxicity. Our findings validated the hypothesis that a peptide inhibitor targeting the two BoNT structural regions which were responsible for substrate recognition and cleavage respectively could exhibit excellent inhibitory effect, thereby providing insight on future development of more potent inhibitors against BoNTs.
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Affiliation(s)
- Jiubiao Guo
- Shenzhen Key lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, P. R. China
- State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, People’s Republic of China
| | - Shan Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, People’s Republic of China
| | - Bin Ji
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, People’s Republic of China
| | - Edward Waichi Chan
- Shenzhen Key lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, P. R. China
- State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Sheng Chen
- Shenzhen Key lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, P. R. China
- State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
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17
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Kumaran D, Adler M, Levit M, Krebs M, Sweeney R, Swaminathan S. Interactions of a potent cyclic peptide inhibitor with the light chain of botulinum neurotoxin A: Insights from X-ray crystallography. Bioorg Med Chem 2015; 23:7264-73. [PMID: 26522088 DOI: 10.1016/j.bmc.2015.10.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/09/2015] [Accepted: 10/16/2015] [Indexed: 10/22/2022]
Abstract
The seven antigenically distinct serotypes (A-G) of botulinum neurotoxin (BoNT) are responsible for the deadly disease botulism. BoNT serotype A (BoNT/A) exerts its lethal action by cleaving the SNARE protein SNAP-25, leading to inhibition of neurotransmitter release, flaccid paralysis and autonomic dysfunction. BoNTs are dichain proteins consisting of a ∼ 100 kDa heavy chain and a ∼ 50 kDa light chain; the former is responsible for neurospecific binding, internalization and translocation, and the latter for cleavage of neuronal SNARE proteins. Because of their extreme toxicity and history of weaponization, the BoNTs are regarded as potential biowarfare/bioterrorism agents. No post-symptomatic therapeutic interventions are available for BoNT intoxication other than intensive care; therefore it is imperative to develop specific antidotes against this neurotoxin. To this end, a cyclic peptide inhibitor (CPI-1) was evaluated in a FRET assay for its ability to inhibit BoNT/A light chain (Balc). CPI was found to be highly potent, exhibiting a Ki of 12.3 nM with full-length Balc448 and 39.2 nM using a truncated crystallizable form of the light chain (Balc424). Cocrystallization studies revealed that in the Balc424-CPI-1 complex, the inhibitor adopts a helical conformation, occupies a high percentage of the active site cavity and interacts in an amphipathic manner with critical active site residues. The data suggest that CPI-1 prevents SNAP-25 from accessing the Balc active site by blocking both the substrate binding path at the surface and the Zn(2+) binding region involved in catalysis. This differs from linear peptide inhibitors described to date which block only the latter.
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Affiliation(s)
- Desigan Kumaran
- Biological, Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, United States
| | - Michael Adler
- Analytical Toxicology Division, U.S. Army Medical Research Institute of Chemical Defense (USAMRICD), Aberdeen Proving Ground, MD 21010, United States.
| | - Matthew Levit
- Analytical Toxicology Division, U.S. Army Medical Research Institute of Chemical Defense (USAMRICD), Aberdeen Proving Ground, MD 21010, United States
| | - Michael Krebs
- Analytical Toxicology Division, U.S. Army Medical Research Institute of Chemical Defense (USAMRICD), Aberdeen Proving Ground, MD 21010, United States
| | - Richard Sweeney
- Research Division, USAMRICD, Aberdeen Proving Ground, MD 21010, United States
| | - Subramanyam Swaminathan
- Biological, Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, United States
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18
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Monoclonal Antibodies Targeting the Alpha-Exosite of Botulinum Neurotoxin Serotype/A Inhibit Catalytic Activity. PLoS One 2015; 10:e0135306. [PMID: 26275214 PMCID: PMC4537209 DOI: 10.1371/journal.pone.0135306] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 07/20/2015] [Indexed: 12/12/2022] Open
Abstract
The paralytic disease botulism is caused by botulinum neurotoxins (BoNT), multi-domain proteins containing a zinc endopeptidase that cleaves the cognate SNARE protein, thereby blocking acetylcholine neurotransmitter release. Antitoxins currently used to treat botulism neutralize circulating BoNT but cannot enter, bind to or neutralize BoNT that has already entered the neuron. The light chain endopeptidase domain (LC) of BoNT serotype A (BoNT/A) was targeted for generation of monoclonal antibodies (mAbs) that could reverse paralysis resulting from intoxication by BoNT/A. Single-chain variable fragment (scFv) libraries from immunized humans and mice were displayed on the surface of yeast, and 19 BoNT/A LC-specific mAbs were isolated by using fluorescence-activated cell sorting (FACS). Affinities of the mAbs for BoNT/A LC ranged from a KD value of 9.0×10−11 M to 3.53×10−8 M (mean KD 5.38×10−9 M and median KD 1.53×10−9 M), as determined by flow cytometry analysis. Eleven mAbs inhibited BoNT/A LC catalytic activity with IC50 values ranging from 8.3 ~73×10−9 M. The fine epitopes of selected mAbs were also mapped by alanine-scanning mutagenesis, revealing that the inhibitory mAbs bound the α-exosite region remote from the BoNT/A LC catalytic center. The results provide mAbs that could prove useful for intracellular reversal of paralysis post-intoxication and further define epitopes that could be targeted by small molecule inhibitors.
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19
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Farrow B, Wong M, Malette J, Lai B, Deyle KM, Das S, Nag A, Agnew HD, Heath JR. Epitope Targeting of Tertiary Protein Structure Enables Target-Guided Synthesis of a Potent In-Cell Inhibitor of Botulinum Neurotoxin. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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20
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Farrow B, Wong M, Malette J, Lai B, Deyle KM, Das S, Nag A, Agnew HD, Heath JR. Epitope targeting of tertiary protein structure enables target-guided synthesis of a potent in-cell inhibitor of botulinum neurotoxin. Angew Chem Int Ed Engl 2015; 54:7114-9. [PMID: 25925721 DOI: 10.1002/anie.201502451] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/09/2015] [Indexed: 12/14/2022]
Abstract
Botulinum neurotoxin (BoNT) serotype A is the most lethal known toxin and has an occluded structure, which prevents direct inhibition of its active site before it enters the cytosol. Target-guided synthesis by in situ click chemistry is combined with synthetic epitope targeting to exploit the tertiary structure of the BoNT protein as a landscape for assembling a competitive inhibitor. A substrate-mimicking peptide macrocycle is used as a direct inhibitor of BoNT. An epitope-targeting in situ click screen is utilized to identify a second peptide macrocycle ligand that binds to an epitope that, in the folded BoNT structure, is active-site-adjacent. A second in situ click screen identifies a molecular bridge between the two macrocycles. The resulting divalent inhibitor exhibits an in vitro inhibition constant of 165 pM against the BoNT/A catalytic chain. The inhibitor is carried into cells by the intact holotoxin, and demonstrates protection and rescue of BoNT intoxication in a human neuron model.
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Affiliation(s)
- Blake Farrow
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA).,Department of Applied Physics and Materials Science, California Institute of Technology (USA)
| | - Michelle Wong
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Jacquie Malette
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Bert Lai
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Kaycie M Deyle
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Samir Das
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Arundhati Nag
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Heather D Agnew
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA).
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21
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Videnović M, Opsenica DM, Burnett J, Gomba L, Nuss JE, Selaković Ž, Konstantinović J, Krstić M, Šegan S, Zlatović M, Sciotti RJ, Bavari S, Šolaja BA. Second generation steroidal 4-aminoquinolines are potent, dual-target inhibitors of the botulinum neurotoxin serotype A metalloprotease and P. falciparum malaria. J Med Chem 2014; 57:4134-53. [PMID: 24742203 PMCID: PMC4032193 DOI: 10.1021/jm500033r] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Indexed: 01/25/2023]
Abstract
Significantly more potent second generation 4-amino-7-chloroquinoline (4,7-ACQ) based inhibitors of the botulinum neurotoxin serotype A (BoNT/A) light chain were synthesized. Introducing an amino group at the C(3) position of the cholate component markedly increased potency (IC50 values for such derivatives ranged from 0.81 to 2.27 μM). Two additional subclasses were prepared: bis(steroidal)-4,7-ACQ derivatives and bis(4,7-ACQ)cholate derivatives; both classes provided inhibitors with nanomolar-range potencies (e.g., the Ki of compound 67 is 0.10 μM). During BoNT/A challenge using primary neurons, select derivatives protected SNAP-25 by up to 89%. Docking simulations were performed to rationalize the compounds' in vitro potencies. In addition to specific residue contacts, coordination of the enzyme's catalytic zinc and expulsion of the enzyme's catalytic water were a consistent theme. With respect to antimalarial activity, the compounds provided better IC90 activities against chloroquine resistant (CQR) malaria than CQ, and seven compounds were more active than mefloquine against CQR strain W2.
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Affiliation(s)
- Milica Videnović
- Faculty
of Chemistry, University of Belgrade, Studentski trg 16, P.O. Box 51, 11158, Belgrade, Serbia
| | - Dejan M. Opsenica
- Institute
of Chemistry, Technology, and Metallurgy, University of Belgrade, Njegoseva 12, 11000 Belgrade, Serbia
| | - James
C. Burnett
- Computational
Drug Development Group, Leidos Biomedical
Research, Inc., FNLCR at Frederick, P.O.
Box B, Frederick, Maryland 21701, United States
| | - Laura Gomba
- Department
of Bacteriology, United States Army Medical
Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, Maryland 21702, United States
| | - Jonathan E. Nuss
- Department
of Bacteriology, United States Army Medical
Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, Maryland 21702, United States
| | - Života Selaković
- Faculty
of Chemistry, University of Belgrade, Studentski trg 16, P.O. Box 51, 11158, Belgrade, Serbia
| | - Jelena Konstantinović
- Faculty
of Chemistry Innovative Centre, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Maja Krstić
- Faculty
of Chemistry, University of Belgrade, Studentski trg 16, P.O. Box 51, 11158, Belgrade, Serbia
| | - Sandra Šegan
- Institute
of Chemistry, Technology, and Metallurgy, University of Belgrade, Njegoseva 12, 11000 Belgrade, Serbia
| | - Mario Zlatović
- Faculty
of Chemistry, University of Belgrade, Studentski trg 16, P.O. Box 51, 11158, Belgrade, Serbia
| | - Richard J. Sciotti
- Division
of Experimental Therapeutics, Walter Reed
Army Institute of Research, Silver
Spring, Maryland 20910, United States
| | - Sina Bavari
- Target
Discovery and Experimental Microbiology, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, Maryland 21702, United States
| | - Bogdan A. Šolaja
- Faculty
of Chemistry, University of Belgrade, Studentski trg 16, P.O. Box 51, 11158, Belgrade, Serbia
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22
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Patel K, Cai S, Singh BR. Current strategies for designing antidotes against botulinum neurotoxins. Expert Opin Drug Discov 2014; 9:319-33. [DOI: 10.1517/17460441.2014.884066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kruti Patel
- University of Massachusetts Dartmouth, Department of Chemistry and Biochemistry, North Dartmouth, MA 02747, USA
| | - Shuowei Cai
- University of Massachusetts Dartmouth, Department of Chemistry and Biochemistry, North Dartmouth, MA 02747, USA
| | - Bal Ram Singh
- University of Massachusetts Dartmouth, Department of Chemistry and Biochemistry, North Dartmouth, MA 02747, USA
- Institute of Advanced Sciences and Prime Bio, Inc., Botulinum Research Center, 166 Chase Road, North Dartmouth, MA 02747, USA
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23
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Silhár P, Eubanks LM, Seki H, Pellett S, Javor S, Tepp WH, Johnson EA, Janda KD. Targeting botulinum A cellular toxicity: a prodrug approach. J Med Chem 2013; 56:7870-9. [PMID: 24127873 DOI: 10.1021/jm400873n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The botulinum neurotoxin light chain (LC) protease has become an important therapeutic target for postexposure treatment of botulism. Hydroxamic acid based small molecules have proven to be potent inhibitors of LC/A with nanomolar Ki values, yet they lack cellular activity conceivably due to low membrane permeability. To overcome this potential liability, we investigated two prodrug strategies, 1,4,2-dioxazole and carbamate, based on our 1-adamantylacetohydroxamic acid scaffold. The 1,4,2-dioxazole prodrug did not demonstrate cellular activity, however, carbamates exhibited cellular potency with the most active compound displaying an EC50 value of 20 μM. Cellular trafficking studies were conducted using a "fluorescently silent" prodrug that remained in this state until cellular uptake was complete, which allowed for visualization of the drug's release inside neuronal cells. In sum, this research sets the stage for future studies leveraging the specific targeting and delivery of these prodrugs, as well as other antibotulinum agents, into neuronal cells.
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Affiliation(s)
- Peter Silhár
- Departments of Chemistry and Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, and The Worm Institute for Research and Medicine, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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24
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Mizanur RM, Frasca V, Swaminathan S, Bavari S, Webb R, Smith LA, Ahmed SA. The C terminus of the catalytic domain of type A botulinum neurotoxin may facilitate product release from the active site. J Biol Chem 2013; 288:24223-33. [PMID: 23779108 DOI: 10.1074/jbc.m113.451286] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Botulinum neurotoxins are the most toxic of all compounds. The toxicity is related to a poor zinc endopeptidase activity located in a 50-kDa domain known as light chain (Lc) of the toxin. The C-terminal tail of Lc is not visible in any of the currently available x-ray structures, and it has no known function but undergoes autocatalytic truncations during purification and storage. By synthesizing C-terminal peptides of various lengths, in this study, we have shown that these peptides competitively inhibit the normal catalytic activity of Lc of serotype A (LcA) and have defined the length of the mature LcA to consist of the first 444 residues. Two catalytically inactive mutants also inhibited LcA activity. Our results suggested that the C terminus of LcA might interact at or near its own active site. By using synthetic C-terminal peptides from LcB, LcC1, LcD, LcE, and LcF and their respective substrate peptides, we have shown that the inhibition of activity is specific only for LcA. Although a potent inhibitor with a Ki of 4.5 μm, the largest of our LcA C-terminal peptides stimulated LcA activity when added at near-stoichiometric concentration to three versions of LcA differing in their C-terminal lengths. The result suggested a product removal role of the LcA C terminus. This suggestion is supported by a weak but specific interaction determined by isothermal titration calorimetry between an LcA C-terminal peptide and N-terminal product from a peptide substrate of LcA. Our results also underscore the importance of using a mature LcA as an inhibitor screening target.
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Affiliation(s)
- Rahman M Mizanur
- Integrated Toxicology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
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25
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Dadgar S, Ramjan Z, Floriano WB. Paclitaxel is an inhibitor and its boron dipyrromethene derivative is a fluorescent recognition agent for botulinum neurotoxin subtype A. J Med Chem 2013; 56:2791-803. [PMID: 23484537 DOI: 10.1021/jm301829h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have successfully identified one new inhibitor and one new fluorescent recognition agent for the botulinum neurotoxin subtype A (BoNT/A) using the virtual screening protocol "protein scanning with virtual ligand screening" (PSVLS). Hit selection used an in-house developed holistic binding scoring method. Selected hits were tested experimentally for inhibitory activity using fluorescence resonance energy transfer (FRET) assays against the light chain (catalytic domain) of BoNT/A. Ligand binding was determined against the light and heavy chain BoNT/A complex through either radiolabeled ligand binding assays (nonfluorescent ligands) or fluorescence intensity assays (fluorescent ligands). These experimental assays have confirmed one compound (paclitaxel) to inhibit BoNT/A's proteolytic activity experimentally with an IC50 of 5.2 μM. A fluorescent derivative was also confirmed to bind to the toxin and therefore is a suitable candidate for the rational design of new detection agents and for the development of fluorescence-based multiprobe detection assays.
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Affiliation(s)
- Saedeh Dadgar
- Department of Chemistry, Lakehead University and Thunder Bay Regional Research Institute, Thunder Bay, Ontario P7B 5E1, Canada
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26
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The thioredoxin reductase-thioredoxin system is involved in the entry of tetanus and botulinum neurotoxins in the cytosol of nerve terminals. FEBS Lett 2012. [DOI: 10.1016/j.febslet.2012.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Singh P, Singh MK, Chaudhary D, Chauhan V, Bharadwaj P, Pandey A, Upadhyay N, Dhaked RK. Small-molecule quinolinol inhibitor identified provides protection against BoNT/A in mice. PLoS One 2012; 7:e47110. [PMID: 23071727 PMCID: PMC3469547 DOI: 10.1371/journal.pone.0047110] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 09/10/2012] [Indexed: 11/18/2022] Open
Abstract
Botulinum neurotoxins (BoNTs), etiological agents of the life threatening neuroparalytic disease botulism, are the most toxic substances currently known. The potential for the use as bioweapon makes the development of small-molecule inhibitor against these deadly toxins is a top priority. Currently, there are no approved pharmacological treatments for BoNT intoxication. Although an effective vaccine/immunotherapy is available for immuno-prophylaxis but this cannot reverse the effects of toxin inside neurons. A small-molecule pharmacological intervention, especially one that would be effective against the light chain protease, would be highly desirable. Similarity search was carried out from ChemBridge and NSC libraries to the hit (7-(phenyl(8-quinolinylamino)methyl)-8-quinolinol; NSC 84096) to mine its analogs. Several hits obtained were screened for in silico inhibition using AutoDock 4.1 and 19 new molecules selected based on binding energy and Ki. Among these, eleven quinolinol derivatives potently inhibited in vitro endopeptidase activity of botulinum neurotoxin type A light chain (rBoNT/A-LC) on synaptosomes isolated from rat brain which simulate the in vivo system. Five of these inhibitor molecules exhibited IC(50) values ranging from 3.0 nM to 10.0 µM. NSC 84087 is the most potent inhibitor reported so far, found to be a promising lead for therapeutic development, as it exhibits no toxicity, and is able to protect animals from pre and post challenge of botulinum neurotoxin type A (BoNT/A).
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Affiliation(s)
- Padma Singh
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
| | - Manglesh Kumar Singh
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
| | - Dilip Chaudhary
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
| | - Vinita Chauhan
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
| | - Pranay Bharadwaj
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
| | - Apurva Pandey
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
| | - Nisha Upadhyay
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
| | - Ram Kumar Dhaked
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
- * E-mail:
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Eichhorn T, Dolimbek BZ, Deeg K, Efferth T, Atassi MZ. Inhibition in vivo of the activity of botulinum neurotoxin A by small molecules selected by virtual screening. Toxicon 2012; 60:1180-90. [PMID: 22960451 DOI: 10.1016/j.toxicon.2012.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 07/24/2012] [Accepted: 07/25/2012] [Indexed: 10/28/2022]
Abstract
To search for small molecular size inhibitors of botulinum neurotoxin A (BoNT/A) endopeptidase activity, we have screened the NCI library containing about 1 million structures against the substrate binding pocket of BoNT/A. Virtual screening (VS) was performed with the software Glide (Grid-based ligand docking energetics) and the findings were confirmed by AutoDock. Ten compounds were found that had favorable energetic and glide criteria and 5 of these compounds were selected for their ability to protect mice in vivo against a lethal dose of BoNT/A. Each compound was incubated at different molar excesses with a lethal dose of the toxin and then the mixture injected intravenously into mice. At 4690 M excess, compounds NSC94520 and NSC99639 protected all (100%) the mice from lethal toxicity. Compounds NSC48461 and NSC627733 gave 75% protection. Compound NSC348884 showed the least inhibition of toxicity allowing only a fraction (25%) of the mice to survive challenge with a lethal dose; and in the case of the mice that did not survive there was a considerable delay of mortality. At 2400 M excess compounds NSC94520 remained fully protective while and NSC99639 afforded 75% protection and at 1200 M excess each of these two compounds gave 50% protection. The two compounds gave no protection at 600 or less molar excess. When each compound was administered intravenously at 4690 M excess at different times (from 1 h to 6 h) after the intravenous injection of the active toxin, none of the compounds was able to protect the animals from toxicity. The findings show the value of VS in identifying potential inhibitors of the toxin for further development and improvement.
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Affiliation(s)
- Tolga Eichhorn
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
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Stura EA, Le Roux L, Guitot K, Garcia S, Bregant S, Beau F, Vera L, Collet G, Ptchelkine D, Bakirci H, Dive V. Structural framework for covalent inhibition of Clostridium botulinum neurotoxin A by targeting Cys165. J Biol Chem 2012; 287:33607-14. [PMID: 22869371 DOI: 10.1074/jbc.m112.396697] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Clostridium botulinum neurotoxin type A (BoNT/A) is one of the most potent toxins for humans and a major biothreat agent. Despite intense chemical efforts over the past 10 years to develop inhibitors of its catalytic domain (catBoNT/A), highly potent and selective inhibitors are still lacking. Recently, small inhibitors were reported to covalently modify catBoNT/A by targeting Cys(165), a residue located in the enzyme active site just above the catalytic zinc ion. However, no direct proof of Cys(165) modification was reported, and the poor accessibility of this residue in the x-ray structure of catBoNT/A raises concerns about this proposal. To clarify this issue, the functional role of Cys(165) was first assessed through a combination of site-directed mutagenesis and structural studies. These data suggested that Cys(165) is more involved in enzyme catalysis rather than in structural property. Then by peptide mass fingerprinting and x-ray crystallography, we demonstrated that a small compound containing a sulfonyl group acts as inhibitor of catBoNT/A through covalent modification of Cys(165). The crystal structure of this covalent complex offers a structural framework for developing more potent covalent inhibitors catBoNT/A. Other zinc metalloproteases can be founded in the protein database with a cysteine at a similar location, some expressed by major human pathogens; thus this work should find broader applications for developing covalent inhibitors.
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Affiliation(s)
- Enrico A Stura
- Commissariat à l'Energie Atomique, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines, CE-Saclay, 91191 Gif-sur-Yvette, Cedex, France
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Majgier-Baranowska H, Williams JD, Li B, Peet NP. Studies on the mechanism of the Cadogan–Sundberg indole synthesis. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.06.146] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Opsenica I, Filipovic V, Nuss JE, Gomba LM, Opsenica D, Burnett JC, Gussio R, Solaja BA, Bavari S. The synthesis of 2,5-bis(4-amidinophenyl)thiophene derivatives providing submicromolar-range inhibition of the botulinum neurotoxin serotype A metalloprotease. Eur J Med Chem 2012; 53:374-9. [PMID: 22516424 PMCID: PMC3361628 DOI: 10.1016/j.ejmech.2012.03.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/22/2012] [Accepted: 03/25/2012] [Indexed: 10/28/2022]
Abstract
Botulinum neurotoxins (BoNTs), composed of a family of seven serotypes (categorized A-G), are the deadliest of known biological toxins. The activity of the metalloprotease, light chain (LC) component of the toxins is responsible for causing the life-threatening paralysis associated with the disease botulism. Herein we report significantly more potent analogs of novel, lead BoNT serotype A LC inhibitor 2,5-bis(4-amidinophenyl)thiophene (K(i) = 10.88 μM ± 0.90 μM). Specifically, synthetic modifications involved simultaneously replacing the lead inhibitor's terminal bis-amidines with secondary amines and the systematic tethering of 4-amino-7-chloroquinoline substituents to provide derivatives with K(i) values ranging from 0.302 μM (± 0.03 μM) to 0.889μM (± 0.11 μM).
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Affiliation(s)
- Igor Opsenica
- Faculty of Chemistry, University of Belgrade, Studentski trg16, P.O. Box 51, Belgrade, Serbia
| | - Vuk Filipovic
- Faculty of Chemistry, University of Belgrade, Studentski trg16, P.O. Box 51, Belgrade, Serbia
| | - Jon E. Nuss
- United States Army Medical Research Institute of Infectious Diseases, Department of Bacteriology, 1425 Porter Street, Frederick, MD 21702, USA
| | - Laura M. Gomba
- United States Army Medical Research Institute of Infectious Diseases, Department of Bacteriology, 1425 Porter Street, Frederick, MD 21702, USA
| | - Dejan Opsenica
- Institute of Chemistry, Technology, and Metallurgy, 12 Njegoseva 12, 11001, P.O. Box 473, Belgrade, Serbia
| | - James C. Burnett
- SAIC-Frederick, Inc., National Cancer Institute at Frederick, Target Structure-Based Drug Discovery Group, P.O. Box B, Frederick, MD 21702, USA
| | - Rick Gussio
- National Cancer Institute at Frederick, Developmental Therapeutics Program, P.O. Box B, Frederick, MD 21702, USA
| | - Bogdan A. Solaja
- Faculty of Chemistry, University of Belgrade, Studentski trg16, P.O. Box 51, Belgrade, Serbia
| | - Sina Bavari
- Chief, Target Discovery and Experimental Microbiology, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD 21702, USA
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Ivarsson ME, Leroux JC, Castagner B. Targeting bacterial toxins. Angew Chem Int Ed Engl 2012; 51:4024-45. [PMID: 22441768 DOI: 10.1002/anie.201104384] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/21/2011] [Indexed: 12/18/2022]
Abstract
Protein toxins constitute the main virulence factors of several species of bacteria and have proven to be attractive targets for drug development. Lead candidates that target bacterial toxins range from small molecules to polymeric binders, and act at each of the multiple steps in the process of toxin-mediated pathogenicity. Despite recent and significant advances in the field, a rationally designed drug that targets toxins has yet to reach the market. This Review presents the state of the art in bacterial toxin targeted drug development with a critical consideration of achieved breakthroughs and withstanding challenges. The discussion focuses on A-B-type protein toxins secreted by four species of bacteria, namely Clostridium difficile (toxins A and B), Vibrio cholerae (cholera toxin), enterohemorrhagic Escherichia coli (Shiga toxin), and Bacillus anthracis (anthrax toxin), which are the causative agents of diseases for which treatments need to be improved.
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Affiliation(s)
- Mattias E Ivarsson
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology Zurich, Wolfgang-Pauli-Strasse 10, Zurich, Switzerland
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Structure-Based Drug Discovery for Botulinum Neurotoxins. Curr Top Microbiol Immunol 2012; 364:197-218. [DOI: 10.1007/978-3-642-33570-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Time-dependent botulinum neurotoxin serotype A metalloprotease inhibitors. Bioorg Med Chem 2011; 19:7338-48. [PMID: 22082667 DOI: 10.1016/j.bmc.2011.10.062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 10/13/2011] [Accepted: 10/19/2011] [Indexed: 11/21/2022]
Abstract
Botulinum neurotoxins (BoNTs) are the most lethal of biological substances, and are categorized as class A biothreat agents by the Centers for Disease Control and Prevention. There are currently no drugs to treat the deadly flaccid paralysis resulting from BoNT intoxication. Among the seven BoNT serotypes, the development of therapeutics to counter BoNT/A is a priority (due to its long half-life in the neuronal cytosol and its ease of production). In this regard, the BoNT/A enzyme light chain (LC) component, a zinc metalloprotease responsible for the intracellular cleavage of synaptosomal-associated protein of 25 kDa, is a desirable target for developing post-BoNT/A intoxication rescue therapeutics. In an earlier study, we reported the high throughput screening of a library containing 70,000 compounds, and uncovered a novel class of benzimidazole acrylonitrile-based BoNT/A LC inhibitors. Herein, we present both structure-activity relationships and a proposed mechanism of action for this novel inhibitor chemotype.
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Abstract
The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here.
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Thompson AA, Jiao GS, Kim S, Thai A, Cregar-Hernandez L, Margosiak SA, Johnson AT, Han GW, O’Malley S, Stevens RC. Structural characterization of three novel hydroxamate-based zinc chelating inhibitors of the Clostridium botulinum serotype A neurotoxin light chain metalloprotease reveals a compact binding site resulting from 60/70 loop flexibility. Biochemistry 2011; 50:4019-28. [PMID: 21434688 PMCID: PMC3092028 DOI: 10.1021/bi2001483] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Neurotoxins synthesized by Clostridium botulinum bacteria (BoNT), the etiological agent of human botulism, are extremely toxic proteins making them high-risk agents for bioterrorism. Small molecule inhibitor development has been focused on the light chain zinc-dependent metalloprotease domain of the neurotoxin, an effort that has been hampered by its relatively flexible active site. Developed in concert with structure--activity relationship studies, the X-ray crystal structures of the complex of BoNT serotype A light chain (BoNT/A LC) with three different micromolar-potency hydroxamate-based inhibitors are reported here. Comparison with an unliganded BoNT/A LC structure reveals significant changes in the active site as a result of binding by the unique inhibitor scaffolds. The 60/70 loop at the opening of the active site pocket undergoes the largest conformational change, presumably through an induced-fit mechanism, resulting in the most compact catalytic pocket observed in all known BoNT/A LC structures.
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Affiliation(s)
- Aaron A. Thompson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Guan-Sheng Jiao
- Department of Chemistry, PanThera Biopharma LLC, Aiea, HI 96701
| | - Seongjin Kim
- Department of Chemistry, PanThera Biopharma LLC, Aiea, HI 96701
| | - April Thai
- Department of Chemistry, PanThera Biopharma LLC, Aiea, HI 96701
| | | | | | - Alan T. Johnson
- Department of Chemistry, PanThera Biopharma LLC, Aiea, HI 96701
| | - Gye Won Han
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Sean O’Malley
- Department of Chemistry, PanThera Biopharma LLC, Aiea, HI 96701
| | - Raymond C. Stevens
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037,Address correspondence to: The Scripps Research Institute, 10550 North Torrey Pines Rd., GAC-1200, La Jolla, CA 92037. Tel.: 858-784-9416; Fax: 858-784-9483;
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Ruge DR, Dunning FM, Piazza TM, Molles BE, Adler M, Zeytin FN, Tucker WC. Detection of six serotypes of botulinum neurotoxin using fluorogenic reporters. Anal Biochem 2011; 411:200-9. [PMID: 21216216 DOI: 10.1016/j.ab.2011.01.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 01/03/2011] [Accepted: 01/04/2011] [Indexed: 12/01/2022]
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Opsenica I, Burnett JC, Gussio R, Opsenica D, Todorović N, Lanteri CA, Sciotti RJ, Gettayacamin M, Basilico N, Taramelli D, Nuss JE, Wanner L, Panchal RG, Šolaja BA, Bavari S. A chemotype that inhibits three unrelated pathogenic targets: the botulinum neurotoxin serotype A light chain, P. falciparum malaria, and the Ebola filovirus. J Med Chem 2011; 54:1157-69. [PMID: 21265542 PMCID: PMC3056319 DOI: 10.1021/jm100938u] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A 1,7-bis(alkylamino)diazachrysene-based small molecule was previously identified as an inhibitor of the botulinum neurotoxin serotype A light chain metalloprotease. Subsequently, a variety of derivatives of this chemotype were synthesized to develop structure-activity relationships, and all are inhibitors of the BoNT/A LC. Three-dimensional analyses indicated that half of the originally discovered 1,7-DAAC structure superimposed well with 4-amino-7-chloroquinoline-based antimalarial agents. This observation led to the discovery that several of the 1,7-DAAC derivatives are potent in vitro inhibitors of Plasmodium falciparum and, in general, are more efficacious against CQ-resistant strains than against CQ-susceptible strains. In addition, by inhibiting β-hematin formation, the most efficacious 1,7-DAAC-based antimalarials employ a mechanism of action analogous to that of 4,7-ACQ-based antimalarials and are well tolerated by normal cells. One candidate was also effective when administered orally in a rodent-based malaria model. Finally, the 1,7-DAAC-based derivatives were examined for Ebola filovirus inhibition in an assay employing Vero76 cells, and three provided promising antiviral activities and acceptably low toxicities.
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Affiliation(s)
- Igor Opsenica
- Faculty of Chemistry, University of Belgrade, Studentski trg 16, P.O. Box 51, 11158, Belgrade, Serbia
| | - James C. Burnett
- Target Structure-Based Drug Discovery Group, SAIC-Frederick, Inc., National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
| | - Rick Gussio
- Developmental Therapeutics Program, National Cancer Institute at Frederick, P.O. Box B, F.V.C. 310, Frederick, MD 21702, USA
| | - Dejan Opsenica
- Institute of Chemistry, Technology, and Metallurgy, Belgrade, Serbia
| | - Nina Todorović
- Institute of Chemistry, Technology, and Metallurgy, Belgrade, Serbia
| | - Charlotte A. Lanteri
- Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Richard J. Sciotti
- Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Montip Gettayacamin
- United States Army Medical Component, Armed Forces Research Institute of Medical Science, Department of Veterinary Medicine, Bangkok, Thailand
| | - Nicoletta Basilico
- Dipartimento di Sanità Pubblica- Microbiologia-Virologia, Università di Milano, Via Pascal 36, 20133 Milano, Italy
| | - Donatella Taramelli
- Dipartimento di Sanità Pubblica- Microbiologia-Virologia, Università di Milano, Via Pascal 36, 20133 Milano, Italy
| | - Jonathan E. Nuss
- United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD 21702; USA
| | - Laura Wanner
- United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD 21702; USA
| | - Rekha G. Panchal
- United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD 21702; USA
| | - Bogdan A. Šolaja
- Faculty of Chemistry, University of Belgrade, Studentski trg 16, P.O. Box 51, 11158, Belgrade, Serbia
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD 21702; USA
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Šilhár P, Alakurtti S, Čapková K, Xiaochuan F, Shoemaker CB, Yli-Kauhaluoma J, Janda KD. Synthesis and evaluation of library of betulin derivatives against the botulinum neurotoxin A protease. Bioorg Med Chem Lett 2011; 21:2229-31. [PMID: 21421315 DOI: 10.1016/j.bmcl.2011.02.115] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 02/25/2011] [Accepted: 02/28/2011] [Indexed: 10/18/2022]
Abstract
Botulinum neurotoxins (BoNTs) are the most toxic proteins currently known. Current treatments for botulinum poisoning are all protein based with a limited window of opportunity. Inhibition of the BoNT light chain protease (LC) has emerged as a new therapeutic strategy for the treatment of botulism as it may provide an effective post-exposure remedy. As such, a small library of 40 betulin derivatives was synthesized and screened against the light chain of BoNT serotype A (LC/A); five positive hits (IC(50) <100 μM) were uncovered. Detailed evaluation of inhibition mechanism of three most active compounds revealed a competitive model, with sub-micromolar K(i) value for the best inhibitor (7). Unfortunately, an in vitro cell-based assay did not show any protection of rat cerebellar neurons against BoNT/A intoxication by 7.
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Affiliation(s)
- Peter Šilhár
- Department of Chemistry, Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037, USA
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Ruthel G, Burnett JC, Nuss JE, Wanner LM, Tressler LE, Torres-Melendez E, Sandwick SJ, Retterer CJ, Bavari S. Post-intoxication inhibition of botulinum neurotoxin serotype A within neurons by small-molecule, non-peptidic inhibitors. Toxins (Basel) 2011; 3:207-17. [PMID: 22069707 PMCID: PMC3202822 DOI: 10.3390/toxins3030207] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 03/10/2011] [Accepted: 03/11/2011] [Indexed: 12/05/2022] Open
Abstract
Botulinum neurotoxins (BoNTs) comprise seven distinct serotypes that inhibit the release of neurotransmitter across neuromuscular junctions, resulting in potentially fatal flaccid paralysis. BoNT serotype A (BoNT/A), which targets synaptosomal-associated protein of 25kDa (SNAP-25), is particularly long-lived within neurons and requires a longer time for recovery of neuromuscular function. There are currently no treatments available to counteract BoNT/A after it has entered the neuronal cytosol. In this study, we examined the ability of small molecule non-peptidic inhibitors (SMNPIs) to prevent SNAP-25 cleavage post-intoxication of neurons. The progressive cleavage of SNAP-25 observed over 5 h following 1 h BoNT/A intoxication was prevented by addition of SMNPIs. In contrast, anti-BoNT/A neutralizing antibodies that strongly inhibited SNAP-25 cleavage when added during intoxication were completely ineffective when added post-intoxication. Although Bafilomycin A1, which blocks entry of BoNT/A into the cytosol by preventing endosomal acidification, inhibited SNAP-25 cleavage post-intoxication, the degree of inhibition was significantly reduced versus addition both during and after intoxication. Post-intoxication application of SMNPIs, on the other hand, was nearly as effective as application both during and after intoxication. Taken together, the results indicate that competitive SMNPIs of BoNT/A light chain can be effective within neurons post-intoxication.
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Affiliation(s)
- Gordon Ruthel
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD 21702; USA; (J.E.N.); (L.M.W.); (L.E.T.); (E.T.-M.); (S.J.S.); (C.J.R.)
| | - James C. Burnett
- SAIC-Frederick, Inc., National Cancer Institute at Frederick, Target Structure-Based Drug Discovery Group, P.O. Box B, Frederick, MD 21702, USA;
| | - Jonathan E. Nuss
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD 21702; USA; (J.E.N.); (L.M.W.); (L.E.T.); (E.T.-M.); (S.J.S.); (C.J.R.)
| | - Laura M. Wanner
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD 21702; USA; (J.E.N.); (L.M.W.); (L.E.T.); (E.T.-M.); (S.J.S.); (C.J.R.)
| | - Lyal E. Tressler
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD 21702; USA; (J.E.N.); (L.M.W.); (L.E.T.); (E.T.-M.); (S.J.S.); (C.J.R.)
| | - Edna Torres-Melendez
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD 21702; USA; (J.E.N.); (L.M.W.); (L.E.T.); (E.T.-M.); (S.J.S.); (C.J.R.)
| | - Sarah J. Sandwick
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD 21702; USA; (J.E.N.); (L.M.W.); (L.E.T.); (E.T.-M.); (S.J.S.); (C.J.R.)
| | - Cary J. Retterer
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD 21702; USA; (J.E.N.); (L.M.W.); (L.E.T.); (E.T.-M.); (S.J.S.); (C.J.R.)
| | - Sina Bavari
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD 21702; USA; (J.E.N.); (L.M.W.); (L.E.T.); (E.T.-M.); (S.J.S.); (C.J.R.)
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Cardinale SC, Butler MM, Ruthel G, Nuss JE, Wanner LM, Li B, Pai R, Peet NP, Bavari S, Bowlin TL. Novel Benzimidazole Inhibitors of Botulinum Neurotoxin/A Display Enzyme and Cell-Based Potency. ACTA ACUST UNITED AC 2011. [PMID: 23205055 DOI: 10.1504/tbj.2011.041813] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Botulinum Neurotoxins (BoNTs) are used therapeutically and in cosmetics, providing potential for bioterrorist activity, thus driving the search for small-molecule BoNT inhibitors. This report describes a 70,000-compound screen for inhibition of BoNT/A using a FRET assay to detect proteolysis of a peptide substrate. Hits were confirmed, followed by evaluation to determine compound specificity. Inhibitors fell into three main chemical classes, and on the basis of potency and specificity of inhibition, the activities of two chemotypes were examined further. Compounds exhibited specificity for BoNT/A LC inhibition with respect to other metalloproteases and displayed activity in a neuronal assay for botulinum intoxication.
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Li B, Peet NP, Butler MM, Burnett JC, Moir DT, Bowlin TL. Small molecule inhibitors as countermeasures for botulinum neurotoxin intoxication. Molecules 2010; 16:202-20. [PMID: 21193845 PMCID: PMC6259422 DOI: 10.3390/molecules16010202] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 12/20/2010] [Accepted: 12/29/2010] [Indexed: 11/18/2022] Open
Abstract
Botulinum neurotoxins (BoNTs) are the most potent of known toxins and are listed as category A biothreat agents by the U.S. CDC. The BoNT-mediated proteolysis of SNARE proteins inhibits the exocytosis of acetylcholine into neuromuscular junctions, leading to life-threatening flaccid paralysis. Currently, the only therapy for BoNT intoxication (which results in the disease state botulism) includes experimental preventative antibodies and long-term supportive care. Therefore, there is an urgent need to identify and develop inhibitors that will serve as both prophylactic agents and post-exposure ‘rescue’ therapeutics. This review focuses on recent progress to discover and develop small molecule inhibitors as therapeutic countermeasures for BoNT intoxication.
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Affiliation(s)
- Bing Li
- Microbiotix, Inc., One Innovation Drive, Worcester, MA 01605, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-508-757-2800; Fax: +1-508-757-1999
| | - Norton P. Peet
- Microbiotix, Inc., One Innovation Drive, Worcester, MA 01605, USA
| | | | - James C. Burnett
- Target, Structure-Based Drug Discovery Group, SAIC-Frederick, Inc., National Cancer Institute at Frederick, 1050 Boyles Street, Frederick, MD 21702, USA; E-Mail: (J.C.B.)
| | - Donald T. Moir
- Microbiotix, Inc., One Innovation Drive, Worcester, MA 01605, USA
| | - Terry L. Bowlin
- Microbiotix, Inc., One Innovation Drive, Worcester, MA 01605, USA
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Hale M, Oyler G, Swaminathan S, Ahmed SA. Basic tetrapeptides as potent intracellular inhibitors of type A botulinum neurotoxin protease activity. J Biol Chem 2010; 286:1802-11. [PMID: 20961849 DOI: 10.1074/jbc.m110.146464] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Botulinum neurotoxins (BoNT) are the most potent of all toxins that cause flaccid muscle paralysis leading to death. They are also potential biothreat agents. A systematic investigation of various short peptide inhibitors of the BoNT protease domain with a 17-residue peptide substrate led to arginine-arginine-glycine-cysteine having a basic tetrapeptide structure as the most potent inhibitor. When assayed in the presence of dithiothreitol (DTT), the inhibitory effect was drastically reduced. Replacing the terminal cysteine with one hydrophobic residue eliminated the DTT effect but with two hydrophobic residues made the pentapeptide a poor inhibitor. Replacing the first arginine with cysteine or adding an additional cysteine at the N terminus did not improve inhibition. When assessed using mouse brain lysates, the tetrapeptides also inhibited BoNT/A cleavage of the endogenous SNAP-25. The peptides penetrated the neuronal cell lines, N2A and BE(2)-M17, without adversely affecting metabolic functions as measured by ATP production and P-38 phosphorylation. Biological activity of the peptides persisted within cultured chick motor neurons and rat and mouse cerebellar neurons for more than 40 h and inhibited BoNT/A protease action inside the neurons in a dose- and time-dependent fashion. Our results define a tetrapeptide as the smallest peptide inhibitor in the backdrop of a large substrate protein of 200+ amino acids having multiple interaction regions with its cognate enzyme. The inhibitors should also be valuable candidates for drug development.
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Affiliation(s)
- Martha Hale
- Department Cell Biology and Biochemistry, Integrated Toxicology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
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Nuss JE, Dong Y, Wanner LM, Ruthel G, Wipf P, Gussio R, Vennerstrom JL, Bavari S, Burnett JC. Pharmacophore Refinement Guides the Rational Design of Nanomolar-Range Inhibitors of the Botulinum Neurotoxin Serotype A Metalloprotease. ACS Med Chem Lett 2010; 1:301-305. [PMID: 21116458 DOI: 10.1021/ml100056v] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Botulinum neurotoxins (BoNTs) are the deadliest of microbial toxins. The enzymes' Zinc(II) metalloprotease, referred to as the light chain (LC) component, inhibits acetylcholine release into neuromuscular junctions, resulting in the disease botulism. Currently, no therapies counter BoNT poisoning post-neuronal intoxication; however, it is hypothesized that small molecules may be used to inhibit BoNT LC activity in the neuronal cytosol. Herein, we describe the pharmacophore-based design and chemical synthesis of potent (non-Zinc(II) chelating) small molecule (non-peptidic) inhibitors (SMNPIs) of the BoNT serotype A LC (the most toxic of the BoNT serotype LCs). Specifically, the three-dimensional superimpositions of 2-[4-(4-amidinephenoxy)-phenyl]-indole-6-amidine-based SMNPI regioisomers (K(i) = 0.600 μM (± 0.100 μM)), with a novel lead bis-[3-amide-5-(imidazolino)-phenyl]-terephthalamide (BAIPT)-based SMNPI (K(i) = 8.52 μM (± 0.53 μM)), resulted in a refined 4-zone pharmacophore. The refined model guided the design of BAIPT-based SMNPIs possessing K(i) values = 0.572 μM (± 0.041 μM) and 0.900 μM (± 0.078 μM).
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Affiliation(s)
- Jonathan E. Nuss
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702
| | - Yuxiang Dong
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Laura M. Wanner
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702
| | - Gordon Ruthel
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702
| | - Peter Wipf
- Department of Chemistry and Combinatorial Chemistry Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Rick Gussio
- Developmental Therapeutics Program, National Cancer Institute at Frederick, Frederick, Maryland 21702
| | - Jonathan L. Vennerstrom
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702
| | - James C. Burnett
- Target Structure-Based Drug Discovery Group, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frederick, Maryland 21702
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Zuniga JE, Hammill JT, Drory O, Nuss JE, Burnett JC, Gussio R, Wipf P, Bavari S, Brunger AT. Iterative structure-based peptide-like inhibitor design against the botulinum neurotoxin serotype A. PLoS One 2010; 5:e11378. [PMID: 20614028 PMCID: PMC2894858 DOI: 10.1371/journal.pone.0011378] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 06/08/2010] [Indexed: 11/26/2022] Open
Abstract
The botulinum neurotoxin serotype A light chain (BoNT/A LC) protease is the catalytic component responsible for the neuroparalysis that is characteristic of the disease state botulism. Three related peptide-like molecules (PLMs) were designed using previous information from co-crystal structures, synthesized, and assayed for in vitro inhibition against BoNT/A LC. Our results indicate these PLMS are competitive inhibitors of the BoNT/A LC protease and their Ki values are in the nM-range. A co-crystal structure for one of these inhibitors was determined and reveals that the PLM, in accord with the goals of our design strategy, simultaneously involves both ionic interactions via its P1 residue and hydrophobic contacts by means of an aromatic group in the P2′ position. The PLM adopts a helical conformation similar to previously determined co-crystal structures of PLMs, although there are also major differences to these other structures such as contacts with specific BoNT/A LC residues. Our structure further demonstrates the remarkable plasticity of the substrate binding cleft of the BoNT/A LC protease and provides a paradigm for iterative structure-based design and development of BoNT/A LC inhibitors.
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Affiliation(s)
- Jorge E. Zuniga
- Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Science, Structural Biology, and Photon Science, Stanford University, Stanford, California, United States of America
| | - Jared T. Hammill
- Center for Chemical Methodologies and Library Development, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Omri Drory
- Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Science, Structural Biology, and Photon Science, Stanford University, Stanford, California, United States of America
| | - Jonathan E. Nuss
- Division of Bacteriology, Department of Immunology, Target Identification, and Translational Research, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - James C. Burnett
- Target Structure-Based Drug Discovery Group, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Rick Gussio
- Information Technology Branch, Developmental Therapeutics Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Peter Wipf
- Center for Chemical Methodologies and Library Development, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (PW); (ATB)
| | - Sina Bavari
- Division of Bacteriology, Department of Immunology, Target Identification, and Translational Research, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Axel T. Brunger
- Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Science, Structural Biology, and Photon Science, Stanford University, Stanford, California, United States of America
- * E-mail: (PW); (ATB)
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Eubanks LM, Šilhár P, Salzameda NT, Zakhari JS, Xiaochuan F, Barbieri JT, Shoemaker CB, Hixon MS, Janda KD. Identification of a Natural Product Antagonist against the Botulinum Neurotoxin Light Chain Protease. ACS Med Chem Lett 2010; 1:268-272. [PMID: 20959871 DOI: 10.1021/ml100074s] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Botulinum neurotoxins (BoNTs) are the etiological agents responsible for botulism, a disease characterized by peripheral neuromuscular blockade and a characteristic flaccid paralysis of humans. BoNTs are the most lethal known poisons affecting humans and has been recognized as a potential bioterrorist threat. Current treatments for botulinum poisoning are predominately prophylactic in nature relying on passive immunization with antitoxins. Inhibition of the BoNT light chain metalloprotease (LC) has emerged as a new therapeutic strategy for the treatment of botulism that may provide an effective post-exposure remedy. A high-throughput screening effort against the light chain of BoNT serotype A (LC/A) was conducted with the John Hopkins Clinical Compound Library comprised of over 1,500 existing drugs. Lomofungin, a natural product first isolated in the late 1960's, was identified as an inhibitor of LC/A, displaying classical noncompetitive inhibition kinetics with a K(i) of 6.7 ± 0.7 µM. Inhibitor combination studies reveal that lomofungin binding is nonmutually exclusive (synergistic). The inhibition profile of lomofungin has been delineated by the use of both an active site inhibitor, 2,4-dichlorocinnamic hydroxamate, and a noncompetitive inhibitor d-chicoric acid; the mechanistic implications of these observations are discussed. Lastly, cellular efficacy was investigated using a rat primary cell model which demonstrated that lomofungin can protect against SNAP-25 cleavage, the intracellular protein target of LC/A.
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Affiliation(s)
- Lisa M. Eubanks
- Departments of Chemistry and Immunology
- The Skaggs Institute for Chemical Biology
- The Worm Institute for Research and Medicine
| | - Peter Šilhár
- Departments of Chemistry and Immunology
- The Skaggs Institute for Chemical Biology
| | | | - Joseph S. Zakhari
- Departments of Chemistry and Immunology
- The Skaggs Institute for Chemical Biology
| | - Feng Xiaochuan
- Department of Biomedical Sciences, Tufts Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, Massachusetts 01536
| | - Joseph T. Barbieri
- Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226
| | - Charles B. Shoemaker
- Department of Biomedical Sciences, Tufts Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, Massachusetts 01536
| | - Mark S. Hixon
- Departments of Chemistry and Immunology
- The Skaggs Institute for Chemical Biology
- The Worm Institute for Research and Medicine
| | - Kim D. Janda
- Departments of Chemistry and Immunology
- The Skaggs Institute for Chemical Biology
- The Worm Institute for Research and Medicine
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Chang TW, Blank M, Janardhanan P, Singh BR, Mello C, Blind M, Cai S. In vitro selection of RNA aptamers that inhibit the activity of type A botulinum neurotoxin. Biochem Biophys Res Commun 2010; 396:854-60. [PMID: 20452328 DOI: 10.1016/j.bbrc.2010.05.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 05/03/2010] [Indexed: 10/19/2022]
Abstract
The category A agent, botulinum neurotoxin (BoNT), is the most toxic molecule known to mankind. The endopeptidase activity of light chain domain of BoNT is the cause for the inhibition of the neurotransmitter release and the flaccid paralysis that leads to lethality in botulism. Currently, antidotes are not available to reverse the flaccid paralysis caused by BoNT. In the present study, we have identified three RNA aptamers through SELEX-process, which bind strongly to the light chain of type A BoNT (BoNT/A) and inhibit the endopeptidase activity, with IC(50) in low nM range. Inhibition kinetic studies reveal low nM K(I) and non-competitive nature of their inhibition. Aptamers are unique group of molecules as therapeutics, and this is first report of their development as an antidote against botulism. These data on K(I) and IC(50) strongly suggest that the aptamers have strong potential as antidotes that can reverse the symptom caused by BoNT/A.
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Affiliation(s)
- Tzuu-Wang Chang
- Department of Chemistry and Biochemistry, and Botulinum Research Center, University of Massachusetts Dartmouth, North Dartmouth, MA 02747, USA
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Pang YP, Davis J, Wang S, Park JG, Nambiar MP, Schmidt JJ, Millard CB. Small molecules showing significant protection of mice against botulinum neurotoxin serotype A. PLoS One 2010; 5:e10129. [PMID: 20405003 PMCID: PMC2854131 DOI: 10.1371/journal.pone.0010129] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 03/21/2010] [Indexed: 11/30/2022] Open
Abstract
Botulinum neurotoxin serotype A (BoNTA) causes a life-threatening neuroparalytic disease known as botulism that could afflict large, unprotected populations if the toxin were employed in an act of bioterrorism. Current post-exposure therapy is limited to symptomatic treatment or passive immunization that is effective for treating infant botulism at a cost of US $45,300 per treatment regimen. Antibodies can neutralize the extracellular but not the intracellular BoNTA. Moreover, antibody production, storage, and administration in a mass casualty scenario pose logistical challenges. Alternatively, small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought to antagonize the extracellular or intracellular toxin. While several such molecules reportedly demonstrated efficacy in protecting cells against BoNTA, there is scant information to show that small molecules can significantly protect mammals against BoNTA. Herein we report the development of effective small-molecules BoNTAe inhibitors with promising in vivo pharmacokinetics. One such molecule has an in vivo half-life of 6.5 hours and is devoid of obvious sign of toxicity. Pre-treatment with this molecule at 2 mg/kg protected 100% and 70% of treated mice against BoNTA at 5 times of its median-lethal dose during the periods of 2 and 4 half-lives of the inhibitor, respectively. In contrast, 40% and 0% of untreated mice survived during the respective periods. Similar levels of protection were also observed with two other small molecules. These results demonstrate that small molecules can significantly protect mice against BoNTA and support the pursuit of small-molecule antagonists as a cost-effective alternative or as an adjunct to passive immunity for treating botulism.
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Affiliation(s)
- Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail: (Y-PP for chemistry); (CBM for biology)
| | - Jon Davis
- Division of Biochemistry, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Shaohua Wang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Jewn Giew Park
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Madhusoodana P. Nambiar
- Division of Biochemistry, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - James J. Schmidt
- Integrated Toxicology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, 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: (Y-PP for chemistry); (CBM for biology)
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Clostridial neurotoxins: mechanism of SNARE cleavage and outlook on potential substrate specificity reengineering. Toxins (Basel) 2010; 2:665-82. [PMID: 22069605 PMCID: PMC3153214 DOI: 10.3390/toxins2040665] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2010] [Revised: 03/30/2010] [Accepted: 04/09/2010] [Indexed: 11/17/2022] Open
Abstract
The clostridial neurotoxin family consists of tetanus neurotoxin and seven distinct botulinum neurotoxins which cause the diseases tetanus and botulism. The extreme potency of these toxins primarily relies not only on their ability to specifically enter motoneurons but also on the activity their catalytic domains display inside presynaptic motoneuronal terminals. Subsequent to neurotoxin binding and endocytosis the catalytic domains become translocated across endosomal membranes and proteolyze unique peptide bonds of one of three soluble N-ethylmaleimide-sensitive fusion protein attachment receptors (SNAREs), vesicle associated membrane protein/synaptobrevin, synaptosome associated protein of 25 kDa, or syntaxin. As these substrate proteins are core components of the vesicular membrane fusion apparatus, cleavage of any of the substrate molecules results in the blockade of neurotransmitter release. This review summarizes the present knowledge about the molecular basis of the specific substrate recognition and cleavage mechanism and assesses the feasibility of reengineering catalytic domains to hydrolyze non-substrate members of the three SNARE families in order to expand the therapeutic application of botulinum neurotoxins.
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